Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

Medvecky, Matej; Cejkova, Darina; Polansky, Ondrej; Karasova, Daniela; Kubasova, Tereza; Cizek, Alois; Rychlik, Ivan

doi:10.1186/s12864-018-4959-4

Table 1 List of strains isolated, sequenced and analysed in this study

From: Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

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

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ISSN: 1471-2164

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