Table 1.
List of strains isolated, sequenced and analysed in this study
| Phylum | Family | Species | ID | rRNA % sim.a | genome (bp) | GC (%) |
|---|---|---|---|---|---|---|
| Actinobacteria | Coriobacteriaceae | Collinsella intestinalis | An268 | 94 | 2,375,164 | 65.28 |
| Actinobacteria | Coriobacteriaceae | Collinsella intestinalis | An7 | 95 | 2,368,937 | 65.33 |
| Actinobacteria | Coriobacteriaceae | Collinsella intestinalis | An307 | 96 | 2,218,890 | 62.95 |
| Actinobacteria | Coriobacteriaceae | Collinsella tanakaei | An271 | 96 | 2,790,023 | 64.34 |
| Actinobacteria | Coriobacteriaceae | Collinsella tanakaei | An2 | 94 | 2,542,639 | 62.39 |
| Actinobacteria | Coriobacteriaceae | Enorma massiliensis | An70 | 99 | 2,374,054 | 62.09 |
| Actinobacteria | Coriobacteriaceae | Enorma timonensis | An5 | 96 | 2,299,978 | 65.99 |
| Actinobacteria | Coriobacteriaceae | Gordonibacter urolithinfaciens | An234A | 99 | 3,542,488 | 65.99 |
| Actinobacteria | Coriobacteriaceae | Gordonibacter urolithinfaciens | An232A | 94 | 3,457,314 | 65.16 |
| Actinobacteria | Coriobacteriaceae | Gordonibacter urolithinfaciens | An230 | 94 | 3,885,330 | 64.16 |
| Actinobacteria | Coriobacteriaceae | Olsenella uli | An188 | 96 | 2,138,506 | 68.68 |
| Actinobacteria | Coriobacteriaceae | Olsenella uli | An290 | 96 | 2,158,343 | 68.09 |
| Actinobacteria | Coriobacteriaceae | Olsenella uli | An285 | 96 | 2,413,556 | 66.98 |
| Actinobacteria | Coriobacteriaceae | Olsenella uli | An293 | 96 | 2,318,914 | 67.87 |
| Actinobacteria | Coriobacteriaceae | Olsenella uli | An270 | 96 | 2,014,154 | 67.55 |
| Bacteroidetes | Bacteroidaceae | Bacteroides clarus | An43 | 99 | 4,226,284 | 45.22 |
| Bacteroidetes | Bacteroidaceae | Bacteroides clarus | An189 | 99 | 4,166,078 | 45.36 |
| Bacteroidetes | Bacteroidaceae | Bacteroides dorei | An16 | 99 | 5,376,103 | 41.79 |
| Bacteroidetes | Bacteroidaceae | Bacteroides dorei | An41 | 99 | 5,463,463 | 42.00 |
| Bacteroidetes | Bacteroidaceae | Bacteroides ovatus | An161 | 99 | 6,700,861 | 42.08 |
| Bacteroidetes | Bacteroidaceae | Bacteroides salanitronis | An322 | 92 | 3,449,415 | 44.84 |
| Bacteroidetes | Bacteroidaceae | Bacteroides uniformis | An67 | 99 | 4,590,834 | 46.36 |
| Bacteroidetes | Bacteroidaceae | Bacteroides xylanisolvens | An109 | 99 | 5,713,108 | 41.57 |
| Bacteroidetes | Bacteroidaceae | Bacteroides xylanisolvens | An107 | 99 | 5,745,201 | 41.89 |
| Bacteroidetes | Bacteroidaceae | Mediterranea massiliensis | An20 | 91 | 3,968,548 | 49.41 |
| Bacteroidetes | Porphyromonadaceae | Barnesiella viscericola | An22 | 98 | 3,264,150 | 53.04 |
| Bacteroidetes | Porphyromonadaceae | Barnesiella viscericola | An55 | 98 | 3,040,531 | 51.37 |
| Bacteroidetes | Porphyromonadaceae | Butyricimonas paravirosa | An62 | 98 | 5,176,855 | 42.63 |
| Bacteroidetes | Porphyromonadaceae | Muribaculum intestinale | An289 | 83 | 2,336,263 | 49.09 |
| Bacteroidetes | Porphyromonadaceae | Muribaculum intestinale | An287 | 83 | 2,349,712 | 49.04 |
| Bacteroidetes | Porphyromonadaceae | Odoribacter splanchnicus | An45 | 99 | 4,610,398 | 43.75 |
| Bacteroidetes | Porphyromonadaceae | Odoribacter splanchnicus | An39 | 99 | 4,722,515 | 43.48 |
| Bacteroidetes | Porphyromonadaceae | Parabacteroides distasonis | An199 | 99 | 5,145,110 | 45.11 |
| Bacteroidetes | Porphyromonadaceae | Parabacteroides johnsonii | An42 | 99 | 4,430,164 | 45.03 |
| Bacteroidetes | Porphyromonadaceae | Parabacteroides merdae | An277 | 92 | 3,709,857 | 46.69 |
| Bacteroidetes | Rikenellaceae | Alistipes onderdonkii | An90 | 100 | 3,488,443 | 58.52 |
| Bacteroidetes | Rikenellaceae | Alistipes senegalensis | An31A | 97 | 2,626,508 | 61.85 |
| Bacteroidetes | Rikenellaceae | Alistipes senegalensis | An116 | 97 | 3,264,205 | 58.57 |
| Bacteroidetes | Rikenellaceae | Alistipes senegalensis | An66 | 97 | 3,064,564 | 59.37 |
| Bacteroidetes | Rikenellaceae | Alistipes shahii | An54 | 96 | 3,272,633 | 58.38 |
| Bacteroidetes | unclassified_"Bacteroidales” | Bacteroides salanitronis | An269 | 92 | 4,466,522 | 45.87 |
| Bacteroidetes | unclassified_"Bacteroidales” | Bacteroides salanitronis | An279 | 92 | 3,976,735 | 45.82 |
| Bacteroidetes | unclassified_"Bacteroidales” | Bacteroides salanitronis | An19 | 92 | 4,779,606 | 45.88 |
| Bacteroidetes | unclassified_"Bacteroidales” | Bacteroides salanitronis | An51A | 92 | 4,415,476 | 45.79 |
| Firmicutes | Enterococcaceae | Enterococcus cecorum | An69 | 100 | 2,010,800 | 36.66 |
| Firmicutes | Enterococcaceae | Enterococcus cecorum | An144 | 100 | 2,521,030 | 36.10 |
| Firmicutes | Lactobacillaceae | Lactobacillus gallinarum | An119 | 99 | 2,068,702 | 36.50 |
| Firmicutes | Lactobacillaceae | Lactobacillus gallinarum | An153 | 99 | 2,042,196 | 36.47 |
| Firmicutes | Lactobacillaceae | Lactobacillus gallinarum | An115 | 99 | 2,039,377 | 36.52 |
| Firmicutes | Lactobacillaceae | Lactobacillus gallinarum | An101 | 99 | 2,051,080 | 36.54 |
| Firmicutes | Lactobacillaceae | Lactobacillus gasseri | An197 | 99 | 1,786,561 | 34.60 |
| Firmicutes | Lactobacillaceae | Lactobacillus reuteri | An71 | 99 | 2,330,171 | 38.47 |
| Firmicutes | Lactobacillaceae | Lactobacillus reuteri | An166 | 99 | 2,293,009 | 38.50 |
| Firmicutes | Lactobacillaceae | Lactobacillus salivarius | An63 | 99 | 1,826,390 | 32.76 |
| Firmicutes | Lactobacillaceae | Lactobacillus salivarius | An84 | 99 | 2,115,320 | 32.74 |
| Firmicutes | Lactobacillaceae | Lactobacillus salivarius | An128 | 99 | 1,900,005 | 32.75 |
| Firmicutes | Erysipelotrichaceae | [Clostridium] spiroforme | An158 | 99 | 2,749,214 | 28.90 |
| Firmicutes | Erysipelotrichaceae | [Clostridium] spiroforme | An15 | 94 | 3,043,058 | 30.24 |
| Firmicutes | Erysipelotrichaceae | [Clostridium] spiroforme | An26 | 99 | 2,686,825 | 28.58 |
| Firmicutes | Erysipelotrichaceae | [Clostridium] spiroforme | An149 | 99 | 2,786,011 | 28.86 |
| Firmicutes | Erysipelotrichaceae | [Clostridium] spiroforme | An173 | 94 | 2,963,161 | 30.12 |
| Firmicutes | Erysipelotrichaceae | [Eubacterium] cylindroides | An64 | 99 | 1,822,768 | 34.80 |
| Firmicutes | Erysipelotrichaceae | [Eubacterium] cylindroides | An178 | 99 | 1,979,688 | 34.75 |
| Firmicutes | Erysipelotrichaceae | Massiliomicrobiota timonensis | An13 | 100 | 2,808,053 | 31.46 |
| Firmicutes | Erysipelotrichaceae | Massiliomicrobiota timonensis | An142 | 98 | 2,805,108 | 31.51 |
| Firmicutes | Erysipelotrichaceae | Massiliomicrobiota timonensis | An134 | 98 | 2,583,105 | 31.58 |
| Firmicutes | Erysipelotrichaceae | Massiliomicrobiota timonensis | An105 | 98 | 2,657,304 | 31.69 |
| Firmicutes | Erysipelotrichaceae | Massiliomicrobiota timonensis | An80 | 98 | 2,632,118 | 31.88 |
| Firmicutes | Clostridiaceae 1 | Clostridium perfringens | An68 | 99 | 3,279,733 | 28.07 |
| Firmicutes | Clostridiaceae 1 | Clostridium perfringens | An185 | 99 | 3,267,175 | 28.06 |
| Firmicutes | Lachnospiraceae | [Clostridium] glycyrrhizinilyticum | An169 | 96 | 4,874,615 | 49.44 |
| Firmicutes | Lachnospiraceae | [Clostridium] glycyrrhizinilyticum | An298 | 96 | 3,190,622 | 46.76 |
| Firmicutes | Lachnospiraceae | [Clostridium] glycyrrhizinilyticum | An76 | 96 | 3,392,322 | 50.34 |
| Firmicutes | Lachnospiraceae | [Clostridium] lactatifermentans | An114 | 95 | 2,765,027 | 31.21 |
| Firmicutes | Lachnospiraceae | [Clostridium] lactatifermentans | An75 | 99 | 3,241,294 | 44.78 |
| Firmicutes | Lachnospiraceae | [Clostridium] oroticum | An181 | 95 | 2,778,317 | 43.19 |
| Firmicutes | Lachnospiraceae | [Clostridium] saccharolyticum | An14 | 95 | 4,319,160 | 54.42 |
| Firmicutes | Lachnospiraceae | [Clostridium] saccharolyticum | An168 | 99 | 3,501,825 | 50.31 |
| Firmicutes | Lachnospiraceae | [Clostridium] saccharolyticum | An196 | 93 | 3,261,385 | 50.05 |
| Firmicutes | Lachnospiraceae | [Eubacterium] contortum | An118 | 95 | 3,480,620 | 52.25 |
| Firmicutes | Lachnospiraceae | [Eubacterium] fissicatena | An131 | 94 | 3,529,099 | 50.87 |
| Firmicutes | Lachnospiraceae | [Eubacterium] fissicatena | An138 | 94 | 3,702,317 | 50.44 |
| Firmicutes | Lachnospiraceae | [Eubacterium] hallii | An3 | 95 | 4,260,545 | 46.43 |
| Firmicutes | Lachnospiraceae | [Eubacterium] hallii | An11 | 95 | 3,929,296 | 46.78 |
| Firmicutes | Lachnospiraceae | Blautia coccoides | An46 | 94 | 3,844,348 | 44.62 |
| Firmicutes | Lachnospiraceae | Blautia producta | An81 | 95 | 4,340,741 | 44.56 |
| Firmicutes | Lachnospiraceae | Blautia schinkii | An249 | 93 | 3,969,115 | 45.08 |
| Firmicutes | Lachnospiraceae | Drancourtella massiliensis | An210 | 95 | 3,049,918 | 45.07 |
| Firmicutes | Lachnospiraceae | Drancourtella massiliensis | An177 | 95 | 2,986,142 | 44.76 |
| Firmicutes | Lachnospiraceae | Drancourtella massiliensis | An57 | 95 | 3,307,621 | 45.72 |
| Firmicutes | Lachnospiraceae | Drancourtella massiliensis | An12 | 96 | 3,637,323 | 46.18 |
| Firmicutes | Ruminococcaceae | Anaerofilum agile | An201 | 91 | 3,232,216 | 60.34 |
| Firmicutes | Ruminococcaceae | Anaeromassilibacillus senegalensis | An200 | 94 | 3,738,663 | 54.30 |
| Firmicutes | Ruminococcaceae | Anaeromassilibacillus senegalensis | An250 | 97 | 3,582,839 | 53.28 |
| Firmicutes | Ruminococcaceae | Anaeromassilibacillus senegalensis | An172 | 92 | 2,820,032 | 41.40 |
| Firmicutes | Ruminococcaceae | Anaerotruncus colihominis | An174 | 99 | 4,104,028 | 53.46 |
| Firmicutes | Ruminococcaceae | Anaerotruncus colihominis | An175 | 99 | 4,098,164 | 53.45 |
| Firmicutes | Ruminococcaceae | Anaerotruncus colihominis | An251 | 99 | 3,446,606 | 54.60 |
| Firmicutes | Ruminococcaceae | Butyricicoccus pullicaecorum | An179 | 99 | 3,474,625 | 53.61 |
| Firmicutes | Ruminococcaceae | Butyricicoccus pullicaecorum | An180 | 99 | 3,016,034 | 54.43 |
| Firmicutes | Ruminococcaceae | Faecalibacterium prausnitzii | An121 | 95 | 2,728,163 | 61.06 |
| Firmicutes | Ruminococcaceae | Faecalibacterium prausnitzii | An77 | 96 | 3,092,450 | 59.48 |
| Firmicutes | Ruminococcaceae | Faecalibacterium prausnitzii | An192 | 97 | 3,520,066 | 58.80 |
| Firmicutes | Ruminococcaceae | Faecalibacterium prausnitzii | An122 | 96 | 3,272,200 | 59.47 |
| Firmicutes | Ruminococcaceae | Faecalibacterium prausnitzii | An58 | 96 | 2,956,350 | 60.63 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An91 | 97 | 3,629,120 | 57.60 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An52 | 97 | 2,845,789 | 59.13 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An92 | 98 | 3,498,453 | 62.13 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An112 | 97 | 2,967,986 | 59.27 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An135 | 98 | 3,907,586 | 61.45 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An82 | 97 | 3,683,590 | 58.85 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An248 | 100 | 3,776,725 | 60.99 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An4 | 97 | 3,239,670 | 58.22 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An9 | 97 | 3,357,728 | 58.20 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An100 | 95 | 3,054,748 | 57.15 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An306 | 98 | 3,967,264 | 59.00 |
| Firmicutes | Ruminococcaceae | Flavonifractor plautii | An10 | 96 | 3,867,419 | 61.74 |
| Firmicutes | Ruminococcaceae | Gemmiger formicilis | An50 | 94 | 3,597,344 | 58.67 |
| Firmicutes | Ruminococcaceae | Gemmiger formicilis | An194 | 95 | 3,080,663 | 59.30 |
| Firmicutes | Ruminococcaceae | Gemmiger formicilis | An87 | 94 | 3,355,244 | 58.58 |
| Firmicutes | Ruminococcaceae | Gemmiger formicilis | An120 | 95 | 3,406,814 | 60.15 |
| Firmicutes | Ruminococcaceae | Pseudoflavonifractor capillosus | An176 | 96 | 2,574,287 | 58.19 |
| Firmicutes | Ruminococcaceae | Pseudoflavonifractor capillosus | An187 | 96 | 2,623,188 | 57.97 |
| Firmicutes | Ruminococcaceae | Pseudoflavonifractor capillosus | An44 | 96 | 2,764,660 | 57.41 |
| Firmicutes | Ruminococcaceae | Pseudoflavonifractor capillosus | An85 | 96 | 3,018,026 | 56.20 |
| Firmicutes | Ruminococcaceae | Pseudoflavonifractor capillosus | An184 | 96 | 3,617,258 | 59.87 |
| Firmicutes | Veillonellaceae | Megamonas hypermegale | An288 | 99 | 2,165,576 | 33.61 |
| Firmicutes | Veillonellaceae | Megasphaera elsdenii | An286 | 95 | 2,396,433 | 53.29 |
| Proteobacteria | Desulfovibrionaceae | Desulfovibrio desulfuricans | An276 | 92 | 3,230,576 | 55.37 |
| Proteobacteria | Enterobacteriaceae | Escherichia fergusonii | An190 | 99 | 5,352,565 | 50.48 |
| Synergistetes | Synergistaceae | Cloacibacillus porcorum | An23 | 93 | 2,902,045 | 57.89 |
| Verrucomicrobia | Verrucomicrobiaceae | Akkermansia muciniphila | An78 | 100 | 2,734,062 | 55.68 |
| Elusimicrobia | Elusimicrobiaceae | Elusimicrobium minutum | An273 | 94 | 1,505,722 | 51.73 |
aPercent similarity along the whole 16S rRNA sequence to the GenBank entry with the highest similarity