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. 2010 Feb;14(1):9–59. doi: 10.1089/omi.2009.0100

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
a

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