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. 2022 Aug 5;17(8):e0272435. doi: 10.1371/journal.pone.0272435

Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics

Rui-Fang Gao 1,2,*, Ying Wang 1,2, Ying Wang 1,2, Zhi-Wen Wang 3, Gui-Ming Zhang 1,2
Editor: Paula V Morais4
PMCID: PMC9355198  PMID: 35930552

Abstract

In this study, we sequenced a bacteria isolate Pandoraea sp. 892iso isolated from a Phytophthora rubi strain which is an important plant pathogenic oomycete, identified through genome and combined the data with existing genomic data from other 28 the genus of Pandoraea species. Next, we conducted a comparative genomic analysis of the genome structure, evolutionary relationships, and pathogenic characteristics of Pandoraea species. Our results identified Pandoraea sp. 892iso as Pandoraea sputorum at both the genome and gene levels. At the genome level, we carried out phylogenetic analysis of single-copy, gene co-linearity, ANI (average nucleotide identity) and AAI (average amino acid identity) indices, rpoB similarity, MLSA phylogenetic analysis, and genome-to-genome distance calculator calculations to identify the relationship between Pandoraea sp. 892iso and P. sputorum. At the gene level, the quorum sensing genes ppnI and ppnR and the OXA-159 gene were assessed. It is speculated that Pandoraea sp. 892iso is the endosymbiont of the Oomycetes strain of Phytophthora rubi.

Introduction

The genus Pandoraea, originating from the term “Pandora’s box”, refers to the source of all evil in Greek mythology and was established by Coenye et al. in 2000 [1]. The species are characterized as nonspore-forming, catalase-positive, aerobic, gram-negative rods with polar flagella. Some species in this genus were once identified closest to Burkholderia cepacia complex (Bcc), Ralstonia pickettii, or Ralstonia paucula based on phenotype. [1–3]. The genus Pandoraea includes 28 named species (Pandoraea anapnoica, P. anhela, P. apista, P. aquatica, P. bronchicola, P. capi, P. captiosa, P. cepalis, P.commovens, P. communis, P. eparura, P. faecigallinarum, P. fibrosis, P. horticolens, P. iniqua, P. morbifera, P. norimbergensis, P. nosoerga, P. oxalativorans, P. pneumonica, P. pnomenusa, P. pulmonicola, P. soli, P. sputorum, P. terrae, P. terrigena, P. thiooxydans and P. vervacti [3–5]. Pandoraea sp. types have been predominantly isolated from patients with septicemia or respiratory tract infections (mostly cystic fibrosis), as well as from food, water, soil, and food [2, 4, 6–9].

Clinical manifestations of this terrorizing pathogen revolve around nosocomial infections and its ability to deteriorate lung function and even cause multiple organ impairment [10–12]. These organisms appear to be potential pathogens for individuals with cystic fibrosis as well for cross-infection [13]. Further, Pandoraea spp. isolated from environmental samples have considerable potential for biotechnological application given various beneficial degradation abilities, such as removing isomers of 1,2,3,4,5,6-hexachlorocyclohexane (HCH) [13], catalyzing the aerobic transformation of biphenyl and various polychlorinated biphenyls (PCBs) [14, 15], catalyzing the decarboxylation of 2,6-dihydroxybenzoate and regioselective carboxylation of 1,3-dihydroxybenzene to 2,6-dihydroxybenzoate, catalyzing the regioselective carboxylation of phenol and 1,2-dihydroxybenzene [16], degrading kraft lignin without any cosubstrate under high alkaline conditions [17], degrading chlorobenzene [18], biodegrading endosulfan classified as an organochlorine pesticide [19], treating malachite green [20], and metabolizing oxalate [21].

Reflecting on previous research, Pandoraea spp. have frequently been misidentified in many clinical laboratories, leading to a lack of clinical documentation on their virulence potential. Therefore, it is important to accurately identify Pandoraea spp.. Earlier classification of prokaryotes was based solely on phenotypic similarities [22], but modern prokaryote characterization has been strongly influenced by advances in genetic methods. One criterion to be considered a species is to be essentially a collection of types that are characterized by at least one diagnostic phenotypic trait and to have purified DNA molecules that show at least 70% cross-hybridization (DNA-DNA hybridization, DDH) [22–25]. This is pragmatic and universally applicable within the bacterial domain, while the lack of this standard has been increasingly found when it comes to reliable diagnosis of infectious disease agents, international regulations for transport, quarantine, and so on [26–28]. Subsequently, this parameter has been applied most frequently in species identification at the whole genome level [29–32]. Genome Blast Distance Phylogeny (GBDP) [33], the core and pangenome [32], and the genomic-distance index based on DNA maximal unique matches (MUM) [34] are used to identify new species. Unfortunately, our understanding of Pandoraea spp. at the genomic level is relatively superficial, whereby the majority of the literature focuses principally on the usage of genotypic data to facilitate accurate genus- and species-level identification and secondarily on biotechnological potential [1, 2, 18, 21].

In the present study, suspected bacteria isolated from an oomycete strain was identified through whole genome sequencing. The taxonomic status of this isolate was verified at the genome and gene levels, and its phylogenetic relationship with similar species was explored using indices, such as ANI/AAI, MLSA (Multi-locus Sequence Analysis) phylogenetic analysis, genome-to-genome distance calculations, quorum sensing, and oxacillinase gene analysis.

Materials and methods

Strains, cultures, and DNA extraction

When we performed morphological observations on the hyphae of a Phytophthora rubi strain (No. 109892) from Westerdijk Fungal Biodiversity Institute, we inadvertently discovered the structure of suspected bacteria present in the mycelia. The structure still existed after the isolation by monofilament isolation and monospore isolation of the fungus. After isolation and culture, we obtained an analytical strain of bacteria, so that part of the name of which is called “892iso isolate”. Separation, purification, and culture were carried out on beef extract peptone medium plates at 30°C for 48 h. A TIANamp Bacteria DNA Kit (Tiangen, China) was used for genomic DNA.

Sequencing, assembly, and annotation

The whole genome was sequenced and assembled by a strategy that combined paired-end and mate-paired libraries. One targeted insert size of 500 bp was constructed using the TruSeq Nano DNA LT Library Prep Kit (Illumina, USA). One mate-paired library (2 kb) was constructed by the Nextera Mate Pair Sample Prep Kit (Illumina, FC-132–1001, USA) on the Illumina HiSeq 2500 platform. SOAPdenovo (v2.04) was used for de novo assembly. The assembled genome was annotated with a web-based tool called RAST (http://rast.nmpdr.org). RAST can identify repeat sequences in the genome, protein-encoding rRNA and tRNA genes, and assign functions to the genes.

Whole genome alignment and some indices calculation

Mauve (version 2.3.1) was used to align genomes for synteny analysis. The calculation of ANI and AAI was based on BLAST alignment results using a Perl script. The genome-to-genome distance calculator calculations were based on a web server (https://ggdc.dsmz.de/) that uses multi-FASTA files as input. The ppnI/ppnR genes of P. pnomenusa were download from NCBI (accession ID KF887500.1 and KF900148.1), then aligned with all Pandoraea gene sets, all matches with the identity greater than 0.3 and score greater than 100 were retained. The ppnI candidates should contain PF00765 domain and ppnR candidates contain PF03472 domain, and the candidate pairs should be adjacent to each other. An intrinsic Carbapenem-Hydrolyzing Oxacillinases gene of Pandoraea sp. HD7676 was download from NCBI (accession ID: KP771987.1). BLAST was employed to identify homolog genes in the 28 Pandoraea species.

Comparative genome analysis

All protein sequences in reference genomes were downloaded and set as the query for all-vs-all BLASTP. OrthoMCL (version 2.0.8) was used to identify single-copy genes with I (inflation) set at 1.5. Next, MUSCLE (version 3.8.425) was used to align the sequences of the associated proteins. PAL2NAL (version 14.0) was used to convert the protein alignment to codon alignment. Gblock (version 0.91b) was used to remove the alignment results that were deemed unreliable. The phylogenetic tree was built by single-copy genes, with Burkholderia cepacia strain LO6 as the outgroup. MCMCTree software in PAML (version 4.7) was used to estimate the divergence time. CAFÉ (version 4) was used to calculate the expansion and contraction of these gene families.

Results

Genome assembly, annotation, and validation of protein-coding genes

The genome of the Pandoraea sp. 892iso isolate was assembled from sequencing data generated by HiSeq 2000 by SOAPDenovo2 assembler. The total length of the top 48 longest scaffolds was 5.83 Mb, representing approximately 82.6-fold genome sequence coverage. The N50 and maximum lengths of scaffolds was 1.43 kb. Most of the length was concentrated on 12 scaffold sequences over 1,000 bp, of which the longest sequence was 2.06 MB (Fig 1). A total of 5,367 protein-coding genes were predicted from the genome assembly, 5,131 (95.60%) of which were supported by the RNA-seq data (coverage > = 90%). Within these protein-coding genes, 4,274 (79.63%) were assigned a biological function. Among the 1,093 ORFs without known function, 736 showed similarity to other database entries. For Pandoraea sp. 892iso isolate, the coding regions from the predicted genes constituted 88.61% of the genome (total length of all genes divide the genome size) and the average gene density was 919 genes per 1 Mb (total number of all genes divide the genome size, times with 100000bp), which were more or fewer than most of other sequenced Pandoraea species. The GC content of the genome, coding sequences, and repetitive elements were 62.66%, 63.32%, and 57.52%, respectively. A total of 63 tRNA genes were predicted from the assembly. The genome characteristics of Pandoraea sp. 892iso and other Pandoraea species are shown in Table 1.

Fig 1. Structure of the genome assembly.

Fig 1

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Table 1. Genome and gene comparison of Pandoraea sp. 892iso and other Pandoraea species.

Content Pandoraea sp. 892iso Pandoraea anapnoica Pandoraea anhela Pandoraea apista Pandoraea aquatica Pandoraea bronchicola Pandoraea capi Pandoraea captiosa Pandoraea cepalis Pandoraea commovens Pandoraea communis
Accession number GCF_902459765.1 GCF_902459655.1 GCF_001465595.2 GCF_902459565.1 GCF_902459805.1 GCF_902459735.1 GCF_902459775.1 GCF_902459625.1 GCF_902459615.1 GCF_902459745.1
Genome
Scaffold Number 48 48 61 2 17 34 31 36 32 26 17
Total Length (Mb) 5.83 6.13 6.05 5.57 5.96 5.35 5.85 6.14 5.16 6.04 5.71
GC Content (%) 62.7 62.4 63.35 62.63 62.89 62.97 63.44 63.3 63.54 62.63 62.57
N50 Length 1,430,084 278,466 256,277 - 442,715 323,330 401,082 280,257 286,967 434,611 434,208
N90 Length 768,040 128,458 71,214 - 244,118 147,078 151,211 137,159 88,384 144,451 240,155
Longest scaffold 2,057,907 677,688 731,537 - 1,296,496 977,860 812,744 1,307,560 1,062,234 1,441,918 1,422,275
Gene
Gene Number 5367 5,348 5,178 4,969 5,197 4,734 5,049 5,328 4,602 5,246 5,051
Gene Length (bp) 5,175,057 5,334,275 5,189,856 4,830,549 5,211,988 4,656,675 5,074,754 5,326,122 4,478,447 5,288,517 4,979,502
GC Content in Gene Region (%) 63.32 63.11 63.92 63.21 63.6 63.52 64.13 63.89 64.03 63.33 63.13
Gene Length/Genome (%) 88.61 87.07 85.84 86.7 87.48 87.02 86.72 86.75 86.8 87.6 87.23
Gene Average Length (bp) 964 997 1,002 972 1,003 984 1,005 1,000 973 1,008 986
Intergenic Region Length (bp) 665,083 792,413 856,156 740,711 746,139 694,448 777,390 813,460 681,119 748,432 729,101
GC Content in Intergenic Region (%) 57.52 57.63 59.87 58.9 57.95 59.27 58.97 59.45 60.3 57.73 58.74
Intergenic Region Length/Genome (%) 11.39 12.93 14.16 13.3 12.52 12.98 13.28 13.25 13.2 12.4 12.77
Content Pandoraea eparura Pandoraea faecigallinarum Pandoraea fibrosis Pandoraea horticolens Pandoraea iniqua Pandoraea morbifera Pandoraea norimbergensis Pandoraea nosoerga Pandoraea oxalativorans Pandoraea pneumonica Pandoraea pnomenusa
Accession number GCF_902459725.1 GCF_001029105.3 GCF_000807775.2 GCF_902459555.1 GCF_902459685.1 GCF_902459575.1 GCF_001465545.3 GCF_902459585.1 GCF_000972785.3 GCF_902459645.1 GCF_000504585.2
Genome
Scaffold Number 35 3 1 68 17 47 1 41 5 12 1
Total Length (Mb) 5.21 5.73 5.59 6.01 6.34 5.23 6.17 4.86 6.5 5.85 5.39
GC Content (%) 63.68 63.45 62.82 62.31 63.06 64.65 63.06 66.13 63.08 62.45 64.89
N50 Length 259,402 - - 290,798 382,973 316,192 - 229,370 - 265,947 -
N90 Length 102,841 - - 73,897 241,289 80,719 - 91,075 - 5,636 -
Longest scaffold 893,217 - - 787,753 1,308,188 801,833 - 664,052 - 2,096,772 -
Gene
Gene Number 4,615 5,027 4,855 5,322 5,499 4,652 5,356 4,297 5,648 5,168 4,759
Gene Length (bp) 4,496,889 4,932,939 4,868,583 5,167,287 5,558,312 4,536,412 5,418,712 4,198,421 5,522,745 5,131,811 4,684,824
GC Content in Gene Region (%) 64.17 63.98 63.39 62.98 63.76 65.1 63.72 66.51 63.59 63.06 65.36
Gene Length/Genome (%) 86.39 86.05 87.06 86 87.68 86.68 87.86 86.35 84.96 87.8 86.98
Gene Average Length (bp) 974 981 1,003 971 1,011 975 1,012 977 978 993 984
Intergenic Region Length (bp) 708,688 799,725 723,482 841,203 780,817 696,886 748,658 663,693 977,986 713,267 701,122
GC Content in Intergenic Region (%) 60.55 60.15 58.94 58.19 58.13 61.77 58.29 63.71 60.23 58.09 61.71
Intergenic Region Length/Genome (%) 13.61 13.95 12.94 14 12.32 13.32 12.14 13.65 15.04 12.2 13.02
Content Pandoraea pulmonicola Pandoraea soli Pandoraea sp. XY-2 Pandoraea sputorum Pandoraea terrae Pandoraea thiooxydans Pandoraea vervacti
Accession number GCF_000815105.2 GCF_902459595.1 GCF_004193915.1 GCF_900187205.1 GCF_902459695.1 GCF_001017775.3 GCF_000934605.2
Genome
Scaffold Number 1 51 1 1 81 1 2
Total Length (Mb) 5.87 4.96 5.06 5.74 6.18 4.46 5.74
GC Content (%) 64.3 63.62 63.76 62.78 62.79 63.19 63.52
N50 Length - 370,563 - - 194,136 - -
N90 Length - 61,129 - - 60,237 - -
Longest scaffold - 921,398 - - 456,896 - -
Gene
Gene Number 4,996 4,393 4,512 4,994 5,590 4,091 4,889
Gene Length (bp) 5,040,965 4,324,589 4,386,412 5,002,422 5,421,742 3,998,582 4,955,787
GC Content in Gene Region (%) 65 64.13 64.26 63.5 63.31 63.76 64.11
Gene Length/Genome (%) 85.91 87.15 86.75 87.1 87.78 89.57 86.39
Gene Average Length (bp) 1,009 984 972 1,002 970 977 1,014
Intergenic Region Length (bp) 826,656 637,393 669,794 740,701 755,081 465,604 780,495
GC Content in Intergenic Region (%) 59.97 60.12 60.47 57.89 58.98 58.3 59.82
Intergenic Region Length/Genome (%) 14.09 12.85 13.25 12.9 12.22 10.43 13.61
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Comparative genomics and identification at the genome level

Comparative genomic analysis

A total of genes in Pandoraea sp. 892iso were classified through cluster analysis. The distribution of best hits within the genus Pandoraea is shown in Fig 2. In total, 3,849 orthologous genes were shared in common between Pandoraea sp. 892iso and the other four Pandoraea species. The cluster analysis of Pandoraea sp. 892iso, 28 Pandoraea species, and Burkholderia cepacia as an outgroup was carried out by orthoMCL to obtain the result of a common single-copy gene family. The phylogenetic relationship in view of these single-copy genes is shown in Fig 3 and S1 Table, which shows the closest phylogenetic relationship to be between Pandoraea sp. 892iso and the P. sputorum strain DSM21091. Meanwhile, eight specific gene families, including 21 genes, were clustered, 17 genes were hypothetical proteins, and the other four are shown in Table 2.

Fig 2. Venn diagram of genes common to Pandoraea sp. 892iso and the four other Pandoraea types.

Fig 2

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Fig 3. Phylogenetic analyses of the evolutionary relationships between Pandoraea sp. 892iso and Pandoraea types.

Fig 3

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A neighbor-joining phylogenetic tree constructed based on single-copy genes common to these nine bacterial genomes. The neighbor-joining method was used in MEGA6, where a bootstrap test (1,000 replicates) is shown next to the branches.

Table 2. Details of the four respective genes of Pandoraea sp. 892iso.
Gene Position direction Detail
fig|93222.8.peg.1 C163_3_104 - DNA-cytosine methyltransferase
fig|93222.8.peg.10 C237_1_126 - DNA-cytosine methyltransferase
fig|93222.8.peg.14 C273_3_104 - DNA-cytosine methyltransferase
fig|93222.8.peg.2519 scaffold3_1641978_1640653 - DNA-cytosine methyltransferase
fig|93222.8.peg.4329 scaffold5_320715_322067 + DNA-cytosine methyltransferase
fig|93222.8.peg.4363 scaffold5_361619_362311 + Transcriptional regulator, GntR family
fig|93222.8.peg.4364 scaffold5_363002_362316 - Transcriptional regulator, GntR family
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The global genome clustering and alignment of Pandoraea types were complicated by Mummer. The results showed the best gene co-linearity among these Pandoraea types and that rearrangement was almost absent, except for P. thiooxydans and P. sputorum, which were phylogenetically closest to Pandoraea sp. 892iso (S1 Fig). It was speculated that the small external selection pressure of the Pandoraea group and the genome evolution occurred in a similar way. More attention should be given to Pandoraea sp. 892iso and its proximal P. sputorum, both of which rearranged compared to other Pandoraea types. Rearrangements existed in the five largest scaffold alignments, especially in scaffolds 3, 4, and 5, as shown in S2 Fig. A special unique insertion sequence in scaffold3_1802763_1803544 of Pandoraea sp. 892iso contains the gene fig|93222.8.peg.2650 with the function of ubiquitin in the NR database, which may be related to the function of covalent attachment to other cellular proteins associated with stability changing, localization, and activity of the target protein [35]. The ubiquitin gene in Pandoraea sp. 892iso was found to be different from that in human, mouse, zebrafish, rice, Arabidopsis, yeast, or other model organisms by phylogenetic analysis (Fig 4).

Fig 4. Phylogenetic analyses of evolutionary relationships of ubiquitin genes among Pandoraea sp. 892iso and Pandoraea types.

Fig 4

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A neighbor-joining phylogenetic tree constructed based on single-copy genes common to these nine bacterial genomes. The neighbor-joining method was used in MEGA6, where a bootstrap test (1,000 replicates) is shown next to the branches.

ANI and AAI

ANI (average nucleotide identity), as the new method for bacterial species definition, provides several benefits, avoids misplacement based on phenotypic similarities or chemical characteristics, provides a scalable and uniform approach that works for both culturable and nonculturable species, is faster and cheaper than traditional taxonomic methods, and, most importantly, falls in line with Darwin’s vision of classification [30]. AAI (average amino acid identity), a method that compares all conserved protein-coding genes present in a given set of genomes, clusters types into groups that share more than 95% AAI [36]. ANI and AAI characteristics have been used to evaluate the accuracy of these genotypic methods in the identification of Pandoraea species. Given the availability of whole genome sequence data and Pandoraea sp. 892iso nucleotide and amino acid data as query, Blastn by CDS sequence coverage was ≥ 50% and tblastn by protein coverage was ≥ 70%. We performed sequence-based genotypic microbial identification analysis using the RefSeq database by genome comparison between Pandoraea sp. 892iso and Pandoraea sputorum and generated an ANI value of 98.81% and an AAI value of 91.18%; genome comparison with other in-house sequenced Pandoraea species provided an ANI value of less than 93.34% and an AAI value of 84.90% (Table 3). Based on previous results using the ANI value for species definition, ANI and AAI values of ≥ 95% corresponded to the traditional 70% DNA-DNA. Using the ANI and AAI values of Pandoraea sp. 892iso, it can be unequivocally stated that Pandoraea sp. 892iso is phylogenetically close to P. sputorum.

Table 3. Average nucleotide identity (ANI) and average amino acid identity (AAI) analyses.

Genome comparisons of Pandoraea sp. 892iso and other Pandoraea-type species.

Species ID ANI AAI
value percent value percent
Pandoraea anapnoica GCF_902459765.1 94.10 83.55 93.57 89.88
Pandoraea anhela GCF_902459655.1 87.56 61.88 85.97 84.01
Pandoraea apista GCF_001465595.2 86.43 54.74 84.98 83.38
Pandoraea aquatica GCF_902459565.1 92.99 83.01 93.06 89.25
Pandoraea bronchicola GCF_902459805.1 86.63 55.10 84.51 81.14
Pandoraea capi GCF_902459735.1 87.77 67.77 88.02 87.59
Pandoraea captiosa GCF_902459775.1 87.24 61.15 86.49 85.41
Pandoraea cepalis GCF_902459625.1 86.48 48.39 82.57 77.98
Pandoraea commovens GCF_902459615.1 94.51 85.62 94.43 90.55
Pandoraea communis GCF_902459745.1 86.60 53.85 83.93 82.50
Pandoraea eparura GCF_902459725.1 86.58 48.85 81.94 77.51
Pandoraea faecigallinarum GCF_001029105.3 87.43 60.07 85.94 83.10
Pandoraea fibrosis GCF_000807775.2 86.50 57.54 85.87 83.29
Pandoraea horticolens GCF_902459555.1 86.53 53.29 83.58 82.45
Pandoraea iniqua GCF_902459685.1 85.58 54.26 83.99 86.77
Pandoraea morbifera GCF_902459575.1 86.21 51.70 83.57 82.34
Pandoraea norimbergensis GCF_001465545.3 85.45 53.68 83.84 86.68
Pandoraea nosoerga GCF_902459585.1 86.24 50.42 82.72 78.67
Pandoraea oxalativorans GCF_000972785.3 93.57 77.73 90.99 86.06
Pandoraea pneumonica GCF_902459645.1 85.60 52.62 83.58 85.52
Pandoraea pnomenusa GCF_000504585.2 86.27 53.21 83.90 82.50
Pandoraea pulmonicola GCF_000815105.2 86.28 53.72 83.78 82.39
Pandoraea soli GCF_902459595.1 86.52 48.07 82.37 77.75
Pandoraea sp. XY-2 GCF_004193915.1 86.49 48.39 80.31 74.75
Pandoraea sputorum GCF_900187205.1 99.29 88.49 97.03 90.91
Pandoraea terrae GCF_902459695.1 82.67 25.17 72.62 73.04
Pandoraea terrigena GCF_902459705.1 86.36 48.80 82.03 79.21
Pandoraea thiooxydans GCF_001017775.3 80.09 10.79 67.18 62.49
Pandoraea vervacti GCF_000934605.2 87.33 60.28 86.32 83.73
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rpoB similarity and MLSA phylogenetic analysis

The rpoB gene, encoding the β-subunit of RNA polymerase, has emerged as a core gene candidate for phylogenetic analyses and identification of bacteria; it is a single-copy gene, belongs to the common set of genes, and is long enough to contain phylogenetically useful information for some bacterial declination [37–40]. Multilocus sequence analysis (MLSA) is a currently widely used method for prokaryotic taxonomy, which utilizes internal fragments of several protein-coding genes. It was introduced by Gevers et al. and is increasingly being applied to obtain higher resolution power among species within a genus [39, 41]. As a typing technique for type characterization that shows variation in multiple housekeeping genes, a concatenation of five housekeeping genes, shikimate dehydrogenase (aroE), guanylate kinase (gmk), phosphate acetyltransferase (pta), triosephosphate isomerase (tpi), and acetyl coenzyme A acetyltransferase (yqiL), was recommended for our bacterial delineation, as well as for clarifying the taxonomic situation within the Pandoraea family [39, 41]. The phylogenetic tree topologies of Pandoraea sp. 892iso and other Pandoraea spp. by rpoB similarity (Fig 5A) and MLSA analysis (Fig 5B) revealed Pandoraea sp. 892iso to have the closest phylogenetic relationship with Pandoraea sputorum strain DSM21091.

Fig 5. Phylogenetic tree highlighting the position of Pandoraea sp. 892iso relative to the other Pandoraea species.

Fig 5

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The tree was aligned with the characteristics of the rpoB gene (a) and MLSA (b) under the maximum likelihood (ML) criterion.

Genome-to-genome distance calculator

In silico genome-to-genome comparison to obtain an estimate of the overall similarity between the genomes of two types has enabled the taxonomist to perform genome-based species delineation and genome-based subspecies delineation. These distance functions can also cope with heavily reduced genomes and repetitive sequence regions. The Genome-to-Genome Distance Calculator (GGDC) calculates the distances by comparing genomes to obtain HSPs (high-scoring segment pairs) and interfering distances from a set of formulas: 1) HSP length/total length; 2) identities/HSP length; and 3) identities/total length [42]. An estimated GGDC of the overall similarity between Pandoraea sp. 892iso and other Pandoraea species is shown in Table 4. In probability DDG ≥70% index analysis, the pairwise comparison of the genome with P. sputorum was found to be 98.49%, 96.97%, and 99.88% for the HSP length/total length, identities/HSP length, and identities/total length ratios, respectively. Thus, the close relationship of Pandoraea sp. 892iso and P. sputorum was verified.

Table 4. Pairwise comparison of Pandorarae sp. 892iso and Pandoraea species using the GGDC.
Query 　Reference ID HSP length/total length identities/HSP length identities/total length G+C difference
Distance DDH estimate (GLM-based) Prob. DDH>70% Prob. DDH>79% Distance DDH estimate (GLM-based) Prob. DDH>70% Prob. DDH>79% Distance DDH estimate (GLM-based) Prob. DDH>70% Prob. DDH>79%
Pandoraea sp. 892iso Pandoraea anapnoica GCF_902459765.1 78.3 [74.3–81.8%] 0.1411 89.13 52.1 [49.5–54.8%] 0.0669 25.38 74.9 [71.4–78.1%] 0.1985 88.31 0.26
Pandoraea sp. 892iso Pandoraea anhela GCF_902459655.1 48.1 [44.7–51.5%] 0.3215 8.92 29 [26.6–31.5%] 0.1476 0.07 42.4 [39.4–45.4%] 0.4217 0.31 0.69
Pandoraea sp. 892iso Pandoraea apista GCF_001465595.2 48 [44.6–51.4%] 0.322 8.82 26.6 [24.3–29.1%] 0.1626 0.02 41.3 [38.3–44.3%] 0.4323 0.21 0.03
Pandoraea sp. 892iso Pandoraea aquatica GCF_902459565.1 80.7 [76.8–84.1%] 0.1286 91.75 46.5 [43.9–49.1%] 0.0803 10.85 74.9 [71.4–78.1%] 0.1985 88.3 0.23
Pandoraea sp. 892iso Pandoraea bronchicola GCF_902459805.1 48.6 [45.2–52%] 0.3173 9.79 27 [24.6–29.5%] 0.1603 0.03 41.8 [38.9–44.9%] 0.4268 0.26 0.31
Pandoraea sp. 892iso Pandoraea capi GCF_902459735.1 61 [57.3–64.6%] 0.2337 45.76 29.3 [27–31.8%] 0.1458 0.08 51.6 [48.5–54.7%] 0.3455 4.22 0.78
Pandoraea sp. 892iso Pandoraea captiosa GCF_902459775.1 48.7 [45.3–52.2%] 0.3164 9.99 28.4 [26–30.9%] 0.1515 0.05 42.6 [39.6–45.6%] 0.42 0.32 0.64
Pandoraea sp. 892iso Pandoraea cepalis GCF_902459625.1 38.3 [34.9–41.8%] 0.4098 1.11 26.9 [24.6–29.4%] 0.1605 0.03 34.5 [31.6–37.6%] 0.5045 0.02 0.88
Pandoraea sp. 892iso Pandoraea commovens GCF_902459615.1 85.3 [81.6–88.4%] 0.1056 95.14 54.2 [51.5–56.9%] 0.0625 32.2 81.4 [78–84.3%] 0.1615 96.5 0.03
Pandoraea sp. 892iso Pandoraea communis GCF_902459745.1 43.9 [40.5–47.4%] 0.3559 4.04 26.8 [24.4–29.3%] 0.1614 0.02 38.5 [35.6–41.6%] 0.4599 0.08 0.09
Pandoraea sp. 892iso Pandoraea eparura GCF_902459725.1 36.8 [33.4–40.3%] 0.426 0.75 27.5 [25.1–30%] 0.1571 0.03 33.6 [30.6–36.7%] 0.5161 0.01 1.02
Pandoraea sp. 892iso Pandoraea faecigallinarum GCF_001029105.3 49.8 [46.4–53.2%] 0.3082 11.94 28.8 [26.4–31.3%] 0.1492 0.06 43.5 [40.5–46.5%] 0.4115 0.44 0.79
Pandoraea sp. 892iso Pandoraea fibrosis GCF_000807775.2 52.1 [48.6–55.5%] 0.2918 16.86 26.7 [24.4–29.2%] 0.1618 0.02 44.1 [41.1–47.1%] 0.4064 0.52 0.16
Pandoraea sp. 892iso Pandoraea horticolens GCF_902459555.1 41.6 [38.3–45.1%] 0.3767 2.47 26.8 [24.5–29.3%] 0.1612 0.02 36.9 [33.9–40%] 0.4771 0.04 0.35
Pandoraea sp. 892iso Pandoraea iniqua GCF_902459685.1 39.5 [36.2–43%] 0.397 1.51 25.6 [23.3–28.1%] 0.1697 0.01 35 [32–38%] 0.4994 0.02 0.41
Pandoraea sp. 892iso Pandoraea morbifera GCF_902459575.1 43.2 [39.9–46.7%] 0.3621 3.49 26.5 [24.1–29%] 0.1636 0.02 37.9 [34.9–40.9%] 0.4665 0.06 2
Pandoraea sp. 892iso Pandoraea norimbergensis GCF_001465545.3 39.3 [36–42.8%] 0.3992 1.44 25.5 [23.2–28%] 0.1702 0.01 34.8 [31.8–37.9%] 0.5015 0.02 0.4
Pandoraea sp. 892iso Pandoraea nosoerga GCF_902459585.1 40.8 [37.4–44.2%] 0.3849 2.03 26.8 [24.4–29.3%] 0.1615 0.02 36.3 [33.3–39.3%] 0.4842 0.03 3.47
Pandoraea sp. 892iso Pandoraea oxalativorans GCF_000972785.3 62.6 [58.9–66.2%] 0.2242 51.57 49.4 [46.8–52%] 0.073 17.48 61 [57.7–64.2%] 0.2809 29.7 0.43
Pandoraea sp. 892iso Pandoraea pneumonica GCF_902459645.1 39.9 [36.6–43.4%] 0.393 1.67 25.3 [23–27.8%] 0.1718 0.01 35.1 [32.2–38.2%] 0.4973 0.02 0.21
Pandoraea sp. 892iso Pandoraea pnomenusa GCF_000504585.2 43.6 [40.2–47%] 0.3588 3.78 26.6 [24.3–29.1%] 0.1626 0.02 38.2 [35.3–41.3%] 0.463 0.07 2.23
Pandoraea sp. 892iso Pandoraea pulmonicola GCF_000815105.2 41.3 [37.9–44.8%] 0.3797 2.29 26.6 [24.2–29.1%] 0.163 0.02 36.6 [33.6–39.6%] 0.4809 0.04 1.64
Pandoraea sp. 892iso Pandoraea soli GCF_902459595.1 39.4 [36–42.9%] 0.3985 1.46 27 [24.7–29.5%] 0.16 0.03 35.4 [32.4–38.4%] 0.4948 0.02 0.96
Pandoraea sp. 892iso Pandoraea sp. XY-2 GCF_004193915.1 39.7 [36.3–43.1%] 0.3957 1.56 27 [24.6–29.5%] 0.1603 0.03 35.5 [32.6–38.6%] 0.4926 0.03 1.1
Pandoraea sp. 892iso Pandoraea sputorum GCF_900187205.1 94.2 [91.7–96%] 0.0565 98.49 94 [92.2–95.4%] 0.0077 96.97 96.1 [94.4–97.3%] 0.0638 99.88 0.12
Pandoraea sp. 892iso Pandoraea terrae GCF_902459695.1 18.2 [15.1–21.7%] 0.7652 0 22.6 [20.3–25%] 0.194 0 17.9 [15.3–20.9%] 0.8108 0 0.13
Pandoraea sp. 892iso Pandoraea terrigena GCF_902459705.1 39 [35.6–42.4%] 0.403 1.31 26.7 [24.4–29.2%] 0.1621 0.02 34.9 [32–38%] 0.4998 0.02 0.82
Pandoraea sp. 892iso Pandoraea thiooxydans GCF_001017775.3 14.2 [11.4–17.6%] 0.9145 0 20.2 [18–22.6%] 0.2177 0 14.4 [12–17.2%] 0.9331 0 0.54
Pandoraea sp. 892iso Pandoraea vervacti GCF_000934605.2 50.9 [47.5–54.4%] 0.2999 14.26 28.4 [26–30.9%] 0.1512 0.05 44.1 [41.1–47.2%] 0.4058 0.53 0.87
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Some special genes among Pandoraea sp

Quorum sensing (QS)

The most studied QS molecule is N-acyl homoserine lactone (AHL), which is secreted by gram-negative proteobacteria. AHLs are secreted by LuxI homologs until a threshold concentration of AHL is attained before they bind to LuxR homologs and subsequently activate a cascade of QS-regulated gene expression [43]. The predicted putative AHL synthase (ppnI) and AHL receptor protein (ppnR) in Pandoraea sp. 892iso and the nine Pandoraea species are shown in Table 5. The phylogenetic trees of putative AHL synthase (ppnI) and AHL receptor protein (ppnR) are shown in Fig 6.

Table 5. The identified ppnI and ppnR genes in Pandoraea sp. 892iso and nine Pandoraea species.
Species Accession number scaffold gene start end strand
Pandoraea sp. 892iso fig|93222.8.peg.1246 scaffold3 ppnI 215501 216286 +
Pandoraea sp. 892iso fig|93222.8.peg.1247 scaffold3 ppnR 216253 216966 -
Pandoraea oxalativorans WP_046292715.1 NZ_CP011253.3 ppnI 4024825 4025493 -
Pandoraea oxalativorans WP_046293945.1 NZ_CP011253.3 ppnR 4024031 4024732 +
Pandoraea anapnoica WP_150739377.1 NZ_CABPSP010000011.1 ppnI 57228 57914 -
Pandoraea anapnoica WP_150739515.1 NZ_CABPSP010000011.1 ppnR 56433 57134 +
Pandoraea pneumonica WP_150681584.1 NZ_CABPSK010000004.1 ppnI 583193 583867 -
Pandoraea pneumonica WP_174988328.1 NZ_CABPSK010000004.1 ppnR 582433 583146 +
Pandoraea morbifera WP_150566717.1 NZ_CABPSD010000005.1 ppnI 208906 209694 -
Pandoraea morbifera WP_150566716.1 NZ_CABPSD010000005.1 ppnR 208206 208919 +
Pandoraea sputorum WP_174555901.1 NZ_LT906435.1 ppnI 1348270 1349055 +
Pandoraea sputorum WP_039402529.1 NZ_LT906435.1 ppnR 1349022 1349723 -
Pandoraea terrae WP_150700195.1 NZ_CABPRZ010000043.1 ppnI 19106 19732 -
Pandoraea terrae WP_150700194.1 NZ_CABPRZ010000043.1 ppnR 18360 19076 +
Pandoraea vervacti WP_044456583.1 NZ_CP010897.2 ppnI 4037152 4037835 -
Pandoraea vervacti WP_044458339.1 NZ_CP010897.2 ppnR 4036372 4037073 +
Pandoraea captiosa WP_150627103.1 NZ_CABPSQ010000011.1 ppnI 88267 88950 -
Pandoraea captiosa WP_150627162.1 NZ_CABPSQ010000011.1 ppnR 87492 88193 +
Pandoraea pnomenusa WP_023871914.1 NC_023018.2 ppnI 3778787 3779572 -
Pandoraea pnomenusa WP_080685145.1 NC_023018.2 ppnR 3778087 3778800 +
Pandoraea commovens WP_174985011.1 NZ_CABPSA010000008.1 ppnI 204518 205333 +
Pandoraea commovens WP_150666021.1 NZ_CABPSA010000008.1 ppnR 205300 206013 -
Burkholderia cepacia WP_042976961.1 NZ_CP045236.1 ppnI 471746 472354 -
Burkholderia cepacia WP_021162347.1 NZ_CP045236.1 ppnR 473082 473801 +
Pandoraea faecigallinarum WP_167362711.1 NZ_CP011807.3 ppnI 3690884 3691549 -
Pandoraea faecigallinarum WP_053059408.1 NZ_CP011807.3 ppnR 3690044 3690820 +
Pandoraea capi WP_150721274.1 NZ_CABPRV010000004.1 ppnI 224554 225237 -
Pandoraea capi WP_150721396.1 NZ_CABPRV010000004.1 ppnR 223772 224473 +
Pandoraea norimbergensis WP_157125706.1 NZ_CP013480.3 ppnI 1418662 1419441 +
Pandoraea norimbergensis WP_064675185.1 NZ_CP013480.3 ppnR 1419408 1420109 -
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Fig 6. Phylogenetic tree of ppnI and ppnR.

Fig 6

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Intrinsic carbapenem-hydrolyzing oxacillinases

Oxacillinases are serine β-lactamases of molecular class D. Many bacterial species could produce OXA-type enzymes, some of them with carbapenem-hydrolyzing activity. The nine Pandoraea-derived oxacillinase genes, named OXA-159, encode 292 amino acids and were found to be new oxacillinase variants [44]. The predicted genes with the function of OXA-159 in Pandoraea sp. 892iso and the nine Pandoraea species are shown in Table 6. The phylogenetic trees of genes with the putative function of OXA-159 are shown in Fig 7.

Table 6. The identified genes with the function of OXA-159 in Pandoraea sp. 892iso and nine Pandoraea species.
Species Accession number
Pandoraea sp. 892iso fig|93222.8.peg.176
Pandoraea oxalativorans WP_052653498.1
Pandoraea nosoerga WP_150556387.1
Pandoraea morbifera WP_150567617.1
Pandoraea sputorum WP_063861062.1
Pandoraea communis WP_150690981.1
Pandoraea fibrosis WP_052240481.1
Pandoraea pnomenusa WP_023872076.1
Burkholderia cepacia WP_153490194.1
Pandoraea faecigallinarum WP_053059421.1
Pandoraea capi WP_150719552.1
Pandoraea norimbergensis WP_058375744.1
Pandoraea anapnoica WP_150740206.1
Pandoraea bronchicola WP_150559740.1
Pandoraea iniqua WP_150791439.1
Pandoraea apista WP_048627819.1
Pandoraea pneumonica WP_150680540.1
Pandoraea cepalis WP_150607462.1
Pandoraea sp. XY-2 WP_130026801.1
Pandoraea pulmonicola WP_052266736.1
Pandoraea soli WP_150552526.1
Pandoraea vervacti WP_063389849.1
Pandoraea aquatica WP_150576315.1
Pandoraea captiosa WP_150626879.1
Pandoraea commovens WP_150664304.1
Pandoraea horticolens WP_150619975.1
Pandoraea anhela WP_150669648.1
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Fig 7. Phylogenetic tree of OXA-159 genes.

Fig 7

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The neighbor-joining method was used in MEGA7, where a bootstrap test (1,000 replicates) is shown next to the branch.

Conclusions

We sequenced Pandoraea sp. 892iso from the genome of a Phytophthora rubi strain (numbered 109892) and combined the data with existing genomic data for other Pandoraea species. Next, we conducted a comparative genomic analysis of the genome structure, evolutionary relationships, and pathogenic characteristics of Pandoraea species. Our results identified Pandoraea sp. 892iso as Pandoraea sputorum at both the genome and gene levels. At the genome level, we carried out phylogenetic analysis of single-copy, gene co-linearity, ANI and AAI indices, rpoB similarity, MLSA phylogenetic analysis, and genome-to-genome distance calculator calculations to identify the relationship between Pandoraea sp. 892iso and P. sputorum. At the gene level, the quorum sensing genes ppnI and ppnR and the OXA-159 gene were analyzed. It is speculated that Pandoraea sp. 892iso is the endosymbiont of the Phytophthora rubi strain.

Supporting information

S1 Fig. Diagram of linear genomic organization among Pandoraea types.

(DOC)

Click here for additional data file. (70KB, doc)
S2 Fig. Diagram of linear genomic organization between Pandoraea sp. 892iso and Pandoraea sputorum.

Scaffold1, scaffold2, scaffold3, scaffold4, and scaffold5 were the five largest sequences.

(DOC)

Click here for additional data file. (44KB, doc)
S1 Table. The list of single copy gene in the genome of Pandoraea sp. 892iso.

(XLSX)

Click here for additional data file. (303.1KB, xlsx)

Data Availability

All relevant data are within the manuscript and its Supporting Information files.

Funding Statement

Grant funds of National Key R&D Programme of China (No. 2016YFF0203204) and National Key Technology Research and Development Programme of China (No. 2012BAK11B06) for Gui-Ming Zhang are used in study design, data collection and analysis. The funds of Scientific Research Project of General Administration of Customs. P. R. China (No. 2021HK171) for Ying Wang is used for the decision to publish, and preparation of the manuscript.

References

  • 1.Coenye T, Falsen E, Hoste B, Ohlén M, Goris J, Govan JR, et al. Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov. Int J Syst Evol Micr. 2000; 50(2):887–99. doi: 10.1099/00207713-50-2-887 [DOI] [PubMed] [Google Scholar]
  • 2.Schneider I, Queenan AM, Bauernfeind A. Novel carbapenem-hydrolyzing oxacillinase OXA-62 from Pandoraea pnomenusa. Antimicrob Agents Ch. 2006; 50(4):1330–5. doi: 10.1128/AAC.50.4.1330-1335.2006 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Stryjewski ME, LiPuma JJ, Messier RH Jr, Reller LB, Alexander BD. Sepsis, multiple organ failure, and death due to Pandoraea pnomenusa infection after lung transplantation. J Clin Microbiol. 2003; 41(5):2255–7. doi: 10.1128/JCM.41.5.2255-2257.2003 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Daneshvar MI, Hollis DG, Steigerwalt AG, Whitney AM, Spangler L, Douglas MP, et al. Assignment of CDC weak oxidizer group 2 (WO-2) to the genus Pandoraea and characterization of three new Pandoraea genome species. J Clin Microbiol. 2001; 39(5):1819–26. doi: 10.1128/JCM.39.5.1819-1826.2001 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Anandham R, Indiragandhi P, Kwon SW, Sa TM, Jeon CO, Kim YK, et al. Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.). Int J Syst Evol Micr. 2010; 60(1):21–6. doi: 10.1099/ijs.0.012823-0 [DOI] [PubMed] [Google Scholar]
  • 6.Peeters C, De Canck E, Cnockaert M, Brandt ED, Snauwaert C, Verheyde B, et al. Comparative genomics of Pandoraea, a genus enriched in xenobiotic biodegradation and metabolism. Front Microbiol, 2019; 10: 2556. doi: 10.3389/fmicb.2019.02556 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Sahin N, Tani A, Kotan R, Sedláček I, Kimbara K, Tamer AU, et al. Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. Int J Syst Evol Micr, 2011; 61(9): 2247–2253. doi: 10.1099/ijs.0.026138-0 [DOI] [PubMed] [Google Scholar]
  • 8.Jeong SE, Lee HJ, Jia B, Jeon CO. Pandoraea terrae sp. nov., isolated from forest soil, and emended description of the genus Pandoraea Coenye et al. 2000. Int J Syst Evol Micr, 2016; 66(9): 3524–3530. doi: 10.1099/ijsem.0.001229 [DOI] [PubMed] [Google Scholar]
  • 9.Johnson LN, Han J, Moskowitz SM, Burns JL, Qin X, Englund JA. Pandoraea bacteremia in a cystic fibrosis patient with associated systemic illness. The Pediatric infectious disease journal 2004; 23(9):881–882. doi: 10.1097/01.inf.0000136857.74561.3c [DOI] [PubMed] [Google Scholar]
  • 10.Caraher E, Collins J, Herbert G, Murphy PG, Gallagher CG, Crowe MJ, et al. Evaluation of in vitro virulence characteristics of the genus Pandoraea in lung epithelial cells. J Med Microbiol. 2008; 57(1):15–20. doi: 10.1099/jmm.0.47544-0 [DOI] [PubMed] [Google Scholar]
  • 11.Costello A, Herbert G, Fabunmi L, Schaffer K, Kavanagh KA, Caraher EM, et al. Virulence of an emerging respiratory pathogen, genus Pandoraea, in vivo and its interactions with lung epithelial cells. J Med Microbiol. 2011; 60(3):289–99. doi: 10.1099/jmm.0.022657-0 [DOI] [PubMed] [Google Scholar]
  • 12.Jones AM, Webb AK. Recent advances in cross-infection in cystic fibrosis: Burkholderia cepacia complex, Pseudomonas aeruginosa, MRSA and Pandoraea spp. J Roy Soc Med. 2003; 96(Suppl 43):66. doi: 10.1258/jrsm.96.1.54 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Okeke BC, Siddique T, Arbestain MC, Frankenberger WT. Biodegradation of γ-hexachlorocyclohexane (lindane) and α-hexachlorocyclohexane in water and a soil slurry by a Pandoraea species. J Agr Food Chem. 2002; 50(9):2548–55. doi: 10.1021/jf011422a [DOI] [PubMed] [Google Scholar]
  • 14.Gómez-Gil L, Kumar P, Barriault D, Bolin JT, Sylvestre M, Eltis LD. Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme. J Bacteriol. 2007; 189(15):5705–15. doi: 10.1128/JB.01476-06 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Liz JAZ, Jan-Roblero J, de la Serna JZ, de León AV, Hernández-Rodríguez C. Degradation of polychlorinated biphenyl (PCB) by a consortium obtained from a contaminated soil composed of Brevibacterium, Pandoraea and Ochrobactrum. World Journal of Microbiology and Biotechnology 2009; 25(1):165–170. doi: 10.1007/s11274-008-9875-3 [DOI] [Google Scholar]
  • 16.Matsui T, Yoshida T, Yoshimura T, Nagasawa T. Regioselective carboxylation of 1, 3-dihydroxybenzene by 2, 6-dihydroxybenzoate decarboxylase of Pandoraea sp. 12B-2. Appl Microbiol Biot. 2006; 73(1):95–102. doi: 10.1007/s00253-006-0437-z [DOI] [PubMed] [Google Scholar]
  • 17.Shi Y, Chai L, Tang C, Yang Z, Zheng Y, Chen Y, et al. Biochemical investigation of kraft lignin degradation by Pandoraea sp. B-6 isolated from bamboo slips. Bioproc Biosyst Eng. 2013; 36(12):1957–65. doi: 10.1007/s00449-013-0972-9 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Jiang X, Liu H, Xu Y, Wang S, Leak DJ, Zhou N. Genetic and biochemical analyses of chlorobenzene degradation gene clusters in Pandoraea sp. strain MCB032. Arch Microbiol. 2009; 191(6):485–92. doi: 10.1007/s00203-009-0476-9 [DOI] [PubMed] [Google Scholar]
  • 19.Siddique T, Okeke BC, Arshad M, Frankenberger WT. Biodegradation kinetics of endosulfan by Fusarium ventricosum and a Pandoraea species. J Agr Food Chem. 2003; 51(27):8015–9. doi: 10.1021/jf030503z [DOI] [PubMed] [Google Scholar]
  • 20.Chen C, Kuo J, Cheng C, Huang Y, Ho I, Chung Y. Biological decolorization of dye solution containing malachite green by Pandoraea pulmonicola YC32 using a batch and continuous system. J Hazard Mater. 2009; 172(2):1439–45. doi: 10.1016/j.jhazmat.2009.08.009 [DOI] [PubMed] [Google Scholar]
  • 21.Ee R, Yong D, Lim YL, Yin W, Chan K. Complete genome sequence of oxalate-degrading bacterium Pandoraea vervacti DSM 23571 T. J Biotechnol. 2015; 204:5–6. doi: 10.1016/j.jbiotec.2015.03.020 [DOI] [PubMed] [Google Scholar]
  • 22.Tindall BJ, Rosselló-Móra R, Busse H, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Micr. 2010; 60(1):249–66. doi: 10.1099/ijs.0.016949-0 [DOI] [PubMed] [Google Scholar]
  • 23.McCarthy BJ, Bolton ET. An approach to the measurement of genetic relatedness among organisms. P Natl Acad Sci Usa. 1963; 50(1):156. doi: 10.2307/71689 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Schildkraut CL, Marmur J, Doty P. The formation of hybrid DNA molecules and their use in studies of DNA homologies. J Mol Biol. 1961; 3(5):516–95. doi: 10.1016/s0022-2836(61)80024-7 [DOI] [PubMed] [Google Scholar]
  • 25.Wayne LG, Brenner DJ, Colwell RR, Grimont P, Kandler O, Krichevsky MI, et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Micr 1987; 37(4):463–464. doi: 10.1099/00207713-37-4-463 [DOI] [Google Scholar]
  • 26.Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Micr. 1994; 44(4):846–9. doi: 10.1099/00207713-44-4-846 [DOI] [Google Scholar]
  • 27.Brenner FW, Villar RG, Angulo FJ, Tauxe R, Swaminathan B. Salmonella nomenclature. J Clin Microbiol. 2000; 38(7):2465–7. doi: 10.1128/JCM.38.7.2465-2467.2000 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Rosselló-Mora R, Amann R. The species concept for prokaryotes. Fems Microbiol Rev. 2001; 25(1):39–67. doi: 10.1111/j.1574-6976.2001.tb00571.x [DOI] [PubMed] [Google Scholar]
  • 29.Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philosophical Transactions of the Royal Society B: Biological Sciences 2006; 361(1475):1929–1940. doi: 10.1098/rstb.2006.1920 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Chan JZ, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ. Defining bacterial species in the genomic era: insights from the genus Acinetobacter. Bmc Microbiol 2012; 12(1):1–11. doi: 10.1186/1471-2180-12-302 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Micr. 2007; 57(1):81–91. doi: 10.1099/ijs.0.64483-0 [DOI] [PubMed] [Google Scholar]
  • 32.Grim CJ, Kotewicz ML, Power KA, Gopinath G, Franco AA, Jarvis KG, et al. Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation. Bmc Genomics. 2013; 14(1):366. doi: 10.1186/1471-2164-14-366 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC. Whole-genome prokaryotic phylogeny. Bioinformatics. 2005; 21(10):2329–35. doi: 10.1093/bioinformatics/bth324 [DOI] [PubMed] [Google Scholar]
  • 34.Deloger M, El Karoui M, Petit M. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J Bacteriol. 2009; 191(1):91–9. doi: 10.1128/JB.01202-08 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Pickart CM, Eddins MJ. Ubiquitin: structures, functions, mechanisms. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research 2004; 1695(1–3):55–72. doi: 10.1016/j.bbamcr.2004.09.019 [DOI] [PubMed] [Google Scholar]
  • 36.Thompson CC, Chimetto L, Edwards RA, Swings J, Thompson FL. Microbial genomic taxonomy. Bmc Genomics. 2013; 14(1):1–8. doi: 10.1186/1471-2164-14-913 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 37.Adékambi T, Drancourt M, Raoult D. The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 2009; 17(1):37–45. doi: 10.1016/j.tim.2008.09.008 [DOI] [PubMed] [Google Scholar]
  • 38.Adékambi T, Shinnick TM, Raoult D, Drancourt M. Complete rpoB gene sequencing as a suitable supplement to DNA–DNA hybridization for bacterial species and genus delineation. Int J Syst Evol Micr 2008; 58(8):1807–1814. doi: 10.1099/ijs.0.65440-0 [DOI] [PubMed] [Google Scholar]
  • 39.Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, et al. Re-evaluating prokaryotic species. Nat Rev Microbiol 2005; 3(9):733–739. doi: 10.1038/nrmicro1236 [DOI] [PubMed] [Google Scholar]
  • 40.Estrada-De Los Santos P, Vinuesa P, Martínez-Aguilar L, Hirsch AM, Caballero-Mellado J. Phylogenetic analysis of Burkholderia species by multilocus sequence analysis. Curr Microbiol 2013; 67(1):51–60. doi: 10.1007/s00284-013-0330-9 [DOI] [PubMed] [Google Scholar]
  • 41.Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10(5):504–509. doi: 10.1016/j.mib.2007.08.006 [DOI] [PubMed] [Google Scholar]
  • 42.Auch AF, Klenk H, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2(1):142–148. doi: 10.4056/sigs.541628 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 43.Fuqua C, Parsek MR, Greenberg EP. Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu Rev Genet. 2001; 35(1):439–68. doi: 10.1146/annurev.genet.35.102401.090913 [DOI] [PubMed] [Google Scholar]
  • 44.Schneider I, Bauernfeind A. Intrinsic carbapenem-hydrolyzing oxacillinases from members of the genus Pandoraea. Antimicrob Agents Ch. 2015; 59(11):7136–41. doi: 10.1128/AAC.01112-15 [DOI] [PMC free article] [PubMed] [Google Scholar]

Decision Letter 0

Paula V Morais

13 Dec 2021

PONE-D-21-31328Genome insights from the identification of a Pandoraea sputorum strainPLOS ONE

Dear Dr. Gao,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Pleased, take into consideration all the comments of the reviewer. The comparison of your strain with the other bacteria has to be made with all relevant species, taking into account the updated information. Many additional species have been added to this genus in the last few years. Do not forget that you need to give all accession numbers of the sequences used.

Please, submit your revised manuscript by Jan 24 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

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If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Paula V Morais, Ph.D

Academic Editor

PLOS ONE

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This work was supported by National Key R&D Programme of China (No. 2016YFF0203204) and National Key Technology Research and Development Programme of China (No. 2012BAK11B06) for G.-M. Z. Scientific research project of General Administration of Customs. P. R. China (2021HK171) for Y. W.

We note that you have provided additional information within the Acknowledgements Section that is not currently declared in your Funding Statement. Please note that funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. 

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- https://journals.asm.org/doi/10.1128/AAC.01112-15

- https://www.cell.com/heliyon/fulltext/S2405-8440(21)00422-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2405844021004229%3Fshowall%3Dtrue

- https://pubmed.ncbi.nlm.nih.gov/15571809/

We would like to make you aware that copying extracts from previous publications, especially outside the methods section, word-for-word is unacceptable. In addition, the reproduction of text from published reports has implications for the copyright that may apply to the publications.

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We will carefully review your manuscript upon resubmission, so please ensure that your revision is thorough.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: PONE-D-21-31328: Genome insights from the identification of a Pandoraea sputorum strain

The authors describe the relationship between a strain of Pandoraea derived from Phytophthora rubi with some previously described Pandoraea species at the genomic level and conclude that it is likely to belong to the species P. sputorum. They also compare quorum sensing and oxacillinase genes from their strain with those from other species of this genus.

Major comments: While the authors have been quite systematic in their comparison of strain Pandoraea sp. 892iso with other species at the genomic level, they have not included a large number of species which have been added to this genus in the last few years. In addition, while the analysis is thorough, a considerable portion of their manuscript focuses on the description of where this strain sits in the taxonomy of this genus and this seems to be out of proportion with respect to the final conclusion i.e. that this strain belongs to P. sputorum. It would be better if the authors focused less on the where their strain fits in this genus and more on the interesting aspects concerning their quorum sensing and oxacillinase gene comparisons and their MLSA typing approach.

Minor comments:

Please avoid using the word “strain”, unless required, or else preface it with “type” or “reference” where appropriate (for example in the legend for figure 3).

Title:

This should be more informative.

Abstract:

Line 13-would be useful to explain what Phytophthora rubi is.

Line 15: Would be useful to clarify which Pandoraea species you are referring to.

Line 21: Please make it clear which Oomycetes strain you are referring to.

Introduction:

Line 27: Use “genus” rather than “species”

Line 30: Please re-structure this sentence as it is unclear.

Line 33: Many additional species have been added to this genus in the last few years. Please see Peeters et al., (2019) Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism.Front. Microbiol. 10:2556 and the following for additional species: Anandham et al., 2010; Sahin et al., 2011; Jeong et al., 2016). Please update your manuscript with this information.

Line 40: “Further”

Line 67: “were identified through whole genome sequencing”

Lines 68 and 75: Please use “isolate” rather than strain

Materials and Methods:

Line 90: Do you mean “calculations” rather than “calculate”?

Line 95 and 100: please clarify what you mean by “11 species”.

Results:

Line 114: Which Pandoraea sputorum isolate are you referring to? If it is Pandoraea sp. 892iso It may be better to use the name of the strain at this stage as the evidence for the WGS-based identification has not yet been presented.

Line 134: It would be helpful if the authors included some details about the types of single copy genes chosen for their generating their phylogenetic tree, with the genes listed in a table, or in supplementary information.

Lines 183-188: The decision to choose these particular house-keeping genes should be explained.

Line 207: A much shorter title to this section should be chosen.

Figures and Tables:

Figure 2: The legend for this figure needs further information about the methods used to generate this data.

Table 1: Please clarify the accession numbers and details for the P. pulmonicola, P. sputorum genomes used, and also for the other species for which this information had not been provided.

Table 2: This table needs some description in the legend, and further details in the main text to explain what it depicts.

**********

6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2022 Aug 5;17(8):e0272435. doi: 10.1371/journal.pone.0272435.r002

Author response to Decision Letter 0

19 Jan 2022

Dear reviewer and editor,

Thank you very much for your help on our manuscript entitled ‘Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics’.

According to your suggestion, we have revised one by one, and now we resubmit again.

We hope our revisions will meet with approval.

Best wishes,

Sincerely yours,

Ruifang Gao

Attachment

Submitted filename: renamed_7c11c.docx

Click here for additional data file. (21.2KB, docx)

Decision Letter 1

Paula V Morais

6 Apr 2022

PONE-D-21-31328R1Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristicsPLOS ONE

Dear Dr. Gao,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please, take into consideration all the comments raised by me and the reviewer.

Please submit your revised manuscript by May 21 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Paula V Morais, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments:

1- The number of species of Pandorea is not correct. See https://lpsn.dsmz.de/genus/pandoraea

2- To consider a strain a new species we have 3 criteria and not 2. 16S rRNA gene sequence has to be considered (introduction).

3- What made you suspect that the fungus culture was contaminated? Give some detail (material and methods).

4- You still have the number of Pandorea wrong "...KP771987.1). BLAST was employed to identify homolog genes in the 11 Pandoraea species." Did you repeat the comparison with the 28 Pandorea strains?

5- Please, clarify "...per 1 Mb, which is more/fewer than most of the other sequenced bacteria...."

6- Table 1. What was the criteria to include 30 strains of Pandorea species? What was the criteria for the order they are included? I would like to see them by alphabetic order.

7- "In total, 3,456 849

orthologous genes were shared in common between Pandoraea sp. 892iso and the other four Pandoraea straintypes." Which ones?

8- "fig|93222.8.peg.2650 with the function of ubiquitin in the NR database." Do you mean predicted function?

9- Table 3 and Table 4. List the species by alphabetic order unless you could present a relevant criterium for not doing it.

10- "...AHL receptor protein (ppnR) in Pandoraea sp. 892iso and the nine Pandoraea species are shown..." Why 9 Pandorea species?

11- Table 6. I do not understand. How many genes? How namy species type strains?

12- "...and combined the data with existing genomic data for five other Pandoraea" Is it correct?

13. "It is speculated that Pandoraea sp. 892iso is the endosymbiont of the Phytophthora rubi strain." I do not see in your manuscript any result that supports this sentence. Why the isolate is not a contaminant of your culture? This comment is related with the 3 comment. If you want to include this senetence you have to explain in detail the fungus isolation and culture and the bacteria isolation story.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: (No Response)

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #2: There should be unification for the term that used after Pandoraea. Three different terms (types, sp., and previously strains) were employed throughout the manuscript. The term “species” is usually used in the literature.

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #2: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2022 Aug 5;17(8):e0272435. doi: 10.1371/journal.pone.0272435.r004

Author response to Decision Letter 1

12 May 2022

Dear editor,

Thank you very much for your help on our manuscript entitled ‘Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics’.

A list of the single copy genes in the genome of Pandoraea sp. 892iso had been shown in Supporting Information files, which was noted in the section Comparative genomic analysis in the manuscript.

"The phylogenetic relationship in view of these single-copy genes is shown in Fig 3 and S1 Table, ....."

The separate caption of S1 Table also has been added at the end of manuscript.

We hope our revisions will meet with approval.

Best wishes,

Sincerely yours,

Ruifang Gao

Attachment

Submitted filename: renamed_7c11c.docx

Click here for additional data file. (21.2KB, docx)

Decision Letter 2

Paula V Morais

3 Jun 2022

PONE-D-21-31328R2

Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics

PLOS ONE

Dear Dr. Gao,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Figures 4 and 5 need to be improved so they can be published as supplementary figures. The manuscript has to be revised to be adapted and the figures numbered according.

Please submit your revised manuscript by Jul 18 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Paula V Morais, Ph.D

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2022 Aug 5;17(8):e0272435. doi: 10.1371/journal.pone.0272435.r006

Author response to Decision Letter 2

4 Jun 2022

Dear editor,

Thank you very much for your help on our manuscript entitled ‘Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics’.

According to your suggestion, we have revised and now we resubmit again.

We hope our revisions will meet with approval.

Best wishes,

Sincerely yours,

Ruifang Gao

Attachment

Submitted filename: 4th-Response to editor.doc

Click here for additional data file. (23.5KB, doc)

Decision Letter 3

Paula V Morais

20 Jul 2022

Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics

PONE-D-21-31328R3

Dear Dr. Gao,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Paula V Morais, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Acceptance letter

Paula V Morais

27 Jul 2022

PONE-D-21-31328R3

Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics

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Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Fig. Diagram of linear genomic organization among Pandoraea types.

    (DOC)

    Click here for additional data file. (70KB, doc)
    S2 Fig. Diagram of linear genomic organization between Pandoraea sp. 892iso and Pandoraea sputorum.

    Scaffold1, scaffold2, scaffold3, scaffold4, and scaffold5 were the five largest sequences.

    (DOC)

    Click here for additional data file. (44KB, doc)
    S1 Table. The list of single copy gene in the genome of Pandoraea sp. 892iso.

    (XLSX)

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    Data Availability Statement

    All relevant data are within the manuscript and its Supporting Information files.

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