A Persistent and Diverse Airway Microbiota Present during Chronic Obstructive Pulmonary Disease Exacerbations

Abstract

Acute exacerbations of chronic obstructive pulmonary disease (COPD) are a major source of morbidity and contribute significantly to healthcare costs. Although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in COPD airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. The aim of this study was to comprehensively profile airway bacterial communities using a culture-independent microarray, the 16S rRNA PhyloChip, of a cohort of COPD patients requiring ventilatory support and antibiotic therapy for exacerbation-related respiratory failure. PhyloChip analysis revealed the presence of over 1,200 bacterial taxa representing 140 distinct families, many previously undetected in airway diseases; bacterial community composition was strongly influenced by the duration of intubation. A core community of 75 taxa was detected in all patients, many of which are known pathogens. Bacterial community diversity in COPD airways is substantially greater than previously recognized and includes a number of potential pathogens detected in the setting of antibiotic exposure. Comprehensive assessment of the COPD airway microbiota using high-throughput, culture-independent methods may prove key to understanding the relationships between airway bacterial colonization, acute exacerbation, and clinical outcomes in this and other chronic inflammatory airway diseases.

Introduction

Chronic obstructive pulmonary disease (COPD) affects more than 12 million individuals in the United States and is the fourth leading cause of chronic morbidity and mortality (Rabe et al., 2007). A significant proportion of COPD-related healthcare costs are attributable to hospitalization for respiratory exacerbations (Mannino and Braman, 2007), with severe exacerbations having been associated with high mortality rates (Connors et al., 1996; Nseir et al., 2006). Bacterial infections are implicated in approximately 50% of COPD exacerbations (Sethi and Murphy, 2008). However, in most studies to date, bacterial identification has primarily relied on culture-based methods (Papi et al., 2006; Rosell et al., 2005; Soler et al., 2007) or species-specific, targeted PCR approaches (Murphy et al., 2004). Therefore, the true depth of bacterial diversity present in COPD airways is unknown, and the potential role for mixed-species bacterial communities in the pathogenesis of chronic airway colonization and acute exacerbations have been largely overlooked.

It is increasingly recognized that the human host is colonized by diverse, site-specific microbial communities that constitute the human microbiome (Dethlefsen et al., 2007; Eckburg et al., 2005). Growing interest in characterizing these consortia and their interactions with the host, is exemplified by the formation in 2008 of the International Human Microbiome Consortium (IHMC), a collaborative effort to merge data generated through the U.S. NIH Human Microbiome Project (HMP; http://nihroadmap.nih.gov/hmp) and the E.U. Metagenomics of the Human Intestinal Tract (MetaHIT; www.metahit.eu) initiatives. Constant exposure of the respiratory tract with the external environment could conceivably lead to important microbe–microbe and microbe–host interactions, yet the human airway microbiota, particularly that present in the context of pulmonary disease, remains largely uncharacterized. Given the limitations of culture-based methods, culture-independent approaches that identify species, or groups of closely related species, based on sequence polymorphisms in conserved genes, such as the 16S ribosomal RNA (16S rRNA) gene, enable a more comprehensive assessment of microbial members present in a mixed-species population. Such methods have increasingly been applied to identify bacterial consortia in a variety of human niches with demonstration that community composition is related to disease states such as obesity, ventilator-associated pneumonia and cystic fibrosis airway disease (Flanagan et al., 2007; Harris et al., 2007; Rogers et al., 2004; Turnbaugh et al., 2006).

An alternative approach to traditional culture-independent methods of microbial community analysis is the 16S rRNA PhyloChip, a high-density microarray containing 500,000 probes that can detect approximately 8,500 bacterial taxa [taxa are defined as a group of bacteria sharing at least 97% sequence homology within the 16S rRNA gene sequence; (Brodie et al., 2006)] The PhyloChip has previously been shown to detect substantially greater bacterial diversity compared in parallel with traditional clone library sequencing approaches (Brodie et al., 2006; Desantis et al., 2007; Flanagan et al., 2007). Using this microarray, we analyzed airway specimens from eight COPD patients who were being managed for severe respiratory exacerbations to determine if a more diverse bacterial community is present during pulmonary exacerbation in the setting of antibiotic administration.

Materials and Methods

Subject selection and sample collection

Potential subjects for this study were screened from a database of airway specimens collected between August 2004 and April 2006 from mechanically ventilated patients admitted to the intensive care units at Moffitt-Long Hospital (University of California, San Francisco), who were enrolled in a parent study of Pseudomonas aeruginosa in intubated patients (Flanagan et al., 2007). Subjects admitted to the ICU with a primary diagnosis of “COPD exacerbation” were identified for inclusion in our study. Available endotracheal aspirates (ETAs) from eight patients were processed for 16S rRNA PhyloChip analysis, as detailed below. To compare results from PhyloChip analysis with conventional clinical cultures, we obtained results of quantitative clinical laboratory bacterial cultures (blood agar, chocolate agar, and EMB media) performed on minibronchoalveolar lavage (m-BAL) airway samples, collected within 1–5 days of the ETA specimen analyzed by PhyloChip, as previously described (Flanagan et al., 2007). We have previously found m-BALs to possess a similar bacterial community composition to that of ETAs obtained concurrently from the same patient (Flanagan et al., 2007). Clinical data (Table 1) were recorded in a secure database, including whether a diagnosis of pneumonia by conventional clinical and radiologic criteria (Zhuo et al., 2008) was made during the patient's hospitalization and the time frame between diagnosis and collection of airway samples. The Committee on Human Research at UCSF approved all study protocols, and all patients or their surrogates provided written, informed consent.

Table 1.

Clinical Characteristics of Subjects and Samples

Patient	Age	Gender	Intubation days at sample collection	Antimicrobial therapy received within the past month	Days of active antimicrobial therapy at time of sample collection	Culture resultsa
1	63	M	16	ceftazidime	16	PAb*
2	69	F	6	vancomycin, tobramycin, levofloxacin	5	PAb*
3	78	M	1	vancomycin, piperacillin/tazobactam, levofloxacin	1	PAb*, KPb*, AF
4	78	M	21	piperacillin/tazobactam	31	PAb*, SMb*
5	86	F	17	levofloxacin	17	PAb*
6	85	F	16	doxycycline, moxifloxacin, vancomycin	1	PAb*
7	61	M	5	vancomycin, piperacillin/tazobactam	7	PAb*, SAb
8	73	M	3	piperacillin/tazobactam	3	PAb, EAb*

^amini-BAL, minibronchoalveolar lavage clinical culture. The most recent, available culture data were obtained from within 1–5 days prior to the endotracheal aspirate sample analyzed by PhyloChip.

^bDetected by PhyloChip; *≥10,000 colony-forming units on quantitative mini-BAL culture.

PA, Pseudomonas aeruginosa; KP, Klebsiella pneumoniae; SA, Staphylococcus aureus; EA, Enterobacter aerogenes; SM, Stenotrophomonas maltophilia; AF, Aspergillus fumigatus.

DNA extraction, 16S rRNA gene amplification, PhyloChip processing

Total DNA was extracted from ETAs (200 μL) using a bead-beating step (5.5 m s⁻¹ for 30 s, FastPrep system) (MP Biomedicals, Cleveland, OH) prior to nucleic acid extraction using the Wizard Genomic DNA Purification kit (Promega, Madison, WI). Twelve, 25-cycle PCR reactions, containing 100 ng of DNA, 2.5 mM each of dNTPs, 1.5 μM each primer (Bact-27F and Bact-1492R) (Lane, 1991) and 0.02 U/μL of ExTaq (Takara Bio, Japan), were performed for each sample across a gradient of annealing temperatures (48–58°C), to maximize the diversity recovered. The resulting PCR products were pooled and gel-purified using the MinElute Gel Extraction kit (Qiagen, Chatsworth, CA). Known concentrations of synthetic 16S rRNA gene fragments and non-16S rRNA gene fragments were spiked into the pooled, purified PCR product, which served as internal standards for normalization. A total of 250 ng of purified PCR product per sample was fragmented, biotin-labeled, and hybridized to the microarray as previously described (Brodie et al., 2006). Washing, staining, and scanning of arrays were conducted according to standard Affymetrix protocols. Background subtraction, noise calculations and scaling were carried out as described previously (Brodie et al., 2006; Desantis et al., 2007).

Analysis of PhyloChip data

Relatively conservative detection and quantification criteria for each taxon were applied, as previously described (Desantis et al., 2007). Briefly, probe-pairs consisting of a perfectly matched and mismatched cross hybridization control probe (containing a mismatch at the 13th nucleotide) were scored as positive if they met two criteria: (1) the fluorescence intensity of the perfectly matched probe was ≥1.3 times greater than that of the mismatched probe, and (2) the difference in intensity in each probe pair was 130 times greater than the squared noise value for that array. The positive fraction (pf ) of probe sets (minimum of 11, median of 24 probe-pairs per taxon) was calculated, and a taxon was considered “present” if the calculated pf was ≥90%. Statistical analyses were performed in the R environment (www.R-project.org), using the ecological community analysis package vegan (version 1.16-1). Log-transformed fluorescence intensities were used to calculate Bray-Curtis dissimilarity measures of ecological distance. Nonmetric multidimensional scaling (NMDS), a nonparametric ordination method that maps community relatedness, in this case using the Bray-Curtis distance metric, was used to assess variability in bacterial community structure. The function adonis (Anderson, 2001), which conducts a matrix-based nonparametric analysis of variance, was applied to explore relationships between community composition and clinical variables, including age, gender, number of intubation days, presence of pneumonia, time frame between pneumonia diagnosis and sample collection, antibiotic and corticosteroid treatments, and survival to ICU discharge. Between-group differences in taxon abundance were assessed by two-tailed t-testing with significance adjusted for false discovery using q-values, as previously described (Storey and Tibshirani, 2003). Taxa exhibiting q values <0.05, a p-value ≤0.02 and a change of >1,000 fluorescence units (log-fold change in 16S rRNA copy number) were considered statistically and biologically significant. Phylogenetic trees were constructed using representative 16S rRNA sequences from the Greengenes database (Desantis et al., 2006). A neighbor-joining tree with nearest-neighbor interchange was produced using FastTree (Price et al., 2009) and uploaded to the Interactive Tree of Life project (http://itol.embl.de/) for annotation (Letunic and Bork, 2007).

Quantitative polymerase chain reaction (Q-PCR)

To confirm that changes in array fluorescence intensities were reflective of changes in target organism abundance, triplicate, Q-PCR reactions were performed for selected taxa containing species of interest, using a Stratagene MxP3000 real-time system and the QuantiTect SYBR Green PCR kit (Qiagen). Primers for taxa containing selected species of interest were designed based on PhyloChip probes for the target taxon (Table 2). Reaction conditions were similar to those previously described (Brodie et al., 2007) with the exception that 10 ng of DNA extract were used in 40 cycles of reaction using the annealing temperatures listed in Table 2 for each primer set. Regression analyses of inverse cycle threshold values plotted against PhyloChip fluorescence intensities were determined for each targeted taxon.

Table 2.

Primers Used for Q-PCR Validation of Targeted Species

Species	Primers	Annealing temperature
P. aeruginosa	5′-CAGTAAGTTAATACCTTGCTGTGCTG-3′	55°C
	5′- TGCTGAACCACCTACGCGC-3′
S. maltophilia	5′-GCCGGCTAATACCTGGTTGGGA-3′	55°C
	5′- CTACCCTCTACCACACTCTAGTCGC-3′
H. cetorum	5′-GCGTTACTCGGAATCACTGGGCGTA-3′	48°C
	5′- ATGAGTATTCCTCTTGATCTCTACG-3′
C. mucosalis	5′-ATGTGGTTTAATTCGAAGATACGCG-3′	52°C
	5′- CACGAGCTGACGACAGCCGTGCAGC-3′

Results

16S rRNA PhyloChip analysis identified a total of 1,213 bacterial taxa present in airway samples from COPD patients obtained during the course of acute exacerbations (complete list is provided in Table 3; see at end of article). Despite recent or ongoing exposure to antibiotics across the group, the mean number of taxa detected in each sample was 411 ± 246 taxa (SD). Identified taxa represented a diverse group of species belonging to 38 bacterial phyla and 140 distinct families (Fig. 1A). Bacterial families detected included members of the Pseudomonadaceae, Pasteurellaceae, Helicobacteraceae, Enterobacteriaceae, Comamonadaceae, Burkholderiaceae, and Alteromonadaceae, among many others. In addition, recently described phyla such as the TM7 subgroup of Gram-positive uncultivable bacteria were also detected in the airways of these patients (Table 3).

Table 3.

All Bacterial Taxa Detected by 16S rRNA Phylochip in Airway Samples of COPD Patients Being Treated for Severe Exacerbations

Phylum	Class	Order	Family	S-Fa	Taxon IDb	Representative speciesc
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	508	uranium mining waste pile clone JG37-AG-81 sp.
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	541	uranium mill tailings soil sample clone GuBH2-AG-47 sp.
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	209	uranium mining waste pile clone JG37-AG-29 sp.
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6425	Great Artesian Basin clone B27
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6335	forested wetland clone FW45
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_6	6345	soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-77 bacterium
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6350	soil isolate Ellin337
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6356	forested wetland clone FW47
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_6	6359	PCE-contaminated site clone CLi114
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_6	6362	grassland soil clone DA052
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6366	PCB-polluted soil clone WD228
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6368	soil clone UA2
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6378	Acidobacterium capsulatum
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6410
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6412	acid mine drainage clone TRB82
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_16	6414	PCE-contaminated site clone CLs73
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6421	PCB-polluted soil clone WD217
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_6	6423	coal effluent wetland clone FW92
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_14	6424	sphagnum peat bog clone K-5b10
Acidobacteria	Unclassified	Unclassified	Unclassified	sf_1	572	forested wetland clone FW144
Acidobacteria	Acidobacteria-4	Ellin6075/11-25	Unclassified	sf_1	435	anaerobic VC-degrading enrichment clone VC47 bacterium
Acidobacteria	Acidobacteria-5	Unclassified	Unclassified	sf_1	523	soil metagenomic library clone 17F9
Acidobacteria	Acidobacteria-4	Ellin6075/11-25	Unclassified	sf_1	790	soil clone 11-25
Acidobacteria	Acidobacteria-4	Ellin6075/11-25	Unclassified	sf_1	87	activated sludge clone 2951
Acidobacteria	Acidobacteria-6	Unclassified	Unclassified	sf_1	350	Mammoth cave clone CCM15a
Acidobacteria	Acidobacteria-6	Unclassified	Unclassified	sf_1	897	Mammoth cave clone CCM8b
Acidobacteria	Acidobacteria-6	Unclassified	Unclassified	sf_1	1049	soil clone C112
Acidobacteria	Solibacteres	Unclassified	Unclassified	sf_1	6426	Great Artesian Basin clone B11
Acidobacteria	Acidobacteria-4	Unclassified	Unclassified	sf_1	6363	soil clone 32-11
Acidobacteria	Unclassified	Unclassified	Unclassified	sf_1	4222	forested wetland clone FW105
Actinobacteria	Actinobacteria	Acidimicrobiales	Acidimicrobiaceae	sf_1	1090
Actinobacteria	Actinobacteria	Acidimicrobiales	Acidimicrobiaceae	sf_1	1749	forest soil clone DUNssu275 (-3A) (OTU#188)
Actinobacteria	Actinobacteria	Acidimicrobiales	Acidimicrobiaceae	sf_1	1856	forested wetland clone RCP2-105
Actinobacteria	Actinobacteria	Acidimicrobiales	Acidimicrobiaceae	sf_1	1360	forested wetland clone RCP2-103
Actinobacteria	Actinobacteria	Actinomycetales	Acidothermaceae	sf_1	1399	uranium mill tailings clone Gitt-KF-183
Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	sf_1	1684	Varibaculum cambriense str. CCUG 44998
Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	sf_1	1227	Actinomyces naeslundii
Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	sf_1	1672	Actinomyces odontolyticus str. CCUG 28084
Actinobacteria	Actinobacteria	Actinomycetales	Actinosynnemataceae	sf_1	1463	Saccharothrix texasensis str. NRRL B-16107T
Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	sf_1	1351	Bifidobacterium psychraerophilum str. T16
Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	sf_1	1967	Bifidobacterium pseudocatenulatum str. JCM1200
Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	sf_1	2040	Bifidobacterium adolescentis str. E-981074T
Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	sf_1	1109	Bifidobacterium thermacidophilum porcinum subsp. suis str. P3-14 subsp.
Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	sf_1	1987	human subgingival plaque clone CX010
Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	sf_1	1444	Bifidobacteriaceae genomosp. C1
Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	sf_1	1835	Bifidobacterium breve str. KB 92
Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	sf_1	1875
Actinobacteria	Actinobacteria	Actinomycetales	Cellulomonadaceae	sf_1	1586	Cellulomonas gelida str. DSM 20111T
Actinobacteria	Actinobacteria	Actinomycetales	Cellulomonadaceae	sf_1	1748	Beutenbergia cavernosa str. DSM 12333
Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	sf_1	1258	ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-MN25
Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	sf_1	1800	ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-MN100
Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	sf_1	1958	Atopobium vaginae VA14183_00
Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	sf_1	1517	Corynebacterium xerosis str. DSM 20743
Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	sf_1	1492	Corynebacterium tuscaniae str. ISS-5309
Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	sf_1	1820	Corynebacterium jeikeium str. ATCC 43734
Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	sf_1	1089	Corynebacterium mucifaciens National Microbiology Laboratory Special identifier 01-0118
Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	sf_1	1374
Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	sf_1	1428	Corynebacterium simulans National Microbiology Laboratory Special identifier 00-0186
Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	sf_1	1493	Corynebacterium tuberculostearicum str. CIP102346
Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	sf_1	1803	Corynebacterium spheniscorum str. CCUG 45512
Actinobacteria	Actinobacteria	Actinomycetales	Dermabacteraceae	sf_1	2053	Brachybacterium nesterenkovii str. DSM 9573
Actinobacteria	Actinobacteria	Actinomycetales	Kineosporiaceae	sf_1	1598	lichen-dominated Antarctic cryptoendolithic community clone FBP402
Actinobacteria	Actinobacteria	Actinomycetales	Kineosporiaceae	sf_1	1961	Kineococcus aurantiacus str. IFO 15268
Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	sf_1	1667	Microbacterium lacticum
Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	sf_1	1197	Arctic sea ice ARK10173
Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	sf_1	1437	freshwater clone SV1-16
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1266	Arthrobacter psychrolactophilus
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1557	Arthrobacter oxydans str. DSM 20119
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1593	Arthrobacter globiformis
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1610	Arthrobacter sp str. AC-51
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1966	TCE-contaminated site clone ccspost2208
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1324	glacial ice isolate str. CanDirty1
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1494	Arthrobacter agilis str. DSM 20550
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1573	Arthrobacter nicotianae str. SB42
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1889	Citricoccus sp. str. 2216.25.22
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	2019	Micrococcus luteus str. HN2-11
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1724	Rothia mucilaginosa str. DSM
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	2020	Rothia dentocariosa str. ChDC B200
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	2063	Rothia dentocariosa str. ATCC 17931
Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	sf_1	1213	Kocuria roseus
Actinobacteria	Actinobacteria	Actinomycetales	Micromonosporaceae	sf_1	1876	Couchioplanes subsp. caeruleus str. IFO13939
Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	sf_1	1175	Mycobacterium cf. xenopi 'Hymi_Wue Tb_939/99' str. Hymi_Wue Tb_939/99
Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	sf_1	1262	Mycobacterium holsaticum str. 1406
Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	sf_1	1308	Mycobacterium pyrenivorans str. DSM 44605
Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	sf_1	1365	Mycobacterium chelonae str. CIP 104535T
Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	sf_1	1650	Mycobacterium tuberculosis str. NCTC 7416 H37Rv
Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	sf_1	1726	Mycobacterium terrae str. ATCC 15755
Actinobacteria	Actinobacteria	Actinomycetales	Nocardiaceae	sf_1	1834	Nocardia transvalensis str. DSM 43405
Actinobacteria	Actinobacteria	Actinomycetales	Nocardiopsaceae	sf_1	1385	Streptomonospora salina str. YIM90002
Actinobacteria	Actinobacteria	Actinomycetales	Promicromonosporaceae	sf_1	1671	Cellulosimicrobium cellulans str. NCIMB 11025
Actinobacteria	Actinobacteria	Actinomycetales	Promicromonosporaceae	sf_1	1711	Promicromonospora sukumoe str. DSM 44121
Actinobacteria	Actinobacteria	Actinomycetales	Pseudonocardiaceae	sf_1	1863
Actinobacteria	Actinobacteria	Actinomycetales	Pseudonocardiaceae	sf_1	1343	Saccharomonospora azurea str. M.Goodfel K161 = NA128 (type st
Actinobacteria	Actinobacteria	Rubrobacterales	Rubrobacteraceae	sf_1	1551	soil isolate Ellin301
Actinobacteria	Actinobacteria	Rubrobacterales	Rubrobacteraceae	sf_1	1739
Actinobacteria	Actinobacteria	Rubrobacterales	Rubrobacteraceae	sf_1	1843	uranium mining waste pile soil sample clone JG30-KF-A23
Actinobacteria	Actinobacteria	Actinomycetales	Sporichthyaceae	sf_1	1695	lichen-dominated Antarctic cryptoendolithic community clone FBP417
Actinobacteria	Actinobacteria	Actinomycetales	Streptosporangiaceae	sf_1	1190	Nonomuraea polychroma str. IFO 14345
Actinobacteria	Actinobacteria	Actinomycetales	Thermomonosporaceae	sf_1	1741	Actinomadura pelletieri str. IMSNU 22169T
Actinobacteria	Actinobacteria	Actinomycetales	Thermomonosporaceae	sf_1	1546	Actinomadura fulvescens str. DSM 43923T
Actinobacteria	Actinobacteria	Unclassified	Unclassified	sf_2	1233
Actinobacteria	Actinobacteria	Unclassified	Unclassified	sf_1	1898	termite gut homogenate clone Rs-J10 bacterium
Actinobacteria	Actinobacteria	Unclassified	Unclassified	sf_1	1367
Actinobacteria	Actinobacteria	Unclassified	Unclassified	sf_1	1370	forested wetland clone RCP1-37
Actinobacteria	Actinobacteria	Acidimicrobiales	Unclassified	sf_1	1666
Actinobacteria	Actinobacteria	Actinomycetales	Unclassified	sf_4	1337	Sturt arid-zone soil clone #0425-2M17
Actinobacteria	Actinobacteria	Actinomycetales	Unclassified	sf_3	1486	deep marine sediment clone MB-A2-108
Actinobacteria	Actinobacteria	Unclassified	Unclassified	sf_1	1676
Actinobacteria	Actinobacteria	Acidimicrobiales	Unclassified	sf_1	1217	DCP-dechlorinating consortium clone SHA-34
Actinobacteria	BD2-10 group	Unclassified	Unclassified	sf_2	1652	marine sediment clone Bol7
Actinobacteria	Actinobacteria	Actinomycetales	Unclassified	sf_3	2045	hypersaline lake clone ML602J-44
Actinobacteria	Actinobacteria	Actinomycetales	Unclassified	sf_3	1130	Georgenia muralis str. 1A-C
Actinobacteria	Actinobacteria	Actinomycetales	Unclassified	sf_3	1687	Jonesia quinghaiensis str. DSM 15701
Actinobacteria	Actinobacteria	Actinomycetales	Unclassified	sf_3	1243	termite gut homogenate clone Rs-M95 bacterium
Actinobacteria	Actinobacteria	Actinomycetales	Unclassified	sf_3	1577	termite gut homogenate clone Rs-N91 bacterium
Actinobacteria	Actinobacteria	Actinomycetales	Unclassified	sf_3	1405	Arthrobacter ureafaciens str. DSM 20126
AD3	Unclassified	Unclassified	Unclassified	sf_1	2338	uranium mining waste pile soil clone JG30-KF-C12
Bacteroidetes	Bacteroidetes	Bacteroidales	Bacteroidaceae	sf_12	5256	termite gut homogenate clone Rs-D38 bacterium
Bacteroidetes	Bacteroidetes	Bacteroidales	Bacteroidaceae	sf_12	5320	Bacteroides distasonis
Bacteroidetes	Bacteroidetes	Bacteroidales	Bacteroidaceae	sf_12	5474	Bacteroides acidofaciens str.A24
Bacteroidetes	Bacteroidetes	Bacteroidales	Bacteroidaceae	sf_12	5551	Bacteroides uniformis
Bacteroidetes	Bacteroidetes	Bacteroidales	Bacteroidaceae	sf_12	5979	Bacteroides fragilis str. YCH46
Bacteroidetes	Flavobacteria	Flavobacteriales	Blattabacteriaceae	sf_1	5828	Blattabacterium species
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Crenotrichaceae	sf_11	5334	autotrophic nitrifying biofilm clone NB-11
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Crenotrichaceae	sf_11	5619	anaerobic VC-degrading enrichment clone VC10 bacterium
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Crenotrichaceae	sf_11	5888	penguin droppings sediments clone KD9-169
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Crenotrichaceae	sf_11	6123	Flexibacter japonensis str. IFO 16041
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Crenotrichaceae	sf_11	6267	Cilia-respiratory isolate str. 243-54
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Crenotrichaceae	sf_11	6249	Haliscomenobacter hydrossis
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flammeovirgaceae	sf_5	6084	Microscilla arenaria str. IFO 15982
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	6079	synonym: CFB group clone APe4_42
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5367	patient's bronchoalveolar lavage isolate str. MDA2507 sp.
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5915	groundwater deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-MN27 bacterium
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5997	Flavobacterium aquatile
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	6274
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5317	Tenacibaculum maritimum str. IFO 15946
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5991	Tenacibaculum ovolyticum str. IAM14318
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	6252	Riftia pachyptila's tube clone R103-B20
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5263	subgingival plaque clone DZ074
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5401	Capnocytophaga gingivalis str. ChDC OS45
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5836	Capnocytophaga granulosa str. LMG 12119; FDC SD4
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5423	Aequorivita antarctica str. QSSC9-14
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5942
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5955	Flavobacterium sp. str. V4.MS.29 = MM_2747
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5971	Cytophaga uliginosa
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5436	Arctic sea ice ARK10004
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5473
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5267	bacterioplankton clone AEGEAN_179
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	sf_1	5914	Psychroserpens burtonensis str. S2-64
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_19	5563	Cytophaga sp. I-545
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_19	5542	Cytophaga sp. I-1787
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_19	5307	Microscilla sericea str. IFO 16561
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_19	5357	Flexibacter ruber str. IFO 16677
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_19	5372
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_19	5566	Hongiella mannitolivorans str. IMSNU 14012 JC2050
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_19	5667	penguin droppings sediments clone KD6-118
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_19	5994	Hymenobacter sp. str. NS/50
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_19	6124	Flexibacter flexilis subsp. pelliculosus str. IFO 16028 subsp.
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_19	6297	EBPR sludge lab scale clone HP1A92
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	sf_20	10311	Cytophaga sp. str. BHI60-57B
Bacteroidetes	Bacteroidetes	Bacteroidales	Porphyromonadaceae	sf_1	5295	swine intestine clone p-987-s962-5
Bacteroidetes	Bacteroidetes	Bacteroidales	Porphyromonadaceae	sf_1	5680	termite gut clone Rs-106
Bacteroidetes	Bacteroidetes	Bacteroidales	Porphyromonadaceae	sf_1	5800	Porphyromonas endodontalis str. ATCC 35406
Bacteroidetes	Bacteroidetes	Bacteroidales	Porphyromonadaceae	sf_1	5817	termite gut homogenate clone Rs-N56 bacterium
Bacteroidetes	Bacteroidetes	Bacteroidales	Porphyromonadaceae	sf_1	5961	chlorobenzene-degrading consortium clone IA-16
Bacteroidetes	Bacteroidetes	Bacteroidales	Porphyromonadaceae	sf_1	5454	Dysgonomonas wimpennyi str. ANFA2
Bacteroidetes	Bacteroidetes	Bacteroidales	Porphyromonadaceae	sf_1	5510	sphagnum peat bog clone 26-4b2
Bacteroidetes	Bacteroidetes	Bacteroidales	Porphyromonadaceae	sf_1	6012	mouse feces clone L11-6
Bacteroidetes	Bacteroidetes	Bacteroidales	Porphyromonadaceae	sf_1	5460	mouse feces clone F8
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	5718	Prevotella tannerae str. 29-1
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	5437	cow rumen clone BE1
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	5916	cow rumen clone BE14
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	6011	rumen clone F24-B03
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	6152	rumen clone RF37
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	6259
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	5249	Prevotella denticola str. ATCC 35308
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	5484	oral periodontitis clone FX046
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	5706	oral cavity clone 3.3
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	5769	Bacteroidaceae str. A42
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	5905	swine intestine clone p-2443-18B5
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	5940	Prevotella sp. str. E7_34
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	5946	tongue dorsa clone DO027
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	6047	deep marine sediment clone MB-A2-107
Bacteroidetes	Bacteroidetes	Bacteroidales	Prevotellaceae	sf_1	6239	tongue dorsa clone DO033
Bacteroidetes	Bacteroidetes	Bacteroidales	Rikenellaceae	sf_5	5892	anoxic bulk soil flooded rice microcosm clone BSV73
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Sphingobacteriaceae	sf_1	5513	crevicular epithelial cells clone AZ123
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Sphingobacteriaceae	sf_1	5913	Sphingobacteriaceae str. Ellin160
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	5573	termite gut homogenate clone Rs-D44 bacterium
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Unclassified	sf_6	5439	Mono Lake at depth 35 m station 6 July 2000 clone ML635J-40 bacterium
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	5475	SHA-25 clone
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	5544	marine? clone KD3-17
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	5783	Mono Lake at depth 35 m station 6 July 2000 clone ML635J-15 bacterium
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	5874	Paralvinella palmiformis mucus secretions clone P. palm 53 bacterium
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	5890	penguin droppings sediments clone KD1-125
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	6046	chlorobenzene-degrading consortium clone IIIB-1
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	5820	cow rumen clone BF24
Bacteroidetes	Unclassified	Unclassified	Unclassified	sf_1	5745
Bacteroidetes	Flavobacteria	Flavobacteriales	Unclassified	sf_3	5248	Delaware River estuary clone 1G12
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	5355	DCP-dechlorinating consortium clone SHA-5
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	5481	marine sediment above hydrate ridge clone Hyd89-72 bacterium
Bacteroidetes	Unclassified	Unclassified	Unclassified	sf_4	5703
Bacteroidetes	Unclassified	Unclassified	Unclassified	sf_4	5785	Mono Lake at depth 35 m station 6 July 2000 clone ML635J-56
Bacteroidetes	Unclassified	Unclassified	Unclassified	sf_4	5787	Mono Lake at depth 35 m station 6 July 2000 clone ML635J-1 bacterium
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	5957	Paralvinella palmiformis mucus secretions clone P. palm C/20 bacterium
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	sf_15	6324	temperate estuarine mud clone KM02
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Unclassified	sf_3	6168	Toolik Lake main station at 3 m depth clone TLM11/TLMdgge04
Bacteroidetes	KSA1	Unclassified	Unclassified	sf_1	5951	CFB group clone ML615J-4
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Unclassified	sf_3	6298	travertine hot spring clone SM1C04
BRC1	Unclassified	Unclassified	Unclassified	sf_2	118	penguin droppings sediments clone KD1-1
BRC1	Unclassified	Unclassified	Unclassified	sf_1	5051	soil clone PBS-III-24
BRC1	Unclassified	Unclassified	Unclassified	sf_1	5143	soil clone PBS-II-1
Caldithrix	Unclassified	Caldithrales	Caldithraceae	sf_2	91	benzoate-degrading consortium clone BA059
Caldithrix	Unclassified	Caldithrales	Caldithraceae	sf_1	2384	saltmarsh clone LCP-89
Chlamydiae	Chlamydiae	Chlamydiales	Chlamydiaceae	sf_1	4820	Chlamydophila pneumoniae str. AR39
Chlamydiae	Chlamydiae	Chlamydiales	Parachlamydiaceae	sf_1	4964	neutral pH mine biofilm clone 44a-B1-34
Chlorobi	Chlorobia	Chlorobiales	Chlorobiaceae	sf_1	262	Chlorobium ferrooxidans DSM 13031 str. KofoX
Chlorobi	Chlorobia	Chlorobiales	Chlorobiaceae	sf_1	859	Chlorobium phaeovibrioides str. 2631
Chlorobi	Chlorobia	Chlorobiales	Chlorobiaceae	sf_1	995	Chlorobium limicola str. M1
Chlorobi	Unclassified	Unclassified	Unclassified	sf_8	5822	Saltmarsh mud clone K-790
Chlorobi	Unclassified	Unclassified	Unclassified	sf_6	5294	Mammoth cave clone CCM9b
Chlorobi	Unclassified	Unclassified	Unclassified	sf_9	6146	sludge clone A12b
Chlorobi	Unclassified	Unclassified	Unclassified	sf_8	549	benzene-degrading nitrate-reducing consortium clone Cart-N2 bacterium
Chlorobi	Unclassified	Unclassified	Unclassified	sf_8	636	benzene-degrading nitrate-reducing consortium clone Cart-N3 bacterium
Chloroflexi	Thermomicrobia	Unclassified	Unclassified	sf_1	1041	Antarctic cryptoendolith clone FBP471
Chloroflexi	Unclassified	Unclassified	Unclassified	sf_2	818
Chloroflexi	Unclassified	Unclassified	Unclassified	sf_5	1051	forest soil clone DUNssu055 (-2B) (OTU#087)
Chloroflexi	Anaerolineae	Chloroflexi-1a	Unclassified	sf_1	927	Paralvinella palmiformis mucus secretions clone P. palm C 37 bacterium
Chloroflexi	Thermomicrobia	Unclassified	Unclassified	sf_2	652	uranium mining waste pile soil sample clone JG30-KF-CM45
Chloroflexi	Anaerolineae	Chloroflexi-1a	Unclassified	sf_1	106	DCP-dechlorinating consortium clone SHD-231
Chloroflexi	Anaerolineae	Unclassified	Unclassified	sf_9	375	forest soil clone C043
Chloroflexi	Anaerolineae	Chloroflexi-1a	Unclassified	sf_1	487	thermophilic UASB granular sludge isolate str. IMO-1 bacterium
Chloroflexi	Anaerolineae	Unclassified	Unclassified	sf_9	576	DCP-dechlorinating consortium clone SHA-36
Chloroflexi	Anaerolineae	Chloroflexi-1a	Unclassified	sf_1	583	anaerobic bioreactor clone SHD-238
Chloroflexi	Anaerolineae	Unclassified	Unclassified	sf_9	72	sediments collected at Charon's Cascade near Echo River October 2000 clone CCD21
Chloroflexi	Anaerolineae	Unclassified	Unclassified	sf_9	727	forest soil clone S0208
Chloroflexi	Unclassified	Unclassified	Unclassified	sf_7	757	DCP-dechlorinating consortium clone SHA-8
Chloroflexi	Anaerolineae	Chloroflexi-1a	Unclassified	sf_1	76	DCP-dechlorinating consortium clone SHA-147
Chloroflexi	Anaerolineae	Chloroflexi-1b	Unclassified	sf_2	789	travertine hot spring clone SM1D10
Chloroflexi	Anaerolineae	Unclassified	Unclassified	sf_9	946	temperate estuarine mud clone KM87
Chloroflexi	Dehalococcoidetes	Unclassified	Unclassified	sf_1	2339	uranium mill tailings soil sample clone Sh765B-TzT-20 bacterium
Chloroflexi	Dehalococcoidetes	Unclassified	Unclassified	sf_1	2367	deep marine sediment clone MB-B2-113
Chloroflexi	Dehalococcoidetes	Unclassified	Unclassified	sf_1	2438	deep marine sediment clone MB-A2-110
Chloroflexi	Dehalococcoidetes	Unclassified	Unclassified	sf_1	2445	deep marine sediment clone MB-A2-103
Chloroflexi	Dehalococcoidetes	Unclassified	Unclassified	sf_1	2485
Chloroflexi	Dehalococcoidetes	Unclassified	Unclassified	sf_1	2497	forested wetland clone FW60
Chloroflexi	Unclassified	Unclassified	Unclassified	sf_12	2523	sponge clone TK10
Chloroflexi	Chloroflexi-4	Unclassified	Unclassified	sf_2	2344	forest soil clone C083
Chloroflexi	Unclassified	Unclassified	Unclassified	sf_1	2534	forest soil clone S085
Coprothermobacteria	Unclassified	Unclassified	Unclassified	sf_1	751	Coprothermobacter sp. str. Dex80-3
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	4967	Toolik Lake main station at 3 m depth clone TLM14
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	5147	Emiliania huxleyi str. Plymouth Marine Laborator PML 92
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	5112	Cyanidium caldarium str. 14-1-1
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	5006
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_11	5098	Euglena tripteris str. UW OB
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_11	5123	Lepocinclis fusiformis str. ACOI 1025
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	4966	Adiantum pedatum
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	4976	Calypogeia muelleriana
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_13	5000	Mitrastema yamamotoi
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	5040	Solanum nigrum
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	5182	Epifagus virginiana—chloroplast
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	5183	Pisum sativum—chloroplast
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	5192	Cycas revoluta
Cyanobacteria	Unclassified	Unclassified	Unclassified	sf_5	4998
Cyanobacteria	Cyanobacteria	Thermosynechococcus	Unclassified	sf_1	5012	Synechococcus sp. str. PCC 6312
Cyanobacteria	Unclassified	Unclassified	Unclassified	sf_9	5038	Rumen isolate str. YS2
Cyanobacteria	Unclassified	Unclassified	Unclassified	sf_9	5164	termite gut homogenate clone Rs-H34
Cyanobacteria	Cyanobacteria	Oscillatoriales	Unclassified	sf_1	5189	Oscillatoria sancta str. PCC 7515
Cyanobacteria	Unclassified	Unclassified	Unclassified	sf_5	5015	Chlorogloeopsis fritschii str. PCC 6912
Cyanobacteria	Unclassified	Unclassified	Unclassified	sf_5	5030	Hapalosiphon welwitschii
Cyanobacteria	Cyanobacteria	Nostocales	Unclassified	sf_1	5057	Nodularia sphaerocarpa str. UTEX B 2093
Cyanobacteria	Cyanobacteria	Oscillatoriales	Unclassified	sf_1	5049	Oscillatoria spongeliae str. 520 bg
Cyanobacteria	Cyanobacteria	Plectonema	Unclassified	sf_1	5190	Plectonema sp. str. F3
Cyanobacteria	Unclassified	Unclassified	Unclassified	sf_8	5206
Deinococcus-Thermus	Unclassified	Unclassified	Unclassified	sf_1	178	Thermus sp. str. C4
Deinococcus-Thermus	Unclassified	Unclassified	Unclassified	sf_1	563	Vulcanithermus mediatlanticus str. TR
Deinococcus-Thermus	Unclassified	Unclassified	Unclassified	sf_2	637	hypersaline pond clone LA7-B27N
Deinococcus-Thermus	Unclassified	Unclassified	Unclassified	sf_3	920
DSS1	Unclassified	Unclassified	Unclassified	sf_2	38	DCP-dechlorinating consortium clone SHA-109
DSS1	Unclassified	Unclassified	Unclassified	sf_1	4405	benzoate-degrading consortium clone BA143
Firmicutes	Mollicutes	Acholeplasmatales	Acholeplasmataceae	sf_1	3955	Weeping tea tree witches' broom phytoplasma tree
Firmicutes	Mollicutes	Acholeplasmatales	Acholeplasmataceae	sf_1	3961	Clover yellow edge mycoplasma-like organism
Firmicutes	Mollicutes	Acholeplasmatales	Acholeplasmataceae	sf_1	3975	Black raspberry witches' broom phytoplasma str. BRWB witches' broom room
Firmicutes	Mollicutes	Acholeplasmatales	Acholeplasmataceae	sf_1	3976
Firmicutes	Mollicutes	Acholeplasmatales	Acholeplasmataceae	sf_1	4044
Firmicutes	Mollicutes	Acholeplasmatales	Acholeplasmataceae	sf_1	4045	Chinaberry yellows phytoplasma
Firmicutes	Mollicutes	Acholeplasmatales	Acholeplasmataceae	sf_1	4046	Pigeon pea witches' broom mycoplasma-like organism
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	sf_1	3386	feedlot manure clone B87
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	sf_1	3522	Aerococcus viridans
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	sf_1	3631	Abiotrophia defectiva str. GIFU12707 (ATCC49176)
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	sf_1	3870	Abiotrophia para-adiacens str. TKT1
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	sf_1	3323	Trichococcus flocculiformis str. DSM 2094
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	sf_1	3326	Nostocoida limicola I str. Ben206
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	sf_1	3504	Marinilactibacillus psychrotolerans str. O21
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	sf_1	3553	Desemzia incerta str. DSM 20581
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	sf_1	3833	Carnobacterium alterfunditum
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	sf_1	3840	Trichococcus pasteurii str. KoTa2
Firmicutes	Bacilli	Bacillales	Alicyclobacillaceae	sf_1	3368	geothermal site isolate str. G1
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3612	Bacillus schlegelii str. ATCC 43741T
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3419	Bacillus algicola str. KMM 3737
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3424	uranium mill tailings clone Gitt-KF-76
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3661	Bacillus sp. str. 2216.25.2
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3688	Bacillus sp. str. SAFN-006
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3926	Lake Bogoria isolate 64B4
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	234	Bacillus vulcani str. 3S-1
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	283	Geobacillus thermocatenulatus str. DSM 730
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	305	Bacillus thermoleovorans
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3460	Geobacillus jurassicus str. DS1
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3540	Geobacillus thermoleovorans str. B23
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3763	Geobacillus stearothermophilus
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3836	Geobacillus stearothermophilus str. 46
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	385	Geobacillus stearothermophilus str. T10
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	462	Geobacillus thermodenitrificans str. DSM 466
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	571	Bacillus caldotenax str. DSM 406
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	829	Geobacillus sp. str. YMTC1049
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3635	Bacillus aeolius str. 4-1
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3827	Bacillus acidogenesis str. 105-2
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3845	hot synthetic compost clone pPD15
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3895	Bacillus sporothermodurans str. M215
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3283	Bacillus niacini str. IFO15566
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3439	Bacillus siralis str. 171544
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3589	Bacillus senegalensis str. RS8; CIP 106 669
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3650
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	1050	Bacillus firmus CV93b
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	246	Bacillus sp. 6160m-C1
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3550	Bacillus megaterium str. QM B1551
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3345	Bacillus pumilus str. S9
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3328	Pseudobacillus carolinae
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3370	Bacillus sp. str. TGS437
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3492	Bacillus subtilis str. IAM 12118T
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3579	Bacillus sp. str. TGS750
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3675	Bacillus mojavensis str. M-1
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3706	Bacillus sonorensis str. NRRL B-23155
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3831	Bacillus licheniformis str. KL-068
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3900	Bacillus licheniformis str. DSM 13
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3909	Bacillus subtilis subsp. Marburg str. 168
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3918	Bacillus subtilis
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3467	Bacillus luciferensis str. LMG 18422
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3489	Bacillus silvestris str. SAFN-010
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3482	garbage compost isolate str. M32
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3383
Firmicutes	Bacilli	Bacillales	Bacillaceae	sf_1	3517	Planococcus maritimus str. TF-9
Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	sf_1	3536
Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	sf_1	3792	Carnobacterium sp. str. D35
Firmicutes	Bacilli	Bacillales	Caryophanaceae	sf_1	3285	Caryophanon latum str. DSM 14151
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	2764
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	3021	Clostridium caminithermale str. DVird3
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	2915	Tepidibacter thalassicus str. SC 562
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	3049	Clostridium paradoxum str. DSM 7308T
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	3077	Clostridium glycolicum str. DSM 1288
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4156	MCB-contaminated groundwater-treating reactor clone RA9C1
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4173	termite gut homogenate clone Rs-D81 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4187	Clostridiales oral clone P4PB_122 P3
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4278	granular sludge clone R1p16
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4297
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4300	termite gut clone Rs-060
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4310	termite gut clone Rs-056
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4364	oral endodontic infection clone MCE3_9
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4406	termite gut homogenate clone Rs-J39 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4477	termite gut homogenate clone Rs-N85 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4502
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4584	Clostridium papyrosolvens str. DSM 2782
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4614	Clostridium sp. str. JC3
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4622	termite gut clone Rs-L36
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4638
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4554	termite gut clone Rs-068
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4180	termite gut homogenate clone Rs-M23 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4225	termite gut clone Rs-116
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4265	termite gut homogenate clone Rs-N70 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4266	termite gut homogenate clone Rs-M86 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4272	termite gut homogenate clone Rs-M34 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4321	termite gut homogenate clone Rs-C76 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4357	Lachnospiraceae bacterium 19gly4
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4359	termite gut homogenate clone Rs-C69 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4369	termite gut homogenate clone Rs-N73 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4415	termite gut homogenate clone Rs-K32 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4418	termite gut homogenate clone Rs-H18 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4475	termite gut homogenate clone Rs-N02 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4507	termite gut homogenate clone Rs-N21 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4524	termite gut clone Rs-093
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4550	swine intestine clone p-320-a3
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4559	cow rumen clone BF30
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4566	swine intestine clone p-2657-65A5
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4582	swine intestine clone p-2600-9F5
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4627	termite gut homogenate clone Rs-A13 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4306	UASB reactor granular sludge clone PD-UASB-4 bacterium
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4607	Clostridium novyi str. NCTC538
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4229
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4551	Clostridium acetobutylicum str. ATCC 824 (T)
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4339	Clostridium chauvoei str. ATCC 10092T
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4598	Clostridium sardiniense str. DSM 600
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	sf_12	4169
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3261	Enterococcus mundtii str. LMG 10748
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3288	Isolation and identification hyper-ammonia producing swine storage pits manure
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3298	Enterococcus saccharolyticus str. LMG 11427
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3318	Enterococcus ratti str. ATCC 700914
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3382
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3392	Vagococcus lutrae str. m1134/97/1; CCUG 39187
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3433	Tetragenococcus muriaticus
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3598	Enterococcus solitarius str. DSM 5634
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3680	Melissococcus plutonius str. NCDO 2440
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3713	Enterococcus cecorum str. ATCC43198
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	sf_1	3881	Enterococcus dispar str. LMG 13521
Firmicutes	Mollicutes	Entomoplasmatales	Entomoplasmataceae	sf_1	4074	swine intestine clone p-2013-s959-5
Firmicutes	Mollicutes	Anaeroplasmatales	Erysipelotrichaceae	sf_3	3952	Erysipelothrix rhusiopathiae str. Pecs 56
Firmicutes	Mollicutes	Anaeroplasmatales	Erysipelotrichaceae	sf_3	3965	TCE-contaminated site clone ccslm238
Firmicutes	Mollicutes	Anaeroplasmatales	Erysipelotrichaceae	sf_3	3981	phototrophic sludge clone PSB-M-3
Firmicutes	Mollicutes	Anaeroplasmatales	Erysipelotrichaceae	sf_3	768
Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	sf_1	28	termite gut homogenate clone Rs-H81 bacterium
Firmicutes	Bacilli	Bacillales	Halobacillaceae	sf_1	3633	Bacillus clausii str. GMBAE 42
Firmicutes	Bacilli	Bacillales	Halobacillaceae	sf_1	3344	Halobacillus yeomjeoni str. MSS-402
Firmicutes	Bacilli	Bacillales	Halobacillaceae	sf_1	3488	Halobacillus salinus str. HSL-3
Firmicutes	Bacilli	Bacillales	Halobacillaceae	sf_1	3702	Amphibacillus xylanus str. DSM 6626
Firmicutes	Bacilli	Bacillales	Halobacillaceae	sf_1	3756	Salibacillus sp. str. YIM-kkny16
Firmicutes	Bacilli	Bacillales	Halobacillaceae	sf_1	3769	Gracilibacillus sp. str. YIM-kkny13
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	2698	termite gut homogenate clone Rs-B88 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	2804	Clostridium amygdalinum str. BR-10
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	2961	termite gut homogenate clone Rs-F92 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	3042	swine intestine clone p-2876-6C5
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	3036	termite gut homogenate clone Rs-F27 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	2668	termite gut homogenate clone Rs-G40 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	3017	termite gut homogenate clone Rs-D48 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	3076	Clostridium nexile
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	2825	Butyrivibrio fibrisolvens str. LP1265
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	2834	Butyrivibrio fibrisolvens str. OB156
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	2844	Pseudobutyrivibrio ruminis str. pC-XS2
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	3059	Butyrivibrio fibrisolvens str. NCDO 2249
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	2994	termite gut clone Rs-L15
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	3038	swine intestine clone p-1594-c5
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	3171	Lachnospira pectinoschiza
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	2931	termite gut homogenate clone Rs-G77 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	3060	termite gut homogenate clone Rs-B14 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	3218	termite gut homogenate clone Rs-N53
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	2681	termite gut homogenate clone Rs-K41 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4212	termite gut clone Rs-061
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4273	termite gut homogenate clone Rs-M14 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4281	granular sludge clone UASB_brew_B86
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4315	termite gut homogenate clone Rs-N94 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4331	granular sludge clone UASB_brew_B84
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4335	termite gut homogenate clone Rs-N86 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4434	termite gut homogenate clone Rs-K11 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4510	termite gut homogenate clone Rs-Q53 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4511	ckncm314-B7-17 clone
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4512	granular sludge clone UASB_brew_B25
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4514	termite gut homogenate clone Rs-B34 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4533	termite gut homogenate clone Rs-N06 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4535	ckncm297-B1-1 clone
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4539	termite gut homogenate clone Rs-C61 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4540	termite gut homogenate clone Rs-M18 bacterium
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4567	human colonic clone HuCB5
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4571	Faecalibacterium prausnitzii str. ATCC 27766
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4613	rumen clone 3C0d-3
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4623	human colonic clone HuCA1
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	sf_5	4525	termite gut homogenate clone Rs-Q18 bacterium
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3330	Lactobacillus kitasatonis str. KM9212
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3342	Lactobacillus crispatus str. DSM 20584 T
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3478	Lactobacillus crispatus str. ATCC33197
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3490	Lactobacillus suntoryeus str. LH
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3618	Lactobacillus jensenii str. KC36b
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3696	Lactobacillus kalixensis str. Kx127A2; LMG 22115T; DSM 16043T; CCUG 48459T
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3395	Lactobacillus reuteri str. DSM 20016 T
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3547	Lactobacillus frumenti str. TMW 1.666
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3566	Lactobacillus pontis str. LTH 2587
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3798	Lactobacillus fermentum str. MD-9
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3521	Pediococcus inopinatus str. DSM 20285
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3885	Pediococcus pentosaceus
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3634	Lactobacillus letivazi str. JCL3994
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3767	Lactobacillus suebicus str. CECT 5917T
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3810	Lactobacillus brevis
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3829	Lactobacillus paralimentarius str. DSM 13238
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3366	Lactobacillus saerimneri str. GDA154 LMG 22087 DSM 16049 (T); CCUG 48462 (T)
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3418	Lactobacillus subsp. aviarius
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3703	Lactobacillus salivarius str. RA2115
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3914	Lactobacillus cypricasei str. LMK3
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3821	Lactobacillus casei
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3768	Lactobacillus perolens str. L532
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	sf_1	3526	Lactobacillus sakei
Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	sf_1	3497	Weissella koreensis S-5673
Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	sf_1	3573	Leuconostoc ficulneum str. FS-1
Firmicutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	sf_1	3929	Mycoplasma gypsbengalensis str. Gb-V33
Firmicutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	sf_1	3997	Mycoplasma salivarium str. PG20(T)
Firmicutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	sf_1	4014	Mycoplasma pulmonis str. UAB CTIP
Firmicutes	Bacilli	Bacillales	Paenibacillaceae	sf_1	3415	Paenibacillus nematophilus str. NEM1b
Firmicutes	Bacilli	Bacillales	Paenibacillaceae	sf_1	3630
Firmicutes	Bacilli	Bacillales	Paenibacillaceae	sf_1	3595	Paenibacillus sp. str. MB 2039
Firmicutes	Bacilli	Bacillales	Paenibacillaceae	sf_1	3299	Brevibacillus borstelensis str. LMG 15536
Firmicutes	Bacilli	Bacillales	Paenibacillaceae	sf_1	3641	Brevibacillus sp. MN 47.2a
Firmicutes	Bacilli	Bacillales	Paenibacillaceae	sf_1	319	Ammoniphilus oxalaticus str. RAOx-FF
Firmicutes	Bacilli	Bacillales	Paenibacillaceae	sf_1	625	Ammoniphilus oxalivorans str. RAOx-FS
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	304	Selenomonas ruminantium str.JCM6582
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	709	Selenomonas ruminantium str.S20
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	710	Centipeda periodontii str. HB-2
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	131	pig feces clone
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	181	Allisonella histaminiformans str. MR2
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	59	swine intestine clone p-1941-s962-3
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	940	Veillonella dispar str. DSM 20735
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	1036	Great Artesian Basin clone G07
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	428	chlorobenzene-degrading consortium clone IIIA-1
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	534	chlorobenzene-degrading consortium clone IIA-26
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	992	anoxic bulk soil flooded rice microcosm clone BSV43 clone
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	242	Desulfosporosinus orientis str. DSMZ 7493
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	300	benzene-contaminated groundwater clone ZZ12C8
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	39	forested wetland clone RCP2-71
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	2721	termite gut homogenate clone Rs-N71 bacterium
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	2729	DCP-dechlorinating consortium clone SHA-58
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	2679	termite gut homogenate clone BCf9-13
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	2694	oral periodontitis clone FX028
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	2714	termite gut homogenate clone Rs-N27 bacterium
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	2913	termite gut homogenate clone Rs-N82 bacterium
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	3080	termite gut homogenate clone Rs-F43 bacterium
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	3112	Evry municipal wastewater treatment plant clone 012C11_B_SD_P15
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	3182	termite gut homogenate clone Rs-Q64 bacterium
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	2993	oral clone P2PB_46 P3
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	2738	Mogibacterium neglectum str. ATCC 700924 (= P9a-h)
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	2805	oral periodontitis clone FX033
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	2797	Isolation and identification hyper-ammonia producing swine storage pits manure
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	619	TCE-dechlorinating microbial community clone 1G
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	224	Finegoldia magna str. ATCC 29328
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	58	Peptostreptococcus sp. str. E3_32
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	1037	Finegoldia magna
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	616	Peptoniphilus lacrimalis str. CCUG 31350
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	sf_5	393	Anaerococcus vaginalis str. CCUG 31349
Firmicutes	Bacilli	Bacillales	Sporolactobacillaceae	sf_1	3365	Bacillus sp. clone ML615J-19
Firmicutes	Bacilli	Bacillales	Sporolactobacillaceae	sf_1	3747	Bacillus sp. str. C-59-2
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3258	Staphylococcus auricularis str. MAFF911484 ATCC33753T
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3284
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3545
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3569	Staphylococcus saprophyticus
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3585
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3592	Staphylococcus caprae str. DSM 20608
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3605
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3628	Staphylococcus haemolyticus str. CCM2737
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3638	Staphylococcus sp str. AG-30
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3654	Staphylococcus pettenkoferi str. B3117
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3684	Staphylococcus sciuri
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3794
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3822	Staphylococcus succinus str. SB72
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3494	Micrococcus luteus B-P 26
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3865	Macrococcus lamae str. CCM 4815
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	sf_1	3432	deep-sea sediment isolate str. P_wp0225
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3722	Lactococcus Il1403 subsp. lactis str. IL1403
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3869	Streptococcus equi subsp. zooepidemicus str. Tokyo1291 subsp.
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3699	Streptococcus agalactiae str. 2603V/R
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3907	aortic heart valve patient with endocarditis clone v6
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3250	Streptococcus bovis str. B315
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3253	derived cheese sample clone 32CR
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3313	Streptococcus salivarius str. ATCC 7073
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3397	Streptococcus macedonicus str. ACA-DC 206 LAB617
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3422	Streptococcus thermophilus str. DSM 20617
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3543
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3588	Streptococcus downei str. ATCC 33748
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3906	Streptococcus bovis str.ATCC 43143
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3499	Streptococcus constellatus str. ATCC27823
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3446	Streptococcus bovis str. HJ50
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3560	Streptococcus gallinaceus str. CCUG 42692
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3753	Streptococcus suis str. 8074
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3251	Streptococcus cristatus str. ATCC 51100
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3287	tongue dorsum scrapings clone FP015
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3290	Streptococcus mitis str. Sm91
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3629	Streptococcus mutans str. UA96
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	sf_1	3685	Streptococcus gordonii str. ATCC 10558
Firmicutes	Clostridia	Clostridiales	Syntrophomonadaceae	sf_5	2456	granular sludge clone R4b14
Firmicutes	Bacilli	Bacillales	Thermoactinomycetaceae	sf_1	3301	Thermoactinomyces sp. str. 700375
Firmicutes	Unclassified	Unclassified	Unclassified	sf_8	546	Ferribacter thermoautotrophicus
Firmicutes	Clostridia	Clostridiales	Unclassified	sf_17	2324
Firmicutes	Desulfotomaculum	Unclassified	Unclassified	sf_1	2351	Desulfotomaculum thermobenzoicum str. DSM 6193
Firmicutes	Desulfotomaculum	Unclassified	Unclassified	sf_1	2359	UASB granular sludge clone JP
Firmicutes	Clostridia	Unclassified	Unclassified	sf_3	2373
Firmicutes	Symbiobacteria	Symbiobacterales	Unclassified	sf_1	2388	G+C Gram-positive clone YNPRH70A
Firmicutes	Unclassified	Unclassified	Unclassified	sf_8	2433	Ferribacter thermoautotrophicus str. JW/JH-Fiji-2
Firmicutes	Desulfotomaculum	Unclassified	Unclassified	sf_1	2443	Desulfotomaculum thermoacetoxidans str. DSM 5813
Firmicutes	Desulfotomaculum	Unclassified	Unclassified	sf_1	2490	Desulfotomaculum solfataricum str. V21
Firmicutes	Clostridia	Unclassified	Unclassified	sf_4	2398	deep marine sediment clone MB-C2-106
Firmicutes	Symbiobacteria	Symbiobacterales	Unclassified	sf_1	77	thermal soil clone YNPFFP9
Firmicutes	Clostridia	Clostridiales	Unclassified	sf_17	926
Firmicutes	Desulfotomaculum	Unclassified	Unclassified	sf_1	198	Pelotomaculum sp. str. JT
Firmicutes	Catabacter	Unclassified	Unclassified	sf_4	2716	termite gut homogenate clone Rs-F76 bacterium
Firmicutes	Clostridia	Clostridiales	Unclassified	sf_17	3476
Firmicutes	Bacilli	Lactobacillales	Unclassified	sf_1	3289	Isobaculum melis CCUG 37660T
Firmicutes	Bacilli	Lactobacillales	Unclassified	sf_1	3481
Firmicutes	Clostridia	Clostridiales	Unclassified	sf_17	4168
Firmicutes	Catabacter	Unclassified	Unclassified	sf_4	4503	termite gut homogenate clone Rs-H83 bacterium
Firmicutes	Unclassified	Unclassified	Unclassified	sf_8	4536	Mono Lake at depth 35m station 6 July 2000 clone ML635J-14 G+C
Firmicutes	Clostridia	Unclassified	Unclassified	sf_7	4216
Firmicutes	Catabacter	Unclassified	Unclassified	sf_1	4261	termite gut homogenate clone Rs-G04 bacterium
Firmicutes	Catabacter	Unclassified	Unclassified	sf_1	4293	termite gut homogenate clone Rs-Q01 bacterium
Firmicutes	gut clone group	Unclassified	Unclassified	sf_1	4298	human mouth clone P4PA_66
Firmicutes	Clostridia	Clostridiales	Unclassified	sf_17	4307
Firmicutes	Catabacter	Unclassified	Unclassified	sf_4	4526	TCE-contaminated site clone ccslm210
Firmicutes	gut clone group	Unclassified	Unclassified	sf_1	4616	rumen clone F23-C12
Fusobacteria	Fusobacteria	Fusobacterales	Fusobacteriaceae	sf_3	367	Leptotrichia amnionii str. AMN-1
Fusobacteria	Fusobacteria	Fusobacterales	Fusobacteriaceae	sf_3	558	Sneathia sanguinegens str. CCUG 41628T
Fusobacteria	Fusobacteria	Fusobacterales	Fusobacteriaceae	sf_1	488	Fusobacterium nucleatum subsp. vincentii str. ATCC 49256
Gemmatimonadetes	Unclassified	Unclassified	Unclassified	sf_5	442	forest soil clone S0134
Gemmatimonadetes	Unclassified	Unclassified	Unclassified	sf_5	227	uranium mining waste pile clone JG37-AG-36
Gemmatimonadetes	Unclassified	Unclassified	Unclassified	sf_5	9464	lodgepole pine rhizosphere soil British Columbia Ministry Forests Long-Term Soil Productivity
Gemmatimonadetes	Unclassified	Unclassified	Unclassified	sf_5	10112	forest soil clone NOS7.157WL
Gemmatimonadetes	Unclassified	Unclassified	Unclassified	sf_5	317	penguin droppings sediments clone KD8-87
Gemmatimonadetes	Unclassified	Unclassified	Unclassified	sf_5	1127	uranium mining waste pile near Johanngeorgenstadt soil clone JG37-AG-21
Gemmatimonadetes	Unclassified	Unclassified	Unclassified	sf_5	1565	uranium mining waste pile clone JG34-KF-418
Gemmatimonadetes	Unclassified	Unclassified	Unclassified	sf_5	2047	soil clone #0319-7G21
LD1PA group	Unclassified	Unclassified	Unclassified	sf_1	10118	anoxic marine sediment clone LD1-PA38
Lentisphaerae	Unclassified	Unclassified	Unclassified	sf_5	10027	Cytophaga sp. str. Dex80-43
Lentisphaerae	Unclassified	Unclassified	Unclassified	sf_5	10330	Mono lake clone ML635J-58
Lentisphaerae	Unclassified	Unclassified	Unclassified	sf_5	9704	Cytophaga sp. str. Dex80-64
marine group A	mgA-2	Unclassified	Unclassified	sf_1	6344	bacterioplankton clone ZA3648c
marine group A	mgA-1	Unclassified	Unclassified	sf_1	6408	Sargasso Sea
marine group A	mgA-1	Unclassified	Unclassified	sf_1	6454	marine clone SAR406
Natronoanaerobium	Unclassified	Unclassified	Unclassified	sf_1	769	fjord ikaite column clone un-c23
Natronoanaerobium	Unclassified	Unclassified	Unclassified	sf_1	2437	Mono Lake at depth 23m station 6 July 2000 clone ML623J-19
Natronoanaerobium	Unclassified	Unclassified	Unclassified	sf_1	3570	Bacillus sp. clone ML1228J-1
Natronoanaerobium	Unclassified	Unclassified	Unclassified	sf_1	3745	Mono Lake at depth 35m station 6 July 2000 clone ML635J-45
Natronoanaerobium	Unclassified	Unclassified	Unclassified	sf_1	4377	Mono Lake at depth 35m station 6 July 2000 clone ML635J-65 G+C
NC10	NC10-1	Unclassified	Unclassified	sf_1	452	vadose clone 5G01
NC10	NC10-1	Unclassified	Unclassified	sf_1	536	uranium mill tailings clone GuBH2-AD-8
NC10	NC10-2	Unclassified	Unclassified	sf_1	10254	uranium mill tailings soil sample clone Sh765B-TzT-35
Nitrospira	Nitrospira	Nitrospirales	Nitrospiraceae	sf_1	984	uranium mining waste pile clone JG37-AG-131 sp.
Nitrospira	Nitrospira	Nitrospirales	Nitrospiraceae	sf_2	542	forested wetland clone FW19
Nitrospira	Nitrospira	Nitrospirales	Nitrospiraceae	sf_2	544	forested wetland clone FW5
Nitrospira	Nitrospira	Nitrospirales	Nitrospiraceae	sf_2	697	forested wetland clone FW118
OP10	CH21 cluster	Unclassified	Unclassified	sf_1	326	geothermal clone ST01-SN3H
OP10	Unclassified	Unclassified	Unclassified	sf_4	484	forested wetland clone FW68
OP10	CH21 cluster	Unclassified	Unclassified	sf_1	514	sludge clone SBRA136
OP10	Unclassified	Unclassified	Unclassified	sf_5	9782	Rocky Mountain alpine soil clone S1a-1H
OP3	Unclassified	Unclassified	Unclassified	sf_4	628	CB-contaminated groundwater clone GOUTB15
OP3	Unclassified	Unclassified	Unclassified	sf_2	349	soil clone PBS-25
OP9/JS1	OP9	Unclassified	Unclassified	sf_1	726	hot spring clone OPB72
OP9/JS1	OP9	Unclassified	Unclassified	sf_1	969	DCP-dechlorinating consortium clone SHA-1
phylum_tax	class_tax	order_tax	family_tax	subfamily	otu_id	rep_prokMSAname
Planctomycetes	Planctomycetacia	Planctomycetales	Anammoxales	sf_2	4683	anoxic basin clone CY0ARA028B09
Planctomycetes	Planctomycetacia	Planctomycetales	Anammoxales	sf_4	4694	USA: Colorado Fort collins Horsetooth Reservoir clone HT2F11
Planctomycetes	Planctomycetacia	Planctomycetales	Anammoxales	sf_4	9662	Great Artesian Basin clone B83
Planctomycetes	Planctomycetacia	Planctomycetales	Pirellulae	sf_3	4670
Planctomycetes	Planctomycetacia	Planctomycetales	Pirellulae	sf_3	4677	aerobic basin clone CY0ARA032A03
Planctomycetes	Planctomycetacia	Planctomycetales	Planctomycetaceae	sf_3	4652	anoxic basin clone CY0ARA028C04
Planctomycetes	Planctomycetacia	Planctomycetales	Planctomycetaceae	sf_3	4948	anoxic basin clone CY0ARA027D01
Proteobacteria	Alphaproteobacteria	Acetobacterales	Acetobacteraceae	sf_1	7529	Gluconacetobacter europaeus str. ZIM B028 V3
Proteobacteria	Gammaproteobacteria	Acidithiobacillales	Acidithiobacillaceae	sf_1	8320	acid mine drainage clone BA11
Proteobacteria	Gammaproteobacteria	Acidithiobacillales	Acidithiobacillaceae	sf_1	8552	Acidithiobacillus ferrooxidans str. D2
Proteobacteria	Gammaproteobacteria	Acidithiobacillales	Acidithiobacillaceae	sf_1	9224	Acidithiobacillus albertensis str. DSM 14366
Proteobacteria	Gammaproteobacteria	Acidithiobacillales	Acidithiobacillaceae	sf_1	9497	Acidithiobacillus ferrooxidans str. ATCC 19859
Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	sf_1	9294	Arctic deep sea Isolation common chemoorganotrophic oxygen-respiring polar current d 1210
Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	sf_1	8340	Aeromonas ichthiosmia
Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	sf_1	8364	Aeromonas allosaccharophila str. CECT 4199
Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	sf_1	8621	Aeromonas sp. PAR2A
Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	sf_1	9000	Aeromonas culicicola str. MTCC 3249
Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	sf_1	9026	Haemophilus piscium str. NCIMB 1952
Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	sf_1	9440	Aeromonas sobria str. NCIMB 12065
Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	sf_1	9494	Aeromonas molluscorum str. 849T
Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	sf_1	7737	atrazine-catabolizing microbial presence methanol clone KRA30+06A
Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	sf_1	7768	swine intestine clone p-861-a5
Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	sf_1	7788	atrazine-catabolizing microbial absence methanol clone KRA30-58
Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	sf_1	7838	Alcaligenes defragrans str. PD-19
Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	sf_1	7902	Alcaligenes faecalis str. M3A
Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	sf_1	7932	Achromobacter subsp. denitrificans str. DSM 30026 (T)
Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	sf_1	7984	Waste-gas biofilter clone BIfciii38
Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	sf_1	7992	Alcaligenes faecalis 5659-H
Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	sf_1	8062	Brackiella oedipodis str. LMG 1945 R8846
Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	sf_1	8094	Alcaligenes sp. str. VKM B-2263 dcm6
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Alcanivoraceae	sf_1	8335	Alcanivorax sp. str. K3-3 (MBIC 4323)
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Alcanivoraceae	sf_1	9658	Alcanivorax sp. str. Haw1
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9035	Microbulbifer sp. str. JAMB-A94
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8348	Arctic sea ice ARK10038
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8484	Alteromonadaceae isolate str. LA50
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8503	Arctic sea ice ARK10244
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8578	Marinobacter lipolyticus str. SM-19
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8594	Marinobacter sp. str. SBS
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9239	Arctic sea ice ARK10228
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8196
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8222
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8600	Colwellia piezophila str. Y223G
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8753	Idiomarina loihiensis str. GSP37
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8174	attached marine recovered surface clone 17 proteobacterium
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8318	Aestuariibacter salexigens str. JC2042
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8374	Agarivorans albus str. MKT 89
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8533
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8695	Arctic pack ice; northern Fram Strait; 80 31.1 N; 01 deg 59.7 min E clone ARKIA-34
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8863	Alteromonas marina str. SW-47
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8970	Arctic seawater isolate str. R9879
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8978	Arctic sea ice ARK10108
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9230	Antarctic pack ice Lasarev Sea Southern Ocean clone ANTXI/4_14-62 sea
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9236	attached marine recovered surface clone 18 proteobacterium
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9288	Alteromonas stellipolaris str. LMG 21861
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9292
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9501	sea water isolate str. BP-PH
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9562	Alteromonadaceae clone PH-B55N
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8172	Pseudoalteromonas sp. str. Bdeep-1
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8336	Alteromonas sp. str. MS23
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8580	Arctic seawater isolate str. R7076
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8932	Pseudoalteromonas antarctica str. N-1
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8975	Alteromonas sp. str. NIBH P1M3
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9058	Pseudoalteromonas carrageenovora str. ATCC 12662T
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9111	Pseudoalteromonas sp. str. E36
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9143	Pseudoalteromonas agarivorans str. KMM 255
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9205	marine clone Arctic96B-17
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9218	Pseudoalteromonas haloplanktis str. ATCC 14393
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9324	Pseudoalteromonas ruthenica str. KMM300
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9386	Alteromonas sp. str. NIBH P2M11
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9640	exposed to diatom detritus isolate str. Tw-10 Tw-10
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8643	Pseudoalteromonas porphyrae str. S2-65
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9369	Pseudoalteromonas luteoviolacea str. NCIMB 1893T
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9222	Shewanella hanedai str. CIP 103207T
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9384	Moritella viscosa str. NVI 88/478T
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8916	Shewanella algae str. 43940
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9067	Shewanella algae str. ACM 4733
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9416	marine isolate str. R8
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9586	Shewanella gaetbuli str. TF-27
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8579	Psychromonas profunda str. 2825
Proteobacteria	Alphaproteobacteria	Rickettsiales	Anaplasmataceae	sf_3	6628	Wolbachia pipientis
Proteobacteria	Alphaproteobacteria	Rickettsiales	Anaplasmataceae	sf_3	6648	Wolbachia sp
Proteobacteria	Alphaproteobacteria	Rickettsiales	Anaplasmataceae	sf_3	6803	Wolbachia sp. Dlem16SWol
Proteobacteria	Alphaproteobacteria	Rickettsiales	Anaplasmataceae	sf_3	6908	Rhinocyllus conicus endosymbiont
Proteobacteria	Alphaproteobacteria	Rickettsiales	Anaplasmataceae	sf_3	7481	Wolbachia pipientis
Proteobacteria	Alphaproteobacteria	Rhizobiales	Bartonellaceae	sf_1	7056	Bartonella schoenbuchensis str. R1
Proteobacteria	Alphaproteobacteria	Rhizobiales	Bartonellaceae	sf_1	7384	aortic heart valve patient with endocarditis clone v9
Proteobacteria	Alphaproteobacteria	Rhizobiales	Bartonellaceae	sf_1	7415	Bartonella quintana str. Toulouse
Proteobacteria	Alphaproteobacteria	Rhizobiales	Bartonellaceae	sf_1	7634	Bartonella henselae str. Houston-1
Proteobacteria	Deltaproteobacteria	Bdellovibrionales	Bdellovibrionaceae	sf_1	10010	uranium mining waste pile clone JG37-AG-139 proteobacterium
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Beijerinck/Rhodoplan/Methylocyst	sf_3	7401	Scrippsiella trochoidea NEPCC 15
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Beijerinck/Rhodoplan/Methylocyst	sf_3	6651	Beijerinckia indica
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Beijerinck/Rhodoplan/Methylocyst	sf_3	7275	Mammoth cave clone CCU18
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Beijerinck/Rhodoplan/Methylocyst	sf_3	7219	Methylosinus sporium
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Beijerinck/Rhodoplan/Methylocyst	sf_3	7640	Methylosinus trichosporium
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Beijerinck/Rhodoplan/Methylocyst	sf_3	6762	acidic forest soil clone UP8
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Beijerinck/Rhodoplan/Methylocyst	sf_3	7153	Methylocella tundrae str. Y1
Proteobacteria	Alphaproteobacteria	Rhizobiales	Bradyrhizobiaceae	sf_1	7029
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7403	Oligotropha carboxidovorans str. S23
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	6927	Nitrobacter hamburgensis str. X14
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	6768	Rhodopseudomonas palustris str. GH
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	6799	Rhodopseudomonas palustris str. ATCC 17001
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7316
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7333	Afipia genosp. 4 str. G3644
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	6941	Rhodopseudomonas rhenobacensis str. Klemme Rb
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7087	Bradyrhizobium japonicum HA1
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7398	Bradyrhizobium japonicum str. USDA 38
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	6636	Bradyrhizobium elkanii str. USDA 76
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	6867	heavy metal-contaminated soil clone a13131
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	6887	Bradyrhizobium str. YB2
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7044	Afipia genosp. 2 str. G4438
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7126	ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-MN96 proteobacterium
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7390	Afipia genosp. 10 str. G8996
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7477	Bradyrhizobium elkanii str. SEMIA 6028
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7522	Bradyrhizobium sp. str. KKI14
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	6878	Bradyrhizobium japonicum SD5
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	6917	Bradyrhizobium japonicum str. IAM 12608
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Bradyrhizobiaceae	sf_1	7353	temperate estuarine mud clone HC65
Proteobacteria	Alphaproteobacteria	Rhizobiales	Brucellaceae	sf_1	6757	Ochrobactrum anthropi str. ESC1
Proteobacteria	Alphaproteobacteria	Rhizobiales	Brucellaceae	sf_1	6981	Ochrobactrum gallinifaecis str. Iso 196
Proteobacteria	Alphaproteobacteria	Rhizobiales	Brucellaceae	sf_1	6995
Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	sf_1	7720	penguin droppings sediments clone KD1-79
Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	sf_1	7771	Burkholderia glathei str. ATCC 29195T
Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	sf_1	7782	Burkholderia hospita str. LMG 20598T
Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	sf_1	7969	Burkholderia sp.
Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	sf_1	8059	Burkholderia caribensis str. MWAP71
Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	sf_1	8068	Burkholderia caryophylli str. ATCC 25418
Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	sf_1	7747
Proteobacteria	Alphaproteobacteria	Consistiales	Caedibacteraceae	sf_4	7157	acid mine drainage clone ASL45
Proteobacteria	Alphaproteobacteria	Consistiales	Caedibacteraceae	sf_5	6947	termite gut homogenate clone Rs-B60 proteobacterium
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10446
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10461	deepest cold-seep area Japan Trench clone JTB360 proteobacterium
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10523	Riftia pachyptila's tube clone R103-B70
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10538	Arcobacter cryaerophilus
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10447	Sulfurospirillum deleyianum str. Spirillum 5175
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10464	Campylobacter sp. str. NO2B
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10434	Campylobacter gracilis
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10456	Campylobacter showae
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10463	Campylobacter subsp. fetus
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10484	Campylobacter helveticus
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10540	Campylobacter showae str. LMG 12636
Proteobacteria	Gammaproteobacteria	Cardiobacteriales	Cardiobacteriaceae	sf_1	8536	Cardiobacterium hominis
Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	sf_1	7486	Asticcacaulis excentricus str. ATCC15261
Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	sf_1	6781	Brevundimonas intermedia str. MBIC2712 ATCC15262
Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	sf_1	6904	Brevundimonas vesicularis str. IAM 12105T
Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	sf_1	6909	Brevundimonas diminuta str. DSM 1635
Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	sf_1	6968	Brevundimonas diminuta str. IAM 12691T
Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	sf_1	7359	Brevundimonas bacteroides str. CB7
Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	sf_1	7366	Brevundimonas subvibrioides str. CB81
Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	sf_1	7436	Brevundimonas sp. str. FWC40
Proteobacteria	Gammaproteobacteria	Chromatiales	Chromatiaceae	sf_1	9048	Allochromatium sp. AT2202
Proteobacteria	Gammaproteobacteria	Chromatiales	Chromatiaceae	sf_1	8546	Thiocapsa litoralis
Proteobacteria	Gammaproteobacteria	Chromatiales	Chromatiaceae	sf_1	8527
Proteobacteria	Gammaproteobacteria	Chromatiales	Chromatiaceae	sf_1	8697	Thiococcus sp. AT2204
Proteobacteria	Gammaproteobacteria	Chromatiales	Chromatiaceae	sf_1	9054
Proteobacteria	Gammaproteobacteria	Chromatiales	Chromatiaceae	sf_1	9052
Proteobacteria	Gammaproteobacteria	Chromatiales	Chromatiaceae	sf_1	9356
Proteobacteria	Gammaproteobacteria	Chromatiales	Chromatiaceae	sf_1	9370	isolate str. HTB019
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	8112	Comamonas testosteroni str. SMCC B329
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7704	freshwater clone PRD01b009B
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7705	penguin droppings sediments clone KD4-7
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7801	Toolik Lake main station at 3 m depth clone TLM05/TLMdgge10 proteobacterium
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7829	Xylophilus ampelinus str. ATCC 33914
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7928	penguin droppings sediments clone KD5-43
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7941	MCB-contaminated groundwater-treating reactor clone RB9C10
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7986	Arctic sea ice ARK10281
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	8138	Pseudomonas lanceolata str. ATCC 14669T
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	8139	Delftia tsuruhatensis str. AD9
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7856	Variovorax paradoxus
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7964	napthalene-contaminated sediment clone 76
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7888	Hydrogenophaga flava str. DSM 619T
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7919	strain isolate str. rM4
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7987	Acidovorax sp. str. OS-6
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	8012	Acidovorax konjaci str. DSM 7481
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	8018	Acidovorax delafieldii str. ATCC 17505
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	8021	Acidovorax facilis str. CCUG 2113
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	8022	Acidovorax avenae subsp. cattleyae str. NCPPB 961 subsp.
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	8031	strain isolate str. rJ10
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	8046	Acidovorax defluvii str. BSB411
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	8152	nephridia Octolasion lacteum clone Ol2-2
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7807	Aquaspirillum metamorphum str. DSM 1837
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7884	Germany:Elbe River clone Elb37
Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	sf_1	7965	Anoxobacterium dechloraticum
Proteobacteria	Gammaproteobacteria	Legionellales	Coxiellaceae	sf_3	7893	agricultural soil clone SC-I-71
Proteobacteria	Gammaproteobacteria	Legionellales	Coxiellaceae	sf_3	8457	5' clone CHAB-XI-27
Proteobacteria	Gammaproteobacteria	Legionellales	Coxiellaceae	sf_3	9198	uranium mining waste pile clone KF-JG30-B15 KF-JG30-B15
Proteobacteria	Gammaproteobacteria	Legionellales	Coxiellaceae	sf_3	8969	uranium mining waste pile soil sample clone JG30-KF-C15 proteobacterium
Proteobacteria	Gammaproteobacteria	Legionellales	Coxiellaceae	sf_3	9444	forested wetland clone FW23
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfoarculaceae	sf_2	10227	marine sediment clone Bol11
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	sf_5	9666	marine sediment above hydrate ridge clone Hyd89-13 proteobacterium
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	sf_5	9875	hydrothermal sediment clone AF420354
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	sf_5	9800	forested wetland clone FW57
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	sf_5	10268
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	sf_5	10046	Desulfobacterium cetonicum str. DSM 7267 oil recovery water
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	sf_5	10239
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	sf_5	10319	sulfate-reducing habitat clone SLM-CP-116
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	sf_5	10031	Antarctic sediment clone SB1_49
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	sf_5	10083	Desulfobacter curvatus str. DSM 3379
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	sf_5	9940	Antarctic sediment clone SB2_56
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobulbaceae	sf_1	10047	epibiontic clone C11-D3
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobulbaceae	sf_1	10187	Mono Lake at depth 23 m station 6 July 2000 clone ML623J-57 proteobacterium
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobulbaceae	sf_1	9734	Riftia pachyptila's tube clone R103-B13
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobulbaceae	sf_1	9739	gas hydrate clone Hyd89-51
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfohalobiaceae	sf_1	9894	Desulfonauticus submarinus str. 6N
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfomicrobiaceae	sf_1	10079	Desulfomicrobium baculatum str. DSM 1742
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	sf_1	10262	Desulfovibrio sp. str. Ac5.2
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	sf_1	10248	Desulfovibrio giganteus str. DSM 4370
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	sf_1	10016	termite gut homogenate clone Rs-N35 proteobacterium
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	sf_1	9826	termite gut homogenate clone Rs-M72 proteobacterium
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	sf_1	10071	Desulfovibrio desulfuricans
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	sf_1	10212
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	sf_1	9709	termite gut homogenate clone Rs-N31 proteobacterium
Proteobacteria	Deltaproteobacteria	Desulfuromonadales	Desulfuromonaceae	sf_1	10020	uranium mill tailings soil sample clone GuBH2-AG-114 proteobacterium
Proteobacteria	Gammaproteobacteria	Chromatiales	Ectothiorhodospiraceae	sf_1	9450	Halorhodospira neutrophila str. SG 3304
Proteobacteria	Gammaproteobacteria	Chromatiales	Ectothiorhodospiraceae	sf_1	9598	Mono Lake at depth 2 m station 6 July 2000 clone ML602J-47 proteobacterium
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_6	433	coal effluent wetland clone RCP2-6
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_6	646	Opitutus sp. str. SA-9
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9309	Buchnera sp
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8742	USA:New York isolate str. KN4
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_6	8783	Alterococcus agarolyticus str. ADT3; CCRC17102
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9135	intestine Zophobas mori clone
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9358	Salmonella subsp. enterica serovar Waycross str. Swy1 subsp.
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9496
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8886	Salmonella typhimurium LT2 str. SGSC1412
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8740	Erwinia chrysanthemi str. 573
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9651	Pectobacterium subsp. atrosepticum str. GSPB 1710
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8379	Erwinia amylovora EA G-5
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9142	Erwinia amylovora str. DSM 30165
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9252	Pantoea cedenensis str. A34
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9345	Erwinia amylovora str. BC199(= Ea528)
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8554	Kluyvera ascorbata 69
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8885	Morganella morganii str. AP28
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9363	Citrobacter freundii str. CDC 621-64
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9594	Morganella morganii str. ATCC35200
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8758	Pectobacterium cypripedii str. ATCC 29267
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8282	Antonina pretiosa symbiont
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8693	Pantoea agglomerans str. A40
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8700	Baumannia cicadellinicola
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9302	Pantoea subsp. stewartii str. GSPB 2626
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8236	Vryburgia amaryllidis symbiont
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8504	Dysmicoccus neobrevipes symbiont
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8603	Melanococcus albizziae symbiont
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8607	Amonostherium lichtensioides symbiont
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8624	Erium globosum symbiont
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9290	Baumannia cicadellinicola
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9293	USA clone 14/7
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9420
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8934	Pectobacterium subsp. carotovorum str. E155 subsp.
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9266	Parasite BEV of E.variegatus
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8467	Serratia marcescens subsp. sakuensis str. KRED subsp.
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9348
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8505	Buttiauxella warmboldiae str. DSM 9404
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8528	Enterobacter cloacae Nr. 3
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8530	Enterobacteriaceae CF01Ent-1
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8640
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8936	Klebsiella oxytoca str. ChDC OS31
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9060	Enterobacter ludwigii str. EN-119 = DSMZ 16688
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9274	Enterobacter sp. CC1
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9361	Enterobacter intermedius str. JCM1238
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9390	Enterobacter nimipressuralis str. LMG 10245-T
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8251	Nitrogen-fixing isolate str. CANF3
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8529	Raoultella planticola 7
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8627	Australicoccus grevilleae symbiont
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8770
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8890	Raoultella planticola str. DR3
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8362	Klebsiella pneumoniae str. ASR1
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8510	Klebsiella pneumoniae str. DSM 30104
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8773
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8286	Cyphonococcus alpinus symbiont
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8711	Serratia odorifera str. DSM 4582
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8712	Serratia proteamaculans str. DSM 4543
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8739	Serratia entomophila str. DSM 12358
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8892	Aranicola proteolyticus
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9151
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9417	Serratia fonticola str. DSM 4576
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8631	Planococcus ficus symbiont
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8283	Heteropsylla texana symbiont
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8173	Photorhabdus asymbiotica str. ATCC 43949
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8225
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8642	Erwinia chrysanthemi str. 580
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9029	Photorhabdus asymbiotica subsp. australis str. MB
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8473	Hafnia alvei
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9265	Rahnella aquatilis k 8
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9337	Rahnella genosp. 3 str. DSM 30078
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8564	Rahnella aquatilis str. ATCC 33989
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9157	Secondary symbiont type-U Acyrthosiphon pisum (rrs) clone 5B type-U
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	9262	Yersinia aldovae str. A125
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	1206	Dermacentor variabilis symbiont
Proteobacteria	Gammaproteobacteria	Thiotrichales	Francisellaceae	sf_1	9554	Tilapia parasite TPT-541
Proteobacteria	Gammaproteobacteria	Thiotrichales	Francisellaceae	sf_1	8949	Caedibacter taeniospiralis
Proteobacteria	Deltaproteobacteria	Desulfuromonadales	Geobacteraceae	sf_1	482	trichloroethene-contaminated site clone FTLM205 proteobacterium
Proteobacteria	Deltaproteobacteria	Desulfuromonadales	Geobacteraceae	sf_1	10171
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Halomonadaceae	sf_1	8514	Chromohalobacter israelensis str. ATCC 43985 T
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Halomonadaceae	sf_1	8562	Halomonas sp. str. TNB I20
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Halomonadaceae	sf_1	8576	Halomonas sp. Ko502
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Halomonadaceae	sf_1	8598	Halomonas desiderata str. FB2
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Halomonadaceae	sf_1	8854	Halomonas variabilis str. ANT9112
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Halomonadaceae	sf_1	9471	Boston Harbor surface water isolate str. UMB18C UMB18C
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Halomonadaceae	sf_1	9141	Halomonas sp. SK1
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10385
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10428	Flexispira rappini FH 9702248
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10430	Helicobacter heilmannii str. MM2
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10436	Helicobacter aurati str. MIT 97-5075c
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10442	Helicobacter cetorum str. MIT 99-5656
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10444	Helicobacter suncus str. Kaz-2
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10448	Helicobacter felis str. Dog-1
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10451	Helicobacter heilmannii str. C4S
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10454	Helicobacter pullorum str. NCTC 12826
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10462	Helicobacter rodentium str. MIT 96-1312
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10518	Helicobacter pylori str. ATCC 49396T
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10520	Helicobacter sp. blood isolate 964
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10548	Helicobacter rappini W.Tee-Bat
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10552	Helicobacter winghamensis str. NLEP 97-1611
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10562	Helicobacter rappini W.Tee-Yu
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10425	Sulfurimonas autotrophica str. OK5
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10411	termite gut homogenate clone Rs-P71 proteobacterium
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10432	Riftia pachyptila's tube clone R76-B51
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10438	hydrocarbon seep clone GCA014
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10590	termite gut homogenate clone Rs-H40 proteobacterium
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10614	strain isolate str. BHI80-49
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10417	temperate estuarine mud clone KM61
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10467
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10507	termite gut homogenate clone Rs-M59 proteobacterium
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Hyphomicrobiaceae	sf_1	7646	Hyphomicrobium aestuarii str. DSM 1564
Proteobacteria	Alphaproteobacteria	Rhizobiales	Hyphomicrobiaceae	sf_1	7392
Proteobacteria	Gammaproteobacteria	Legionellales	Legionellaceae	sf_1	8865	Arctic pack ice; northern Fram Strait; 80 31.1 N; 01 deg 59.7 min E clone ARKCH2Br2-23
Proteobacteria	Alphaproteobacteria	Azospirillales	Magnetospirillaceae	sf_1	6922	Dechlorospirillum sp. str. SN1
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Methylobacteriaceae	sf_1	7585	Methylobacterium thiocyanatum str. ALL/SCN-P
Proteobacteria	Gammaproteobacteria	Methylococcales	Methylococcaceae	sf_1	8243	isolate str. IR
Proteobacteria	Gammaproteobacteria	Methylococcales	Methylococcaceae	sf_1	8821	Methylobacter psychrophilus str. Z-0021
Proteobacteria	Gammaproteobacteria	Methylococcales	Methylococcaceae	sf_1	9438	marine sediment above hydrate ridge clone Hyd24-01 proteobacterium
Proteobacteria	Betaproteobacteria	Methylophilales	Methylophilaceae	sf_1	8137	freshwater clone PRD01a011B
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	8366	Psychrobacter frigidicola str. DSM 12411
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	8604	Moraxella oblonga str. IAM 14971
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	8838	Psychrobacter psychrophilus CMS 28
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	8727	Alkanindiges hongkongensis str. HKU9
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	9359	Acinetobacter junii str. S33
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	9428	hydrocarbon-degrading consortium clone AF2-1D
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	9466	Acinetobacter tandoii str. 4N13
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	9641	Acinetobacter haemolyticus
Proteobacteria	Deltaproteobacteria	Myxococcales	Myxococcaceae	sf_1	10358	Myxococcus fulvus str. Mx f2
Proteobacteria	Epsilonproteobacteria	Nautiliales	Nautiliaceae	sf_1	10477	S17sBac5 complete clone
Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	sf_1	7945	Aquaspirillum serpens str. IAM 13944
Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	sf_1	7675	Neisseria sp. str. CCUG 46910
Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	sf_1	7662	Mars Odyssey Orbiter and encapsulation facility clone T5-1 sp.
Proteobacteria	Betaproteobacteria	Nitrosomonadales	Nitrosomonadaceae	sf_1	7789
Proteobacteria	Betaproteobacteria	Nitrosomonadales	Nitrosomonadaceae	sf_1	7976	Nitrosomonas sp. str. Nm86
Proteobacteria	Betaproteobacteria	Nitrosomonadales	Nitrosomonadaceae	sf_1	7770	Nitrosomonas europaea str. ATCC 19718
Proteobacteria	Betaproteobacteria	Nitrosomonadales	Nitrosomonadaceae	sf_1	8145	Nitrosomonas eutropha str. Nm57
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Nitrospinaceae	sf_2	594	uranium mining mill tailing clone GR-296.II.52 GR-296.I.52
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Oceanospirillaceae	sf_1	9351	bacterioplankton clone ZA2333c
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	7743	Herbaspirillum sp. str. NAH4
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	7843	Massilia timonae timone
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	7845	Diaphorina citri symbiont
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	7866	Paucimonas lemoignei str. ATCC 17989T
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	7878	napthalene-contaminated sediment clone 29
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	7921	Collimonas fungivorans str. Ter331
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	7968	Oxalobacter formigenes str. OXB ovinen rumen
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	8013	isolate str. A1020
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	8032	Aquaspirillum arcticum str. IAM 14963
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	8034	Janthinobacterium agaricidamnosum str. W1r3T
Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	sf_1	8058	Herbaspirillum seropedicae str. DSM 6445 ATCC 35892
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	9360	Pasteurella multocida subsp. gallicida str. MCCM 00021 subsp.
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	9349	Pasteurella sp. str. 91985
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	8195	Haemophilus influenzae str. R2866
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	8555	Haemophilus influenzae str. M9741
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	9213	Haemophilus quentini str. MCCM 02026
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	9477	Haemophilus influenzae str. M11105
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	8228	Actinobacillus indolicus str. H1419
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	8861	Haemophilus parasuis 427
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	8614	Acidithiobacillus thiooxidans str. KCTC 8928P
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	8952	Actinobacillus lignieresii
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	9263	Actinobacillus capsulatus
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	8876	Mannheimia sp. R19.2 str. R19.2; CCUG 38463 R19.2
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	9237
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	8409	human colonic mucosal biopsy clone ABLCf1
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	8432
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	8848	str. 86355
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	9533	Haemophilus segnis str. MCCM 00337
Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	sf_1	9628	Histophilus somni str. CCUG 12839
Proteobacteria	Alphaproteobacteria	Rhizobiales	Phyllobacteriaceae	sf_1	6857	Mesorhizobium mediterraneum str. PECA20
Proteobacteria	Alphaproteobacteria	Rhizobiales	Phyllobacteriaceae	sf_1	6692	Phyllobacterium trifolii str. PETP02
Proteobacteria	Alphaproteobacteria	Rhizobiales	Phyllobacteriaceae	sf_1	6916	lake microbial mat isolate str. R-9219
Proteobacteria	Alphaproteobacteria	Rhizobiales	Phyllobacteriaceae	sf_1	6966	Mesorhizobium tianshanense str. -1BS; USDA 3592
Proteobacteria	Alphaproteobacteria	Rhizobiales	Phyllobacteriaceae	sf_1	7009
Proteobacteria	Alphaproteobacteria	Rhizobiales	Phyllobacteriaceae	sf_1	7216	Ahrensia kielensis str. IAM12618
Proteobacteria	Alphaproteobacteria	Rhizobiales	Phyllobacteriaceae	sf_1	7379	Phyllobacterium myrsinacearum HM35
Proteobacteria	Alphaproteobacteria	Rhizobiales	Phyllobacteriaceae	sf_1	7381	Aminobacter aminovorans str. DSM7048T
Proteobacteria	Alphaproteobacteria	Rhizobiales	Phyllobacteriaceae	sf_1	7497	Pseudaminobacter salicylatoxidans str. KTC001
Proteobacteria	Alphaproteobacteria	Rhizobiales	Phyllobacteriaceae	sf_1	7300	marine isolate JP57
Proteobacteria	Gammaproteobacteria	Thiotrichales	Piscirickettsiaceae	sf_3	8664	Thiomicrospira sp. str. Milos-T2
Proteobacteria	Gammaproteobacteria	Thiotrichales	Piscirickettsiaceae	sf_3	9027	Thiomicrospira crunogena str. XCL-2
Proteobacteria	Gammaproteobacteria	Thiotrichales	Piscirickettsiaceae	sf_3	9557	Riftia pachyptila's tube clone R76-B23
Proteobacteria	Gammaproteobacteria	Thiotrichales	Piscirickettsiaceae	sf_3	9291	Methylophaga alcalica str. M39
Proteobacteria	Gammaproteobacteria	Thiotrichales	Piscirickettsiaceae	sf_3	9392	Methylophaga sp. str. V4.ME.29 = MM_2343
Proteobacteria	Deltaproteobacteria	Myxococcales	Polyangiaceae	sf_3	10249	soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-168 proteobacterium
Proteobacteria	Deltaproteobacteria	Myxococcales	Polyangiaceae	sf_3	10298	marine tidal mat clone BTM36
Proteobacteria	Deltaproteobacteria	Myxococcales	Polyangiaceae	sf_3	10353	sludge clone A9
Proteobacteria	Deltaproteobacteria	Myxococcales	Polyangiaceae	sf_3	9671	hydrothermal sediment clone AF420357
Proteobacteria	Deltaproteobacteria	Myxococcales	Polyangiaceae	sf_3	9735	uranium mining waste pile clone JG37-AG-15 proteobacterium
Proteobacteria	Deltaproteobacteria	Myxococcales	Polyangiaceae	sf_3	9755	bacterioplankton clone ZA3704c
Proteobacteria	Deltaproteobacteria	Myxococcales	Polyangiaceae	sf_3	9874	uranium mining waste pile clone JG34-KF-243 proteobacterium
Proteobacteria	Deltaproteobacteria	Myxococcales	Polyangiaceae	sf_3	9900	bioreactor clone mle1-27
Proteobacteria	Deltaproteobacteria	Myxococcales	Polyangiaceae	sf_3	10082	uranium mining waste pile clone JG37-AG-33 proteobacterium
Proteobacteria	Deltaproteobacteria	Myxococcales	Polyangiaceae	sf_4	9733	bacterioplankton clone ZA3735c
Proteobacteria	Betaproteobacteria	Procabacteriales	Procabacteriaceae	sf_1	8136	Acanthamoeba sp. UWC6 symbiont
Proteobacteria	Gammaproteobacteria	Alteromonadales	Pseudoalteromonadaceae	sf_1	9627	Pseudoalteromonas sp
Proteobacteria	Gammaproteobacteria	Alteromonadales	Pseudoalteromonadaceae	sf_1	9339	Pseudoalteromonas sp. str. 05
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8813	Lyrodus pedicellatus symbiont
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9300	Lyrodus pedicellatus symbiont
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8487
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8508	Pseudomonas citronellolis str. TERIDB26
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8691	Pseudomonas aeruginosa str. PAO1
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8754	Pseudomonas sp. str. P400Y-1
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9002	Paederus fuscipes endosymbiont
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9056	Pseudomonas aeruginosa str. #47
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9588	Pseudomonas citronellolis str. TERIDB18
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8288
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8777	Pseudomonas sp. str. KNA6-5
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8852	Pseudomonas stutzeri str. KC
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9068	Pseudomonas stutzeri str. A1501
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9228	Pseudomonas stutzeri HY-105
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9295
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8344	Anabaena circinalis AWQC118C isolate str. UNSW3
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8553	Pseudomonas fulva str. IAM 1587
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8725	Pseudomonas sp. str. 2N1-1
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8850	Agrobacterium agile str. IAM12615
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9238
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9005	Pseudomonas sp. str. KY
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9613	Pseudomonas flavescens str. B62
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8474	ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-MN7 proteobacterium
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8513	Pseudomonas monteilii str. CIP 104883
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9049	uranium mining mill tailing clone GR-Sh2-34 GR-Sh2-34
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9219	Pseudomonas cf. monteilii 9
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9343	Cellvibrio subsp. mixtus str. ACM 2601
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9469	cf. Pseudomonas sp. clone Llangefni 52
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9493	Pseudomonas sp. str. dcm7B
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8209	uranium mining waste pile clone JG37-AG-122 proteobacterium
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8433	Pseudomonas syringae pv. broussonetiae str. KOZ 8101 pv.
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8635
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8853	Pseudomonas cichorii str. ATCC 10857T
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9028	Pseudomonas koreensis str. Ps 9-14
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9240	Pseudomonas fluorescens str. CHA0
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9267	Pseudomonas syringae pv. theae str. PT1
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9310	Pseudomonas sp. str. AC-167
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8338	Pseudomonas synxantha str. DSM 13080 G
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8561	Pseudomonas sp. B65
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8601	Pseudomonas marginalis str. ATCC 10844T
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8687	Pseudomonas putida str. ATCC 17472
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8708
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9175	Pseudomonas extremorientalis str. KMM3447
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9221	Pseudomonas fulgida str. DSM 14938 = LMG 2146 P 515/12
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9243	Pseudomonas tolaasii str. LMG 2342T ()
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9366	Arctic seawater isolate str. R7366
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8755	Pseudomonas sp. SK-1-3-1
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9172	Pseudomonas psychrophila str. E-3
Proteobacteria	Betaproteobacteria	Burkholderiales	Ralstoniaceae	sf_1	7823	Wautersia basilensis str. DSM 11853
Proteobacteria	Betaproteobacteria	Burkholderiales	Ralstoniaceae	sf_1	8110	Wautersia paucula str. LMG 3413
Proteobacteria	Betaproteobacteria	Burkholderiales	Ralstoniaceae	sf_1	8128	Cupriavidus necator
Proteobacteria	Betaproteobacteria	Burkholderiales	Ralstoniaceae	sf_1	7761	Ralstonia detusculanense str. APF11
Proteobacteria	Betaproteobacteria	Burkholderiales	Ralstoniaceae	sf_1	7778	Ralstonia insidiosa str. CCUG 46388
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	7051	Mycoplana dimorpha str. IAM 13154
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	6683	Sinorhizobium fredii str. ATCC35423
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	6725	Sinorhizobium meliloti str. 1021
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	6972	Ensifer adhaerens str. LMG 20582
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	6974	India: Himalayas Kaza Spiti Valley Cold Desert isolate str. Kaza-35 Kaza-35
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	6770	Rhizobium tropici str. LMG 9517
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	6871	Rhizobium mongolense str. USDA 1832
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	7135	Rhizobium gallicum str. FL27
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	7568	Rhizobium etli str. USDA 2667 ATCC 14483 SEMIA 043
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	6798	Agrobacterium tumefaciens TG14
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	6804	Rhizobium sp. str. SH19312
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	6964	Agrobacterium tumefaciens str. C58 Cereon
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	7334	Agrobacterium tumefaciens C4
Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	sf_1	7041	Rhizobium huautlense str. SO2 ()
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	6701	Roseobacter clone NAC11-3
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	6980	Loktanella vestfoldensis str. LMG 22003
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	7433	Scrippsiella trochoidea NEPCC 15
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	7453	Sulfitobacter sp. BIO-11
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	6888	hydrothermal vent strain str. TB66
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	7026	Leisingera methylohalidivorans str. MB2
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	7263
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	7040	Paracoccus alcaliphilus str. JCM 7364
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	7508	lichen-dominated Antarctic cryptoendolithic community clone FBP492 proteobacterium
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	6991	Rhodobacter sphaeroides str. 2.4.1
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	sf_1	7084	Scrippsiella trochoidea NEPCC 15
Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	sf_1	7800	sample taken upstream landfill clone BVC77 landfill
Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	sf_1	7817	TCE-contaminated site clone ccs265
Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	sf_1	7956
Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	sf_1	8127	Zoogloea resiniphila str. PIV-3A2y
Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	sf_1	8131
Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	sf_1	7907	Thauera aromatica str. LG356
Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	sf_1	7925	Thauera selenatis str. ATCC 55363T
Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	sf_1	8156	industrial-phenol-degrading community clone MM1 sp.
Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	sf_1	7824	termite gut homogenate clone Rs-B77 proteobacterium
Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	sf_1	7762	Elbe River snow isolate Iso18 Iso18_1411
Proteobacteria	Alphaproteobacteria	Rickettsiales	Rickettsiaceae	sf_1	7556	Rickettsia bellii str. strains 369-C and G2D42
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Saccharospirillaceae	sf_1	8889	hypersaline Mono Lake clone ML110J-5
Proteobacteria	Alphaproteobacteria	Consistiales	SAR11	sf_2	7043	marine clone Arctic95D-8
Proteobacteria	Gammaproteobacteria	Alteromonadales	Shewanellaceae	sf_1	8581	Shewanella benthica str. DB21MT-2
Proteobacteria	Gammaproteobacteria	Alteromonadales	Shewanellaceae	sf_1	8641	Moritella abyssi str. 2693
Proteobacteria	Gammaproteobacteria	Alteromonadales	Shewanellaceae	sf_1	9081	Shewanella sp. str. MTW-1
Proteobacteria	Gammaproteobacteria	Alteromonadales	Shewanellaceae	sf_1	8662
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	7440	Sphingobium chungbukense str. DJ77
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	7528	Sphingobium yanoikuyae str. GIFU9882
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	7548	Afipia genosp. 13 str. G8991
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	6650	Sphingomonas phyllosphaerae str. FA1
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	7016	Sphingomonas sp. str. SAFR-027
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	7535	Sphingomonas paucimobilis str. GIFU2395
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_15	7035	Sphingomonas asaccharolytica str. IFO 10564-T
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	7215	travertine hot spring clone SM2B06
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	6663	Sphingopyxis flavimaris str. SW-151
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	7100	Novosphingobium capsulatum str. GIFU11526
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	7036	Lutibacterium anuloederans str. LC8
Proteobacteria	Gammaproteobacteria	Aeromonadales	Succinivibrionaceae	sf_1	8822	Anaerobiospirillum sp. str. 3J102
Proteobacteria	Deltaproteobacteria	Syntrophobacterales	Syntrophaceae	sf_3	10067	benzoate-degrading consortium clone BA044
Proteobacteria	Deltaproteobacteria	Syntrophobacterales	Syntrophobacteraceae	sf_1	9864	uranium mining waste pile clone JG37-AG-133 proteobacterium
Proteobacteria	Deltaproteobacteria	Syntrophobacterales	Syntrophobacteraceae	sf_1	10013	hydrothermal sediment clone AF420341
Proteobacteria	Deltaproteobacteria	Syntrophobacterales	Syntrophobacteraceae	sf_1	10021	uranium mill tailings soil sample clone Sh765B-TzT-29 proteobacterium
Proteobacteria	Deltaproteobacteria	Syntrophobacterales	Syntrophobacteraceae	sf_1	9731	uranium mining waste pile clone JG37-AG-90 proteobacterium
Proteobacteria	Deltaproteobacteria	Syntrophobacterales	Syntrophobacteraceae	sf_1	9845	uranium mining waste pile clone JG37-AG-128 proteobacterium
Proteobacteria	Deltaproteobacteria	Syntrophobacterales	Syntrophobacteraceae	sf_1	10184	granular sludge clone R1p32
Proteobacteria	Deltaproteobacteria	Syntrophobacterales	Syntrophobacteraceae	sf_1	10221	granular sludge clone R3p4
Proteobacteria	Deltaproteobacteria	Syntrophobacterales	Syntrophobacteraceae	sf_1	10294	Desulfacinum hydrothermale str. MT-96
Proteobacteria	Deltaproteobacteria	Syntrophobacterales	Syntrophobacteraceae	sf_1	9661	DCP-dechlorinating consortium clone SHD-1
Proteobacteria	Gammaproteobacteria	Thiotrichales	Thiotrichaceae	sf_3	8321	Wadden Sea sediment clone Dangast A9
Proteobacteria	Gammaproteobacteria	Thiotrichales	Thiotrichaceae	sf_3	8741	marine sediment clone Limfjorden L10
Proteobacteria	Gammaproteobacteria	Thiotrichales	Thiotrichaceae	sf_3	8752	Beggiatoa sp. str. MS-81-1c
Proteobacteria	Gammaproteobacteria	Thiotrichales	Thiotrichaceae	sf_3	9015	Beggiatoa alba str. B18LD; ATCC 33555
Proteobacteria	Gammaproteobacteria	Thiotrichales	Thiotrichaceae	sf_3	9321	marine sediment clone Tokyo Bay D
Proteobacteria	Gammaproteobacteria	Thiotrichales	Thiotrichaceae	sf_3	8703	Beggiatoa sp. str. AA5A
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Unclassified	sf_3	468	marine sediment clone Sva0515
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	7377	Rocky Mountain alpine soil clone W2b-8C
Proteobacteria	Alphaproteobacteria	Verorhodospirilla	Unclassified	sf_1	7109	diesel-polluted Bohai Gulf isolate str. M-5 M-5
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	7340	uranium mining waste pile soil sample clone JG30-KF-AS50
Proteobacteria	Alphaproteobacteria	Azospirillales	Unclassified	sf_1	7400	sphagnum peat bog clone K-5b5
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	6694	forested wetland clone RCP2-92
Proteobacteria	Alphaproteobacteria	Azospirillales	Unclassified	sf_1	6732	Anabaena circinalis AWQC118C isolate str. UNSW7
Proteobacteria	Alphaproteobacteria	Acetobacterales	Unclassified	sf_1	7028
Proteobacteria	Alphaproteobacteria	Ellin314/wr0007	Unclassified	sf_1	7123	uranium mining waste pile near Johanngeorgenstadt soil clone JG37-AG-102
Proteobacteria	Alphaproteobacteria	Ellin314/wr0007	Unclassified	sf_1	7222	Great Artesian Basin clone B79
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	7575
Proteobacteria	Alphaproteobacteria	Rhizobiales	Unclassified	sf_1	6726
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	6920	Pseudovibrio denitrificans str. DN34
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	6954
Proteobacteria	Alphaproteobacteria	Ellin329/Riz1046	Unclassified	sf_1	6945	Rhizobiales str. A48
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Unclassified	sf_1	7067	Blastochloris sulfoviridis str. GN1
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Unclassified	sf_1	7264	Bosea thiooxidans TJ1
Proteobacteria	Alphaproteobacteria	Rhizobiales	Unclassified	sf_1	7339
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	6898	heavy metal-contaminated soil clone a13113
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Unclassified	sf_1	7199	uranium mill tailings clone Gitt-KF-194
Proteobacteria	Alphaproteobacteria	Rhizobiales	Unclassified	sf_1	6899
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	6665	hydrocarbon-degrading consortium clone 4-Org2-22
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	7312
Proteobacteria	Alphaproteobacteria	Rhizobiales	Unclassified	sf_1	6789	Shinella zoogloeoides str. ATCC 19623
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_2	6697	termite gut homogenate clone Rs-D84 proteobacterium
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_2	7188	termite gut homogenate clone Rs-B50 proteobacterium
Proteobacteria	Alphaproteobacteria	Consistiales	Unclassified	sf_4	7105	Mariana trough hydrothermal vent water 0.2micro-m filterable fraction clone MT-NB25
Proteobacteria	Alphaproteobacteria	Rhodobacterales	Unclassified	sf_5	7471	sponge clone TK03
Proteobacteria	Alphaproteobacteria	Consistiales	Unclassified	sf_5	6735	Candidatus Pelagibacter ubique str. HTCC1002
Proteobacteria	Unclassified	Unclassified	Unclassified	sf_20	6763
Proteobacteria	Alphaproteobacteria	Rickettsiales	Unclassified	sf_2	6639
Proteobacteria	Alphaproteobacteria	Rickettsiales	Unclassified	sf_1	7156	termite gut homogenate clone Rs-M62 proteobacterium
Proteobacteria	Deltaproteobacteria	AMD clone group	Unclassified	sf_1	6830	coal effluent wetland clone RCP124
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Unclassified	sf_1	6653	Kaistobacter koreensis str. PB229
Proteobacteria	Deltaproteobacteria	Bdellovibrionales	Unclassified	sf_1	7382	marine clone Arctic95C-5
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	6987
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	7572
Proteobacteria	Betaproteobacteria	Burkholderiales	Unclassified	sf_1	8035
Proteobacteria	Betaproteobacteria	MND1 clone group	Unclassified	sf_1	7808	Mammoth cave clone CCU25
Proteobacteria	Betaproteobacteria	Unclassified	Unclassified	sf_3	8007
Proteobacteria	Betaproteobacteria	Unclassified	Unclassified	sf_3	8036	Uranium mill tailings soil sample clone Sh765B-TzT-132 proteobacterium
Proteobacteria	Betaproteobacteria	Unclassified	Unclassified	sf_3	7974
Proteobacteria	Betaproteobacteria	Unclassified	Unclassified	sf_3	8114
Proteobacteria	Betaproteobacteria	MND1 clone group	Unclassified	sf_1	8023	ferromanganous micronodule clone MND1
Proteobacteria	Betaproteobacteria	Unclassified	Unclassified	sf_3	8045
Proteobacteria	Betaproteobacteria	MND1 clone group	Unclassified	sf_1	7818	soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-215 proteobacterium
Proteobacteria	Betaproteobacteria	Neisseriales	Unclassified	sf_1	8037	Chitinimonas taiwanensis str. cf
Proteobacteria	Betaproteobacteria	Unclassified	Unclassified	sf_3	7997
Proteobacteria	Gammaproteobacteria	uranium waste clones	Unclassified	sf_1	8747	uranium waste soil clone JG30-KF-CM35
Proteobacteria	Gammaproteobacteria	GAO cluster	Unclassified	sf_1	9059	activated sludge clone SBRH10
Proteobacteria	Gammaproteobacteria	aquatic clone group	Unclassified	sf_1	9246	Mammoth Cave sediment clone CCD24
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	9498
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	9568	forested wetland clone RCP2-96
Proteobacteria	Gammaproteobacteria	Chromatiales	Unclassified	sf_1	9282
Proteobacteria	Gammaproteobacteria	Legionellales	Unclassified	sf_1	9418	uranium mining waste pile clone JG37-AG-14 proteobacterium
Proteobacteria	Deltaproteobacteria	EB1021 group	Unclassified	sf_4	8169	forested wetland clone RCP2-54
Proteobacteria	Gammaproteobacteria	Symbionts	Unclassified	sf_1	8403	Selenate-reducing isolate str. KE4OH1
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8488
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8646
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8676
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8926	inactive deep-sea hydrothermal vent chimneys clone IheB2-13
Proteobacteria	Gammaproteobacteria	aquatic clone group	Unclassified	sf_1	8957	marine clone Arctic97C-5
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	9105
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	9124	10e-6 dilution marine samples Weser estuary clone DC8-80-1 proteobacterium
Proteobacteria	Gammaproteobacteria	Symbionts	Unclassified	sf_1	9128	Lucina nassula gill symbiont
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	9394
Proteobacteria	Gammaproteobacteria	Symbionts	Unclassified	sf_1	9556	Seepiophila jonesi symbiont
Proteobacteria	Gammaproteobacteria	SUP05	Unclassified	sf_1	8605	bacterioplankton clone ZA2525c
Proteobacteria	Gammaproteobacteria	SUP05	Unclassified	sf_1	8654	inactive deep-sea hydrothermal vent chimneys clone IheB2-31
Proteobacteria	Gammaproteobacteria	SUP05	Unclassified	sf_1	8965	Bathymodiolus thermophilus gill symbiont
Proteobacteria	Gammaproteobacteria	uranium waste clones	Unclassified	sf_1	8231	uranium waste soil clone JG30a-KF-21
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8339	water 5 m downstream manure clone 35ds5
Proteobacteria	Gammaproteobacteria	Ellin307/WD2124	Unclassified	sf_1	8532
Proteobacteria	Gammaproteobacteria	Ellin307/WD2124	Unclassified	sf_1	9458	uranium mining waste pile clone JG37-AG-94 proteobacterium
Proteobacteria	Gammaproteobacteria	SAR86	Unclassified	sf_1	8962	bacterioplankton clone AEGEAN_234
Proteobacteria	Gammaproteobacteria	Legionellales	Unclassified	sf_3	8587	Mars Odyssey Orbiter and encapsulation facility clone T5-3
Proteobacteria	Gammaproteobacteria	GAO cluster	Unclassified	sf_1	9468	activated sludge clone SBRL2_40
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_4	8855
Proteobacteria	Unclassified	Unclassified	Unclassified	sf_8	9558
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Unclassified	sf_3	8230
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8245
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8883
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	9044	hydrothermal sediment clone AF420370
Proteobacteria	Gammaproteobacteria	Thiotrichales	Unclassified	sf_1	8323	hydrothermal sediment clone AF420363
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	8780	uranium mining mill tailing clone GR-296.II.89 GR-296.II.89
Proteobacteria	Gammaproteobacteria	Oceanospirillales	Unclassified	sf_3	8327	Arctic sea ice ARK10148
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8606
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8714	Marinobacter hydrocarbonoclasticus str. ATCC 27132T
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8959	bacterioplankton clone AEGEAN_133
Proteobacteria	Gammaproteobacteria	Alteromonadales	Unclassified	sf_1	8483	Rheinheimera baltica str. OS140 Baltic # 166
Proteobacteria	Gammaproteobacteria	Shewanella	Unclassified	sf_1	9344	Shewanella algae str. ATCC 51192
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	9367	USA: Pacific Ocean seawater Naha Vents Hawaii isolate str. PV-4
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	9473	Arctic pack ice; northern Fram Strait; 80 31.1 N; 01 deg 59.7 min E clone ARKDMS-58
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Unclassified	sf_1	8430	Salmonella bongori str. JEO 4162
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Unclassified	sf_1	9828	termite gut homogenate clone Rs-M89 proteobacterium
Proteobacteria	Deltaproteobacteria	Myxococcales	Unclassified	sf_1	10092	heavy metal-contaminated soil clone a13134
Proteobacteria	Deltaproteobacteria	Myxococcales	Unclassified	sf_1	10259
Proteobacteria	Deltaproteobacteria	Unclassified	Unclassified	sf_7	10048
Proteobacteria	Deltaproteobacteria	Unclassified	Unclassified	sf_9	10049	DCP-dechlorinating consortium clone SHA-72
Proteobacteria	Deltaproteobacteria	Unclassified	Unclassified	sf_9	9760	deep marine sediment clone MB-A2-137
Proteobacteria	Deltaproteobacteria	Unclassified	Unclassified	sf_9	9784	Antarctic sediment clone LH5_30
Proteobacteria	Deltaproteobacteria	Unclassified	Unclassified	sf_9	9798	uranium mill tailings soil sample clone GuBH2-AD/TzT-67 proteobacterium
Proteobacteria	Deltaproteobacteria	Unclassified	Unclassified	sf_9	9876	deep marine sediment clone MB-B2-106
Proteobacteria	Deltaproteobacteria	EB1021 group	Unclassified	sf_4	9884	forested wetland clone RCP2-62
Proteobacteria	Deltaproteobacteria	AMD clone group	Unclassified	sf_1	10084	acid mine drainage clone AS6
Proteobacteria	Deltaproteobacteria	Desulfuromonadales	Unclassified	sf_1	10076	Great Artesian Basin clone G13
Proteobacteria	Deltaproteobacteria	dechlorinating clone group	Unclassified	sf_1	9959	forested wetland clone FW110
Proteobacteria	Deltaproteobacteria	EB1021 group	Unclassified	sf_4	10024	hydrothermal sediment clone AF420338
Proteobacteria	Deltaproteobacteria	AMD clone group	Unclassified	sf_1	9678	coal effluent wetland clone RCP185
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Unclassified	sf_4	9951	forested wetland clone FW13
Proteobacteria	Deltaproteobacteria	Unclassified	Unclassified	sf_9	9738	marine methane seep clone 1513
Proteobacteria	Deltaproteobacteria	AMD clone group	Unclassified	sf_1	9945	acid mine drainage clone BA18
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Unclassified	sf_3	9813	hydrothermal sediment clone AF420340
Proteobacteria	Deltaproteobacteria	Unclassified	Unclassified	sf_9	9890	termite gut homogenate clone Rs-K70 proteobacterium
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Unclassified	sf_1	10543	hydrothermal vent clone PVB_10
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Unclassified	sf_1	10427	hydrothermal vent 9 degrees North East Rise Pacific Ocean clone CH3_17_BAC_16SrRNA_9N_EPR
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Unclassified	sf_1	10475	hydrothermal sediment clone AF420359
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Unclassified	sf_1	10480	Paralvinella palmiformis mucus secretions clone P. palm C 84 proteobacterium
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Unclassified	sf_1	10489	S17sBac16 complete clone
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Unclassified	sf_1	10497	UASB reactor granular sludge clone PD-UASB-2 proteobacterium
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Unclassified	sf_1	10530	hydrothermal vent 9 degrees North East Rise Pacific Ocean clone CH5_6_BAC_16SrRNA_9N_EPR
Proteobacteria	Unclassified	Unclassified	Unclassified	sf_20	2520
Proteobacteria	Deltaproteobacteria	Unclassified	Unclassified	sf_9	244	deep marine sediment clone MB-C2-152
Proteobacteria	Deltaproteobacteria	AMD clone group	Unclassified	sf_1	3084	coal effluent wetland clone RCP216
Proteobacteria	Gammaproteobacteria	Vibrionales	Vibrionaceae	sf_1	8999	Photobacterium leiognathi str. LN101
Proteobacteria	Gammaproteobacteria	Vibrionales	Vibrionaceae	sf_1	8665	Vibrio gallicus str. CIP 107867; HT 3-3
Proteobacteria	Gammaproteobacteria	Vibrionales	Vibrionaceae	sf_1	8267	Vibrio pomeroyi str. LMG 20537
Proteobacteria	Gammaproteobacteria	Vibrionales	Vibrionaceae	sf_1	8798	Vibrio aestuarianus str. KT0901
Proteobacteria	Gammaproteobacteria	Vibrionales	Vibrionaceae	sf_1	8888	Vibrio aestuarianus str. 01/151
Proteobacteria	Alphaproteobacteria	Bradyrhizobiales	Xanthobacteraceae	sf_1	6660	Azorhizobium caulinodans str. ORS 571
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	9167	pea aphid symbiont clone APe4_38
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	8689	Dyemonas todaii str. XD10
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	9332	wetland ecosystem constructed to remediate mine drainage isolate str. WJ2 WJ2
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	8392	penguin droppings sediments clone KD2-14
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	8983	Iron oxidizing strain ES-1
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	9031	municipal wastewater treatment bioreactor clone LB-P bacterium
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	9320	Waste-gas biofilter clone BIyi3
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	8577	Xanthomonas axonopodis pv. citri str. MA
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	9569
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	8538
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	8563	Pseudoxanthomonas mexicana str. AMX 26B
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	9270	Stenotrophomonas rhizophila str. e-p10
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	9286	Stenotrophomonas maltophilia str. LMG 11104
SPAM	Unclassified	Unclassified	Unclassified	sf_1	705	uranium tailings soil clone Sh765B-AG-45
SPAM	Unclassified	Unclassified	Unclassified	sf_1	738	uranium mining waste clone JG34-KF-252
Spirochaetes	Spirochaetes	Spirochaetales	Leptospiraceae	sf_3	6496	Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6459	Spirochaeta sp. str. BHI80-158
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_3	6558	Spironema culicis str. BR91
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6526	Treponema sp. str. 7CPL208
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6479	Treponema sp
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6580	Treponema sp. str. III:C:BA213
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6458	termite gut clone NkS34
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6494	termite gut homogenate clone Rs-C47 sp.
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6562	forested wetland clone RCP1-96
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6507	termite gut clone NkS-Ste2
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6476	termite gut clone NkS50
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6488	Treponema primitia str. ZAS-1
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6490	termite gut homogenate clone BCf4-14
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6491	termite gut homogenate clone BCf8-03
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6506	termite gut homogenate clone Rs-J58 sp.
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6508	termite hindgut clone mpsp2
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6523	termite gut homogenate clone Rs-J64 sp.
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6565	termite gut clone NkS-Oxy25
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	sf_1	6571	Mixotricha paradoxa is flagellate hindgut Mastotermes darwiniensis clone mp4 of
Synergistes	Unclassified	Unclassified	Unclassified	sf_3	117	termite gut homogenate clone Rs-D89
Synergistes	Unclassified	Unclassified	Unclassified	sf_3	353	UASB reactor granular sludge clone PD-UASB-13 G+C
Synergistes	Unclassified	Unclassified	Unclassified	sf_3	60	Flexistipes sp. str. E3_33
Synergistes	Unclassified	Unclassified	Unclassified	sf_3	601	terephthalate-degrading consortium clone TA19
Synergistes	Unclassified	Unclassified	Unclassified	sf_3	719	Synergistes sp. P1 str. P4G_18
Synergistes	Unclassified	Unclassified	Unclassified	sf_3	740	swine intestine clone p-4292-4Wa3
Synergistes	Unclassified	Unclassified	Unclassified	sf_3	808	oral cavity clone BH017
Termite group 1	Unclassified	Unclassified	Unclassified	sf_2	437	termite gut homogenate clone Rs-D43 group
Thermodesulfobacteria	Thermodesulfobacteria	Thermodesulfobacteriales	Thermodesulfobacteriaceae	sf_1	667	Geothermobacterium ferrireducens
Thermotogae	Thermotogae	Thermotogales	Thermotogaceae	sf_4	51	Thermosipho sp. str. MV1063
TM6	Unclassified	Unclassified	Unclassified	sf_1	9803	forest soil clone S1204
TM7	Unclassified	Unclassified	Unclassified	sf_1	5177
TM7	TM7-3	Unclassified	Unclassified	sf_1	8155	oral periodontitis clone EW086
TM7	TM7-3	Unclassified	Unclassified	sf_1	2697	midgut homogenate Pachnoda ephippiata larva clone PeM47
TM7	Unclassified	Unclassified	Unclassified	sf_1	3025
Unclassified	Unclassified	Unclassified	Unclassified	sf_93	925	4MB-degrading consortium clone UASB_TL26
Unclassified	Unclassified	Unclassified	Unclassified	sf_106	243	hot spring clone OPB25
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	485	thermal spring mat clone O1aA90
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	226
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	333
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	651
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	6430
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	6456
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	6360
Unclassified	Unclassified	Unclassified	Unclassified	sf_140	6355
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	7444
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	7767
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	10012
Unclassified	Unclassified	Unclassified	Unclassified	sf_95	2545	anaerobic sludge isolate str. JE
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	2488
Unclassified	Unclassified	Unclassified	Unclassified	sf_156	4291	Mono Lake at depth 35m station 6 July 2000 clone ML635J-21 G+C
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	4410
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Unclassified	sf_4	169	anoxic marine sediment clone LD1-PA26
Verrucomicrobia	Unclassified	Unclassified	Unclassified	sf_3	40	Elbe river clone DEV055
Verrucomicrobia	Unclassified	Unclassified	Unclassified	sf_3	486	Elbe river clone DEV045
Verrucomicrobia	Unclassified	Unclassified	Unclassified	sf_5	686	hydrothermal vent sediment clone a2b018
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Unclassified	sf_3	11	sludge clone H2
Verrucomicrobia	Unclassified	Unclassified	Unclassified	sf_4	288	Prosthecobacter dejongeii
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Unclassified	sf_3	792	termite gut homogenate clone Rs-P07 bacterium
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobia SD 5	sf_1	530	anoxic marine sediment clone LD1-PB20
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobia SD 5	sf_1	533	anoxic marine sediment clone LD1-PB12
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobia SD 5	sf_1	547	anoxic marine sediment clone LD1-PB1
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobia SD 5	sf_1	629	anoxic marine sediment clone LD1-PA50
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobia SD 7	sf_1	446	anoxic marine sediment clone LD1-PA34
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobia SD 7	sf_1	559	anoxic marine sediment clone LD1-PA20
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobia SD 7	sf_1	760	Mono lake clone ML316M-1
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobiaceae	sf_7	29	Fucophilus fucoidanolyticus str. SI-1234
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobiaceae	sf_6	871
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Xiphinematobacteraceae	sf_3	888	Candidatus Xiphinematobacter brevicolli
WS3	Unclassified	Unclassified	Unclassified	sf_3	95	marine sediment above hydrate ridge clone Hyd24-32
WS3	Unclassified	Unclassified	Unclassified	sf_1	2537	anoxic marine sediment clone LD1-PA39
WS5	Unclassified	Unclassified	Unclassified	sf_2	8119	hydrothermal vent sediment clone a2b013

^aS-F, Subfamily identification; ^bTaxon ID, PhyloChip Taxon identification number; ^cRepresentative species, Taxon bacterial species identifier.

FIG. 1.

(A) Phylogenetic tree exhibiting family level bacterial diversity detected in COPD airways despite antimicrobial administration. (B) Bacterial richness detected in individual patient samples.

Interpersonal variation in bacterial richness (number of taxa detected) was noted across the patient samples (Fig. 1B). Four subjects (patients 1, 4, 5, and 6) exhibited communities with significantly fewer taxa (p < 0.002) compared with the other four subjects. Patients in which fewer bacterial taxa were detected tended to possess more members of the Pseudomonadaceae. In contrast, members of the Clostridiaceae, Lachnospiraceae, Bacillaceae, and Peptostreptococcaceae were detected more commonly in those patients with richer communities (patients 2, 3, 7). Patient 8 was observed to possess a large proportion of taxa belonging to the Enterobacteriaceae family, which have been associated with more advanced COPD lung disease (Sethi and Murphy, 2008). Interestingly, this patient had radiographic evidence of coexisting bronchiectasis, which was not present in the other patients.

Given the variation in bacterial richness among samples, which suggested differences in bacterial community composition, NMDS was used to assess variation in bacterial community structure (based on Bray-Curtis dissimilarity measures) across the sample cohort. This revealed two distinct groups of patient samples and confirmed that patient 8 represented a structurally distinct airway community (Fig. 2). Although the cohort was small, given this separation of subjects based on differing bacterial community structures, the influence of available clinical parameters on community composition was explored. Matrix-based, nonparametric multivariate analysis of variance (Anderson, 2001) revealed that across the cohort, the number of elapsed intubation days was significantly associated with bacterial community composition and structure, accounting for the greatest percentage of the observed variability (44%, p < 0.03; Fig. 2). Group 1 patient samples (patients 2, 3, and 7) were characterized by a shorter intubation duration prior to ETA sample collection (≤6 days), while those in Group 2 were intubated for significantly longer periods of time (p < 0.0007; patients 1, 4, 5, and 6; ≥16 days) and exhibited a significantly less rich community composition compared to that of Group 1 (p < 0.025). Given the community variation between Group 1 and Group 2, differences in the relative abundance of all detected taxa were assessed between the groups, which identified 153 taxa with significantly different relative abundances (Table 4; see at end of article). All of these significant taxa were present in higher abundance in Group 1, the majority of which (77%) belonged to the phylum Firmicutes. These included species such as Lactobacillus kitasatonis, L. perolens, L. sakei, and Bacillus clausii, as well as known pathogenic species such as Streptococcus constellatus, which is a member of the Streptoccocus milleri group (SMG; Table 4). No other clinical variable [including diagnosis of pneumonia (n = 6; p < 0.4) or the number of days between pneumonia diagnosis and sample collection (range: 3–52 days; p < 0.6)] demonstrated a significant association with bacterial community composition in this cohort.

FIG. 2.

NMDS analysis demonstrates that bacterial community composition is highly influenced by the duration of intubation (red isotherms). Subjects COPD 5 and COPD 6 are superimposed on the right side of the figure, indicative of highly similar bacterial community composition.

Table 4.

Bacterial Taxa with Significant Differences in Relative Abundance between COPD Patient Group 1 (≤6 Intubation Days) and Group 2 (≥16 Intubation Days)

Phylum	Class	Order	Family	S-Fa	Taxon IDb	Representative speciesc	p-value	q-value	Fluorescence difference (Group 1 – Group 2)
Firmicutes	Symbiobacteria	Symbiobacterales	Unclassified	1	77	thermal soil clone YNPFFP9	<0.001	<0.01	1264
Proteobacteria	Deltaproteobacteria	Unclassified	Unclassified	9	244	deep marine sediment clone MB-C2-152	<0.02	<0.05	1048
Chloroflexi	Anaerolineae	Unclassified	Unclassified	9	375	forest soil clone C043	<0.02	<0.05	1873
Proteobacteria	Deltaproteobacteria	Desulfuromonadales	Geobacteraceae	1	482	trichloroethene-contaminated site clone FTLM205 proteobacterium	≤0.01	<0.05	1092
OP10	CH21 cluster	Unclassified	Unclassified	1	514	sludge clone SBRA136	<0.01	<0.05	1081
Chlorobi	Unclassified	Unclassified	Unclassified	8	636	benzene-degrading nitrate-reducing consortium clone Cart-N3 bacterium	<0.01	<0.05	1475
Unclassified	Unclassified	Unclassified	Unclassified	160	651		<0.01	<0.05	1750
Chloroflexi	Unclassified	Unclassified	Unclassified	7	757	DCP-dechlorinating consortium clone SHA-8	<0.001	<0.01	1619
Natronoanaerobium	Unclassified	Unclassified	Unclassified	1	769	fjord ikaite column clone un-c23	<0.001	<0.01	1305
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	11	940	Veillonella dispar str. DSM 20735	<0.01	<0.05	1150
OP9/JS1	OP9	Unclassified	Unclassified	1	969	DCP-dechlorinating consortium clone SHA-1	<0.02	<0.05	1190
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	1050	Bacillus firmus CV93b	≤0.001	<0.05	1746
Actinobacteria	Actinobacteria	Unclassified	Unclassified	1	1898	termite gut homogenate clone Rs-J10 bacterium	<0.01	<0.05	1906
AD3	Unclassified	Unclassified	Unclassified	1	2338	uranium mining waste pile soil clone JG30-KF-C12	<0.001	<0.01	1148
Chloroflexi	Dehalococcoidetes	Unclassified	Unclassified	1	2339	uranium mill tailings soil sample clone Sh765B-TzT-20 bacterium	<0.02	<0.05	1532
Chloroflexi	Unclassified	Unclassified	Unclassified	1	2534	forest soil clone S085	<0.001	<0.01	1193
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	2668	termite gut homogenate clone Rs-G40 bacterium	<0.01	<0.05	2395
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	5	2694	oral periodontitis clone FX028	<0.02	<0.05	1338
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	5	2714	termite gut homogenate clone Rs-N27 bacterium	<0.01	<0.05	2061
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	5	2729	DCP-dechlorinating consortium clone SHA-58	<0.01	<0.05	1402
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	5	2797	Isolation and identification hyper-ammonia producing swine storage pits manure	<0.01	<0.05	1611
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	5	2805	oral periodontitis clone FX033	<0.02	<0.05	1625
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	2834	Butyrivibrio fibrisolvens str. OB156	<0.01	<0.05	1005
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	2994	termite gut clone Rs-L15	<0.001	<0.01	3929
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	3021	Clostridium caminithermale str. DVird3	<0.01	<0.05	1944
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	3038	swine intestine clone p-1594-c5	<0.01	<0.05	1363
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	3059	Butyrivibrio fibrisolvens str. NCDO 2249	<0.01	<0.05	1069
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	3060	termite gut homogenate clone Rs-B14 bacterium	<0.001	<0.01	3703
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	3076	Clostridium nexile	<0.001	<0.01	1395
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	3077	Clostridium glycolicum str. DSM 1288	<0.01	<0.05	1953
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	3171	Lachnospira pectinoschiza	<0.01	<0.05	1398
Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	5	3182	termite gut homogenate clone Rs-Q64 bacterium	≤0.01	<0.05	1107
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3250	Streptococcus bovis str. B315	<0.001	<0.01	4284
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3251	Streptococcus cristatus str. ATCC 51100	<0.01	<0.05	3986
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3253	derived cheese sample clone 32CR	<0.02	<0.05	2680
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3258	Staphylococcus auricularis str. MAFF911484 ATCC33753T	<0.01	<0.05	1525
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	1	3261	Enterococcus mundtii str. LMG 10748	<0.02	<0.05	2560
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3283	Bacillus niacini str. IFO15566	<0.01	<0.05	1201
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3284		<0.01	<0.05	1347
Firmicutes	Bacilli	Bacillales	Caryophanaceae	1	3285	Caryophanon latum str. DSM 14151	<0.01	<0.05	1499
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3287	tongue dorsum scrapings clone FP015	<0.01	<0.05	3582
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	1	3288	Isolation and identification hyper-ammonia producing swine storage pits manure	<0.01	<0.05	2528
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3290	Streptococcus mitis str. Sm91	≤0.01	<0.05	3971
Firmicutes	Bacilli	Bacillales	Paenibacillaceae	1	3299	Brevibacillus borstelensis str. LMG 15536	<0.02	<0.05	1035
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3313	Streptococcus salivarius str. ATCC 7073	<0.001	<0.01	3189
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	1	3318	Enterococcus ratti str. ATCC 700914	<0.02	<0.05	2272
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	1	3323	Trichococcus flocculiformis str. DSM 2094	<0.01	<0.05	1431
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	1	3326	Nostocoida limicola I str. Ben206	<0.01	<0.05	2363
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3328	Pseudobacillus carolinae	<0.001	<0.01	2370
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	1	3330	Lactobacillus kitasatonis str. KM9212	<0.02	<0.05	1389
Firmicutes	Bacilli	Bacillales	Sporolactobacillaceae	1	3365	Bacillus sp. clone ML615J-19	<0.001	<0.01	1757
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	1	3386	feedlot manure clone B87	<0.01	<0.05	2321
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	1	3392	Vagococcus lutrae str. m1134/97/1; CCUG 39187	<0.001	≤0.01	1976
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3397	Streptococcus macedonicus str. ACA-DC 206 LAB617	<0.01	<0.05	4011
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	1	3418	Lactobacillus subsp. aviarius	<0.01	<0.05	3036
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3419	Bacillus algicola str. KMM 3737	<0.01	<0.05	1590
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3422	Streptococcus thermophilus str. DSM 20617	<0.01	<0.05	3243
Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	1	3433	Tetragenococcus muriaticus	<0.01	<0.05	2715
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3446	Streptococcus bovis str. HJ50	<0.01	<0.05	3846
Firmicutes	Bacilli	Lactobacillales	Unclassified	1	3481		<0.01	<0.05	2102
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3489	Bacillus silvestris str. SAFN-010	<0.001	<0.01	1206
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3492	Bacillus subtilis str. IAM 12118T	<0.01	<0.05	1320
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3494	Micrococcus luteus B-P 26	≤0.01	<0.05	1334
Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	1	3497	Weissella koreensis S-5673	<0.02	<0.05	1457
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3499	Streptococcus constellatus str. ATCC27823	<0.01	<0.05	4476
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	1	3504	Marinilactibacillus psychrotolerans str. O21	<0.01	<0.05	1505
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3517	Planococcus maritimus str. TF-9	<0.01	<0.05	1358
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	1	3521	Pediococcus inopinatus str. DSM 20285	<0.001	<0.05	1122
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	1	3526	Lactobacillus sakei	<0.02	<0.05	1609
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3545		<0.01	<0.05	1372
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	1	3547	Lactobacillus frumenti str. TMW 1.666	<0.01	<0.05	1491
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3550	Bacillus megaterium str. QM B1551	≤0.001	<0.05	1620
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	1	3553	Desemzia incerta str. DSM 20581	<0.001	<0.01	1553
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3560	Streptococcus gallinaceus str. CCUG 42692	<0.001	<0.01	2835
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	1	3566	Lactobacillus pontis str. LTH 2587	<0.01	<0.05	2320
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3569	Staphylococcus saprophyticus	<0.01	<0.05	1391
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3588	Streptococcus downei str. ATCC 33748	<0.01	<0.05	2440
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3589	Bacillus senegalensis str. RS8; CIP 106 669	≤0.02	<0.05	1198
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3592	Staphylococcus caprae str. DSM 20608	≤0.01	<0.05	1322
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3605		<0.01	<0.05	1472
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3612	Bacillus schlegelii str. ATCC 43741T	<0.01	<0.05	1224
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3628	Staphylococcus haemolyticus str. CCM2737	<0.01	<0.05	1572
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3629	Streptococcus mutans str. UA96	<0.01	<0.05	1466
Firmicutes	Bacilli	Bacillales	Halobacillaceae	1	3633	Bacillus clausii str. GMBAE 42	<0.001	<0.01	2363
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	1	3634	Lactobacillus letivazi str. JCL3994	<0.01	<0.05	1586
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3638	Staphylococcus sp str. AG-30	<0.01	<0.05	1359
Firmicutes	Bacilli	Bacillales	Paenibacillaceae	1	3641	Brevibacillus sp. MN 47.2a	<0.02	<0.05	1735
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3654	Staphylococcus pettenkoferi str. B3117	<0.01	<0.05	1310
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3661	Bacillus sp. str. 2216.25.2	<0.01	<0.05	1593
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3675	Bacillus mojavensis str. M-1	<0.01	<0.05	1535
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3684	Staphylococcus sciuri	<0.02	<0.05	1324
Firmicutes	Bacilli	Bacillales	Halobacillaceae	1	3702	Amphibacillus xylanus str. DSM 6626	≤0.01	<0.05	1523
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	1	3703	Lactobacillus salivarius str. RA2115	<0.01	<0.05	1636
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3706	Bacillus sonorensis str. NRRL B-23155	<0.02	<0.05	1324
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3722	Lactococcus Il1403 subsp. lactis str. IL1403	≤0.001	<0.05	2673
Firmicutes	Bacilli	Bacillales	Sporolactobacillaceae	1	3747	Bacillus sp. str. C-59-2	<0.001	<0.01	1959
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3753	Streptococcus suis str. 8074	<0.02	<0.05	3463
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	1	3767	Lactobacillus suebicus str. CECT 5917T	<0.01	<0.05	2031
Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	1	3768	Lactobacillus perolens str. L532	<0.001	<0.001	1593
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3794		<0.01	<0.05	1324
Firmicutes	Bacilli	Bacillales	Staphylococcaceae	1	3822	Staphylococcus succinus str. SB72	<0.01	<0.05	1358
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3827	Bacillus acidogenesis str. 105-2	<0.01	<0.05	1996
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3831	Bacillus licheniformis str. KL-068	<0.01	<0.05	2057
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	1	3833	Carnobacterium alterfunditum	<0.001	<0.01	2781
Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	1	3840	Trichococcus pasteurii str. KoTa2	<0.001	<0.01	2656
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3869	Streptococcus equi subsp. zooepidemicus str. Tokyo1291 subsp.	≤0.01	<0.05	1766
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3900	Bacillus licheniformis str. DSM 13	<0.01	<0.05	1261
Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	1	3906	Streptococcus bovis str.ATCC 43143	<0.001	<0.01	4284
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3909	Bacillus subtilis subsp. Marburg str. 168	<0.01	<0.05	1367
Firmicutes	Bacilli	Bacillales	Bacillaceae	1	3918	Bacillus subtilis	<0.001	<0.01	1486
Firmicutes	Mollicutes	Anaeroplasmatales	Erysipelotrichaceae	3	3965	TCE-contaminated site clone ccslm238	≤0.01	<0.05	1844
Firmicutes	Mollicutes	Anaeroplasmatales	Erysipelotrichaceae	3	3981	phototrophic sludge clone PSB-M-3	<0.01	<0.05	1361
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4180	termite gut homogenate clone Rs-M23 bacterium	<0.01	<0.05	1383
Firmicutes	Clostridia	Unclassified	Unclassified	7	4216		<0.001	<0.01	2447
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4266	termite gut homogenate clone Rs-M86 bacterium	<0.01	<0.05	1302
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	4281	granular sludge clone UASB_brew_B86	≤0.001	<0.05	1333
Firmicutes	gut clone group	Unclassified	Unclassified	1	4298	human mouth clone P4PA_66	<0.01	<0.05	1991
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4306	UASB reactor granular sludge clone PD-UASB-4 bacterium	<0.01	<0.05	1483
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4321	termite gut homogenate clone Rs-C76 bacterium	≤0.01	<0.05	1362
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	4331	granular sludge clone UASB_brew_B84	<0.01	<0.05	1091
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4339	Clostridium chauvoei str. ATCC 10092T	<0.02	<0.05	1542
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4369	termite gut homogenate clone Rs-N73 bacterium	<0.01	<0.05	1579
Natronoanaerobium	Unclassified	Unclassified	Unclassified	1	4377	Mono Lake at depth 35 m station 6 July 2000 clone ML635J-65 G + C	<0.01	<0.05	1585
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4418	termite gut homogenate clone Rs-H18 bacterium	<0.02	<0.05	1173
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	4434	termite gut homogenate clone Rs-K11 bacterium	<0.01	<0.05	1298
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4475	termite gut homogenate clone Rs-N02 bacterium	<0.001	<0.01	1853
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4477	termite gut homogenate clone Rs-N85 bacterium	0.01	<0.05	1505
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4507	termite gut homogenate clone Rs-N21 bacterium	≤0.01	<0.05	1169
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	4510	termite gut homogenate clone Rs-Q53 bacterium	<0.02	<0.05	1896
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	4512	granular sludge clone UASB_brew_B25	<0.01	<0.05	1006
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	4514	termite gut homogenate clone Rs-B34 bacterium	≤0.001	<0.05	1800
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4524	termite gut clone Rs-093	<0.02	<0.05	1269
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	4533	termite gut homogenate clone Rs-N06 bacterium	<0.01	<0.05	1671
Firmicutes	Unclassified	Unclassified	Unclassified	8	4536	Mono Lake at depth 35 m station 6 July 2000 clone ML635J-14 G + C	<0.01	<0.05	1005
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	4540	termite gut homogenate clone Rs-M18 bacterium	<0.01	<0.05	1962
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4598	Clostridium sardiniense str. DSM 600	<0.02	<0.05	1253
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4607	Clostridium novyi str. NCTC538	<0.01	<0.05	1082
Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	5	4613	rumen clone 3C0d-3	<0.02	<0.05	1321
Firmicutes	gut clone group	Unclassified	Unclassified	1	4616	rumen clone F23-C12	<0.01	<0.05	2628
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4622	termite gut clone Rs-L36	≤0.01	<0.05	1112
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	12	4638		<0.01	<0.05	2515
Cyanobacteria	Unclassified	Unclassified	Unclassified	9	5038	Rumen isolate str. YS2	<0.001	<0.01	1724
Bacteroidetes	Bacteroidetes	Unclassified	Unclassified	15	5481	marine sediment above hydrate ridge clone Hyd89-72 bacterium	<0.02	<0.05	2056
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	19	5542	Cytophaga sp. I-1787	<0.01	<0.05	2304
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	15	5783	Mono Lake at depth 35 m station 6 July 2000 clone ML635J-15 bacterium	<0.01	<0.05	1032
Bacteroidetes	Bacteroidetes	Bacteroidales	Unclassified	15	5874	Paralvinella palmiformis mucus secretions clone P. palm 53 bacterium	<0.02	<0.05	1805
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Flexibacteraceae	19	6124	Flexibacter flexilis subsp. pelliculosus str. IFO 16028 subsp.	<0.001	<0.01	1387
Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	1	6459	Spirochaeta sp. str. BHI80-158	<0.001	≤0.01	2558
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Unclassified	3	9813	hydrothermal sediment clone AF420340	<0.01	<0.05	1453
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	5	9875	hydrothermal sediment clone AF420354	<0.01	<0.05	1147
Proteobacteria	Deltaproteobacteria	Desulfuromonadales	Geobacteraceae	1	10171		<0.01	<0.05	1375
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfoarculaceae	2	10227	marine sediment clone Bol11	<0.01	<0.05	1549
Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobacteraceae	5	10319	sulfate-reducing habitat clone SLM-CP-116	<0.01	<0.05	1235

^aS-F, Subfamily identification; ^bTaxon ID, PhyloChip Taxon identification number; ^cRepresentative species, Taxon bacterial species identifier.

A common “core” of 75 bacterial taxa representing 27 classified bacterial families was identified in all patients analyzed (Fig. 3). This core group included members of the Pseudomonadaceae, Enterobacteriaceae, Campylobacteraceae, and Helicobacteraceae, amongst others. In addition, taxa containing species of pathogenic potential, such as Arcobacter cryaerophilus, Brevundimonas diminuta, Leptospira interrogans, as well as P. aeruginosa, were detected in all patients (a complete list of the core taxa is provided in Table 5; see at end of article). We also analyzed the array data for organisms that have previously been associated with COPD airways (Sethi and Murphy, 2008). Haemophilus influenzae was detected by the array in two subjects (patients 2 and 8), although corresponding m-BAL cultures were negative for this organism. Moraxella catarrhalis was not detected by PhyloChip or culture in any patient sample. However, other phylogenetically related members in the Moraxellaceae family, including Moraxella oblonga, Acinetobacter haemolyticus, and Psychrobacter psychrophilus were identified by the array in 80–100% of subjects (Table 3). Streptococcus pneumoniae was detected in four subjects (patients 2, 3, 7 and 8) despite all m-BALs being culture-negative for this species. Finally, we also examined PhyloChip data for the presence of the atypical bacteria, Mycoplasma pneumoniae and Chlamydophila pneumoniae, which are associated with 3–5% percent of exacerbations (Sethi and Murphy, 2008). Neither was detected by the PhyloChip, although a related species, Mycoplasma pulmonis, was identified in a single individual (patient 3).

FIG. 3.

Phylogenetic tree illustrating core bacterial taxa detected in COPD airways samples in this study. Known pathogens are denoted with an asterix; distinct bacterial families are indicated by different colors.

Table 5.

Core Community of Bacterial Taxa Detected in all COPD Patients during Treatment for Severe Exacerbations (Representative Species with a Proven Role in Mammalian Pathogenesis are Highlighted)

Phylum	Class	Order	Family	S-Fa	Taxon IDb	Representative speciesc
Actinobacteria	Actinobacteria	Acidimicrobiales	Acidimicrobiaceae	sf_1	1749	forest soil clone DUNssu275 (-3A) (OTU#188)
Acidobacteria	Acidobacteria	Acidobacteriales	Acidobacteriaceae	sf_6	6362	grassland soil clone DA052
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8578	Marinobacter lipolyticus str. SM-19
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9239	Arctic sea ice ARK10228
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8222
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8753	Idiomarina loihiensis str. GSP37
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	9324	Pseudoalteromonas ruthenica str. KMM300
Proteobacteria	Gammaproteobacteria	Alteromonadales	Alteromonadaceae	sf_1	8579	Psychromonas profunda str. 2825
Proteobacteria	Alphaproteobacteria	Rickettsiales	Anaplasmataceae	sf_3	6648	Wolbachia sp
Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	sf_1	7747
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10538	Arcobacter cryaerophilus
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10447	Sulfurospirillum deleyianum str. Spirillum 5175
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	sf_3	10456	Campylobacter showae
Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	sf_1	6909	Brevundimonas diminuta str. DSM 1635
Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	sf_1	7436	Brevundimonas sp. str. FWC40
Cyanobacteria	Cyanobacteria	Chloroplasts	Chloroplasts	sf_5	5147	Emiliania huxleyi str. Plymouth Marine Laborator PML 92
Proteobacteria	Gammaproteobacteria	Legionellales	Coxiellaceae	sf_3	9198	uranium mining waste pile clone KF-JG30-B15 KF-JG30-B15
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Crenotrichaceae	sf_11	6267	Cilia-respiratory isolate str. 243-54
Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfomicrobiaceae	sf_1	10079	Desulfomicrobium baculatum str. DSM 1742
Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	sf_1	8504	Dysmicoccus neobrevipes symbiont
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10385
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10442	Helicobacter cetorum str. MIT 99-5656
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10444	Helicobacter suncus str. Kaz-2
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10448	Helicobacter felis str. Dog-1
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	sf_3	10451	Helicobacter heilmannii str. C4S
Spirochaetes	Spirochaetes	Spirochaetales	Leptospiraceae	sf_3	6496	Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	8366	Psychrobacter frigidicola str. DSM 12411
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	8838	Psychrobacter psychrophilus CMS 28
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	sf_3	8727	Alkanindiges hongkongensis str. HKU9
Proteobacteria	Betaproteobacteria	Nitrosomonadales	Nitrosomonadaceae	sf_1	7789
Firmicutes	Clostridia	Clostridiales	Peptococc/Acidaminococc	sf_11	992	anoxic bulk soil flooded rice microcosm clone BSV43 clone
Planctomycetes	Planctomycetacia	Planctomycetales	Pirellulae	sf_3	4670
Proteobacteria	Gammaproteobacteria	Thiotrichales	Piscirickettsiaceae	sf_3	9291	Methylophaga alcalica str. M39
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8691	Pseudomonas aeruginosa str. PAO1
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9056	Pseudomonas aeruginosa str. #47
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9068	Pseudomonas stutzeri str. A1501
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9295
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9613	Pseudomonas flavescens str. B62
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9049	uranium mining mill tailing clone GR-Sh2-34 GR-Sh2-34
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9469	cf. Pseudomonas sp. clone Llangefni 52
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9240	Pseudomonas fluorescens str. CHA0
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	9366	Arctic seawater isolate str. R7366
Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	sf_1	8755	Pseudomonas sp. SK-1-3-1
Bacteroidetes	Sphingobacteria	Sphingobacteriales	Sphingobacteriaceae	sf_1	5913	Sphingobacteriaceae str. Ellin160
Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	sf_1	6663	Sphingopyxis flavimaris str. SW-151
Firmicutes	Bacilli	Bacillales	Thermoactinomycetaceae	sf_1	3301	Thermoactinomyces sp. str. 700375
Thermodesulfobacteria	Thermodesulfobacteria	Thermodesulfobacteriales	Thermodesulfobacteriaceae	sf_1	667	Fjonesia
Proteobacteria	Gammaproteobacteria	Thiotrichales	Thiotrichaceae	sf_3	8752	Beggiatoa sp. str. MS-81-1c
Chloroflexi	Unclassified	Unclassified	Unclassified	sf_2	818
Verrucomicrobia	Unclassified	Unclassified	Unclassified	sf_4	288	Prosthecobacter dejongeii
Synergistes	Unclassified	Unclassified	Unclassified	sf_3	117	termite gut homogenate clone Rs-D89
Synergistes	Unclassified	Unclassified	Unclassified	sf_3	719	Synergistes sp. P1 str. P4G_18
OP3	Unclassified	Unclassified	Unclassified	sf_4	628	CB-contaminated groundwater clone GOUTB15
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	485	thermal spring mat clone O1aA90
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	226
Bacteroidetes	KSA1	Unclassified	Unclassified	sf_1	5951	CFB group clone ML615J-4
Chloroflexi	Anaerolineae	Unclassified	Unclassified	sf_9	727	forest soil clone S0208
Cyanobacteria	Unclassified	Unclassified	Unclassified	sf_8	5206
marine group A	mgA-2	Unclassified	Unclassified	sf_1	6344	bacterioplankton clone ZA3648c
Unclassified	Unclassified	Unclassified	Unclassified	sf_160	6430
Proteobacteria	Alphaproteobacteria	Unclassified	Unclassified	sf_6	7575
TM7	TM7-3	Unclassified	Unclassified	sf_1	8155	oral periodontitis clone EW086
Proteobacteria	Gammaproteobacteria	uranium waste clones	Unclassified	sf_1	8747	uranium waste soil clone JG30-KF-CM35
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	9568	forested wetland clone RCP2-96
Proteobacteria	Gammaproteobacteria	SUP05	Unclassified	sf_1	8605	bacterioplankton clone ZA2525c
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_3	8339	water 5 m downstream manure clone 35ds5
Proteobacteria	Gammaproteobacteria	Unclassified	Unclassified	sf_4	8855
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Unclassified	sf_1	10480	Paralvinella palmiformis mucus secretions cloneP. palm C 84 proteobacterium
Proteobacteria	Epsilonproteobacteria	Campylobacterales	Unclassified	sf_1	10530	hydrothermal vent 9 degrees North East Rise PacificOcean clone CH5_6_BAC_16SrRNA_9N_EPR
Actinobacteria	Actinobacteria	Actinomycetales	Unclassified	sf_3	1687	Jonesia quinghaiensis str. DSM 15701
Actinobacteria	Actinobacteria	Actinomycetales	Unclassified	sf_3	1405	Arthrobacter ureafaciens str. DSM 20126
Firmicutes	Clostridia	Unclassified	Unclassified	sf_3	2373
Firmicutes	Catabacter	Unclassified	Unclassified	sf_1	4293	termite gut homogenate clone Rs-Q01 bacterium
Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	sf_3	8689	Dyemonas todaii str. XD10
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Xiphinematobacteraceae	sf_3	888	Candidatus Xiphinematobacter brevicolli

^aS-F, Subfamily identification; ^bTaxon ID, PhyloChip Taxon identification number; ^cRepresentative species, Taxon bacterial species identifier.

Quantitative PCR was performed to validate that changes in reported array fluorescence intensities for targeted taxa correlated with changes in target species copy number for a selection of known airway pathogens (P. aeruginosa and Stenotrophomonas maltophilia) and two characteristic gastrointestinal organisms (Campylobacter mucosalis and Helicobacter cetorum). Regression analysis of species abundance determined by Q-PCR and array fluorescence intensity demonstrated strong concordance between the two independent methods for each target organism (Table 6), confirming their presence in these COPD airway samples and the ability of the array to accurately reflect changes in organism relative abundance.

Table 6.

Correlation Results for Species Abundance by Q-PCR and 16S rRNA PhyloChip

Target species	R value	p Value
P. aeruginosa	0.77	<0.05
S. maltophilia	0.80	<0.05
Campylobacter mucosalis	0.68	<0.10
Helicobacter cetorum	0.79	<0.05

Discussion

Although nearly half of acute COPD exacerbations are associated with bacterial infection, our knowledge of the microbial species associated with these events is limited to a handful of organisms detected primarily by culture-based methods (Papi et al., 2006; Rosell et al., 2005; Soler et al., 2007). The overall aim of this study was to begin to address the overarching question whether previously undetected bacterial species exist in the airways of COPD patients during acute exacerbations. High-resolution, culture-independent analysis using the 16S rRNA PhyloChip revealed a much greater diversity of bacteria than has previously been appreciated in the airways of COPD patients being managed for severe exacerbations, including members of the Pseudomonadaceae, Enterobacteriaceae, and Helicobacteraceae, among others. The potential for a diverse airway bacterial community to play a role in chronic airway colonization and inflammation, a feature of COPD, has not been previously considered.

The identification of a diversity of bacterial communities in respiratory samples from COPD patients experiencing severe exacerbations suggests that the pathogenesis of these events could involve a polymicrobial process. Future studies in a larger cohort of patients, including nonintubated COPD patients with a greater range of exacerbation severity, will be necessary to determine relationships between community composition, structure, and pulmonary health. Only a handful of bacterial species, such as H. influenzae and P. aeruginosa, have previously been associated with COPD exacerbations. The possible role of other bacterial community members with pathogenic potential identified in this study, e.g. A. cryaerophilus, B. diminuta, and L. interrogans, may merit further investigation. Many of these species have been implicated in other pathogenic processes such as endocarditis (Han and Andrade, 2005; Marques da Silva et al., 2006; Paster et al., 2002) and bacteremia (Hsueh et al., 1997; Woo et al., 2001). L. interrogans, the causative agent of human leptospirosis (Gaudie et al., 2008), has recently been shown to induce pulmonary lesions in an experimental animal model of airway infection (Marinho et al., 2009) and pulmonary hemorrhage in severe cases (Dall'Antonia et al., 2008). Their potential for pathogenesis suggests the possibility of a role for these organisms in COPD chronic airway disease. Future studies involving functional and mechanistic analyses will be necessary to further assess this.

Multiple oropharyngeal and gut-associated bacterial species were also identified by PhyloChip analysis, suggesting a potential role in COPD exacerbations. Although contamination by oropharyngeal secretions is always a possibility, samples were collected through an endotracheal tube, diminishing the degree of direct contamination. Ongoing microaspiration during intubation, however, cannot be completely prevented, and it has been suggested that the oral cavity and gastrointestinal tract act as a microbial reservoir for seeding the airways in vulnerable patient populations (Garrouste-Orgeas et al., 1997; Heyland and Mandell, 1992; Orozco-Levi et al., 2003). In our study the relative abundance of targeted gastrointestinal-associated species, H. cetorum and C. mucosalis (Figura et al., 1993; Garcia-Amado et al., 2007), were confirmed by independent Q-PCR in airway samples from these patients. The presence of oropharyngeal or gut-associated bacteria in the lower airways may have significant implications for a disease population with greater risks from pulmonary infections. For example, Duan et al. (2003) demonstrated in a rat model that coinfection of P. aeruginosa with oropharyngeal bacterial species (isolated from cystic fibrosis patient sputa) resulted in enhanced lung damage and upregulation of P. aeruginosa virulence gene expression. In our study, P. aeruginosa and oropharyngeal and gut-associated species were present in the airways of all patients studied, suggesting the potential for enhanced pathogenesis in this patient population.

We recognize that our study numbers are small and represent a severely ill group of COPD patients. Therefore, caution must be exercised in extrapolating these findings to a broader group of COPD patients, especially nonintubated individuals experiencing less severe exacerbations. Although facilitating access to lower respiratory specimens that are otherwise challenging to obtain during severe exacerbations, the intubation status of these patients is an important consideration in weighing these findings. Although protracted intubation was associated with decreased bacterial community richness, the possibility for a more diverse bacterial community to play a role at least at the onset of exacerbation-associated respiratory failure remains. Control samples from nonintubated COPD and non-COPD patients were not available for this study, nor were longitudinal samples from these patients. In a previous study, however, we have found that endotracheal samples obtained from patients briefly intubated for elective surgery produced no detectable 16S rRNA PCR product (Flanagan et al., 2007). The lack of an association between duration of active antimicrobial therapy and bacterial community structure is most likely due to both the small study numbers as well as the administration of previous antibiotic courses up to one month prior to sample collection in the study (e.g., patient 6).

Results of this study highlight the advantages of complementing culture-based methods with higher resolution approaches for bacterial detection to provide a more comprehensive assessment of the airway microbiota present in COPD patients. Culture-independent methods are particularly relevant to identify viable but nonculturable species that produce and exist in biofilms (Rayner et al., 1998), which are characteristic of chronic airway infections (Costerton et al., 1999; Singh et al., 2000) and have recently been implicated in COPD (Martinez-Solano et al., 2008). Because our PhyloChip analysis was based on DNA extracted from airway samples, it does not provide information on the viability of the species detected. However, we have previously noted that within 24 h of antimicrobial administration to cystic fibrosis patients, bacterial richness decreased approximately 10-fold as detected by the PhyloChip (Lynch, unpublished data). This suggests that DNA turnover is relatively rapid in the airways of chronic pulmonary disease patients, and that the taxa detected during antimicrobial administration in our COPD patients largely represent the viable portion of the community. This is supported by the finding that the PhyloChip detected all species that were isolated by concurrent clinical laboratory culture. Independent Q-PCR analysis of selected taxa also demonstrated strong concordance between calculated 16S rRNA copy number and PhyloChip-based fluorescence intensities, validating the abundance of individual species detected by the array. Although both cultures and the microarray demonstrated low detection rates for H. influenzae and M. catarrhalis, two species commonly associated with COPD exacerbation (potentially due to antibiotic-mediated clearance), only the PhyloChip identified other Haemophilus species across the majority of patients in this study, as well as other members of the Moraxellaceae family. Although these molecular methods may identify potentially relevant species undetected by culture, they provide no information on the viability or activity of these species. Hence, the significance of detecting species phylogenetically related to known pathogens in COPD airways is unclear, but may merit further study.

Conclusions

Application of the 16S rRNA PhyloChip to airway secretions from COPD patients during severe respiratory exacerbations requiring ventilatory support and antibiotic administration, demonstrated the presence of diverse bacterial communities, whose structural variation in this cohort was related to the duration of intubation. A core community of bacterial taxa comprised of many known pathogens, some not previously associated with COPD, was common to all patients studied. Given that the disease model of COPD is generally characterized by chronic airway colonization, recurrent infection-related exacerbations, and a persistent state of chronic airway inflammation, these results highlight the need to consider the polymicrobial community present in COPD airways and the potential functional effects of these consortia on immune response and pulmonary health. Identification of relationships that exist between bacterial communities, their collective gene expression, concomitant host response, and clinical outcomes may ultimately lead to improved understanding of the pathogenesis of COPD.

Acknowledgments

The authors thank Yvette Piceno, Todd DeSantis, and Gary Andersen at Lawrence Berkeley National Laboratory for their advice and technical support in this study, and to Homer Boushey, M.D., for his critique of the manuscript. Part of this work was performed at Lawrence Berkeley National Laboratory under the auspices of the University of California under contract number DOE DE-AC02-05CH11231. Research was supported by a Tobacco-Related Disease Research Program (Univ. of California) fellowship to Y.J.H. and an American Lung Association grant to S.V.L. S.V.L. and E.L.B. are funded also by NIH Award (AI075410).

Author Disclosure Statement

The authors declare that no competing financial interests exist.