Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family

Lugli, Gabriele Andrea; Milani, Christian; Turroni, Francesca; Duranti, Sabrina; Mancabelli, Leonardo; Mangifesta, Marta; Ferrario, Chiara; Modesto, Monica; Mattarelli, Paola; Jiří, Killer; van Sinderen, Douwe; Ventura, Marco

doi:10.1186/s12864-017-3955-4

BMC Genomics

Table 1 General features of Bifidobacteriaceae genomes

From: Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family

Taxon number	Bifidobacteriaceae strains	Genome status^a	Genome size	GC content	ORFs number	rRNA loci	tRNA number	GHs number	GH index	Isolation	Accession number
01	B. actinocoloniiforme DSM 22766	Draft (4)	1,823,388	62.71	1484	2	46	41	0.0276	Bumblebee digestive tract	JGYK00000000
02	B. adolescentis ATCC 15703	Complete	2,089,645	59.18	1649	5	54	81	0.0491	Intestine of adult	AP009256.1
03	B. aesculapii DSM 26737	Draft (118)	2,794,396	64.58	2172	6	60	82	0.0378	Faeces of baby common marmosets	BCFK00000000
04	B. angulatum LMG 11039	Draft (6)	2,003,806	59.41	1523	4	48	63	0.0414	Human faeces	JGYL00000000
05	B. animalis subsp. animalis LMG 10508	Draft (13)	1,915,007	60.47	1527	3	52	48	0.0314	Rat feces	JGYM00000000
06	B. animalis subsp. lactis DSM 10140	Complete	1,938,606	60.48	1518	4	52	53	0.0349	Fermented milk	CP001606.1
07	B. aquikefiri LMG 28769	Draft (18)	2,408,364	52.29	2000	2	45	56	0.0280	Household water kefir	MWXA00000000
08	B. asteroides LMG 10735 (PRL2011)	Complete	2,167,304	60.05	1653	2	44	58	0.0351	Honeybee hindgut	CP003325.1
09	B. biavatii DSM 23969	Draft (56)	3,252,147	63.1	2557	5	61	137	0.0536	Feces of tamarin	JGYN00000000
10	B. bifidum LMG 11041	Draft (2)	2,208,468	62.67	1704	3	53	66	0.0387	Brest-feed Infant feaces	JGYO00000000
11	B. bohemicum DSM 22767	Draft (5)	2,052,470	57.45	1632	2	47	56	0.0343	Bumblebee digestive tract	JGYP00000000
12	B. bombi DSM 19703	Draft (4)	1,895,239	56.08	1454	2	48	44	0.0303	Bumblebee digestive tract	ATLK00000000
13	B. boum LMG 10736	Draft (18)	2,171,356	59.31	1726	4	49	45	0.0261	Bovine rumen	JGYQ00000000
14	B. breve LMG 13208	Draft (31)	2,263,780	58.88	1887	2	53	67	0.0355	Infant intestine	JGYR00000000
15	B. callitrichos DSM 23973	Draft (33)	2,887,313	63.52	2364	3	58	105	0.0444	Feces of common marmoset	JGYS00000000
16	B. catenulatum LMG 11043	Draft (11)	2,082,756	56.11	1664	5	55	91	0.0547	Adult intestine	JGYT00000000
17	B. choerinum LMG 10510	Draft (20)	2,096,123	65.53	1672	3	55	54	0.0323	Piglet faeces	JGYU00000000
18	B. commune R-52791	Dreaft (4)	1,633,662	53.93	1303	1	47	31	0.0238	Bumble bee gut	FMBL00000000
19	B. coryneforme LMG 18911	Complete	1,755,151	60.51	1364	3	56	43	0.0315	Honeybee hindgut	CP007287
20	B. crudilactis LMG 23609	Draft (6)	2,362,816	57.72	1883	2	45	51	0.0271	Raw cow milk	JHAL00000000
21	B. cuniculi LMG 10738	Draft (41)	2,531,592	64.87	2194	4	63	70	0.0319	Rabbit faeces	JGYV00000000
22	B. dentium LMG 11045 (Bd1)	Complete	2,636,367	58.54	2129	4	55	113	0.0531	Oral cavity	CP001750.1
23	B. eulemuris DSM 100216	Draft (34)	2,913,389	62.2	2331	2	53	126	0.0541	Faeces of the black lemur	MWWZ00000000
24	B. gallicum LMG 11596	Draft (12)	2,004,594	57.61	1507	2	58	45	0.0299	Adult intestine	JGYW00000000
25	B. gallinarum LMG 11586	Draft (10)	2,160,836	64.22	1654	2	53	78	0.0472	Chicken caecum	JGYX00000000
26	B. hapali DSM 100202	Draft (76)	2,834,308	54.5	2253	3	54	121	0.0537	Faeces of baby common marmosets	MWWY00000000
27	B. indicum LMG 11587	Complete	1,734,546	60.49	1352	3	47	41	0.0303	Insect	CP006018
28	B. kashiwanohense DSM 21854	Draft (30)	2,307,960	56.2	1948	5	53	91	0.0467	Infant feaces	JGYY00000000
29	B. lemurum DSM 28807	Draft (38)	2,944,293	62.64	2321	3	49	122	0.0526	Faeces of the ring-tailed lemur	MWWX00000000
30	B. longum subsp. infantis ATCC 15697	Complete	2,832,748	59.86	2500	4	79	71	0.0284	Intestine of infant	AP010889.1
31	B. longum subsp. longum LMG 13197	Draft (8)	2,384,703	60.33	1899	3	71	73	0.0384	Adult intestine	JGYZ00000000
32	B. longum subsp. suis LMG 21814	Draft (36)	2,335,832	59.96	1955	3	55	74	0.0379	Pig faeces	JGZA00000000
33	B. magnum LMG 11591	Draft (13)	1,822,476	58.72	1507	5	56	46	0.0305	Rabbit faeces	JGZB00000000
34	B. merycicum LMG 11341	Draft (16)	2,280,236	60.33	1741	3	53	66	0.0379	Bovine rumen	JGZC00000000
35	B. minimum LMG 11592	Draft (18)	1,892,860	62.73	1590	2	53	41	0.0258	Sewage	JGZD00000000
36	B. mongoliense DSM 21395	Draft (43)	2,170,490	62.78	1798	2	47	65	0.0362	Fermented mare’s milk	JGZE00000000
37	B. moukalabense DSM 27321	Draft (12)	2,515,335	59.87	2046	4	56	105	0.0513	Feces of wild western lowland gorilla	AZMV00000000
38	B. myosotis DSM 100196	Draft (58)	2,944,195	62.55	2168	4	56	101	0.0466	Faeces of baby common marmosets	MWWW00000000
39	B. pseudocatenulatum LMG 10505	Draft (10)	2,283,767	56.36	1771	6	53	85	0.0480	Infant faeces	JGZF00000000
40	B. pseudolongum subsp. globosum LMG 11569	Draft (26)	1,935,255	63.39	1574	4	52	53	0.0337	Bovine rumen	JGZG00000000
41	B. pseudolongum subsp. pseudolongum LMG 11571	Draft (11)	1,898,684	63.06	1495	3	52	57	0.0381	Swine faeces	JGZH00000000
42	B. psychraerophilum LMG 21775	Draft (11)	2,615,078	58.75	2122	1	45	80	0.0377	Pig caecum	JGZI00000000
43	B. pullorum DSM 20433	Draft (38)	2,100,948	64.31	1678	2	51	81	0.0479	Faeces of chicken	JDUI00000000
44	B. reuteri DSM 23975	Draft (28)	2,847,572	60.45	2149	4	53	85	0.0396	Feces of common marmoset	JGZK00000000
45	B. ruminantium LMG 21811	Draft (23)	2,249,807	59.18	1832	4	50	62	0.0338	Bovine rumen	JGZL00000000
46	B. saeculare LMG 14934	Draft (14)	2,263,283	63.75	1857	2	48	82	0.0442	Rabbit faeces	JGZM00000000
47	B. saguini DSM 23967	Draft (33)	2,787,036	56.35	2321	5	59	104	0.0448	Feces of tamarin	JGZN00000000
48	B. scardovii LMG 21589	Draft (34)	3,141,793	64.63	2480	3	55	128	0.0516	Blood	JGZO00000000
49	B. stellenboschense DSM 23968	Draft (40)	2,812,864	65.34	2202	6	59	80	0.0363	Feces of tamarin	JGZP00000000
50	B. subtile LMG 11597	Draft (27)	2,790,088	60.92	2260	1	47	56	0.0248	Sewage	JGZR00000000
51	B. thermacidophilum subsp. porcinum LMG 21689	Draft (3)	2,079,368	60.2	1738	3	40	46	0.0265	Piglet faeces	JGZS00000000
52	B. thermacidophilum subsp. thermacidophilum LMG 21395	Draft (8)	2,233,072	60.38	1823	4	48	47	0.0258	Anaerobic digester	JGZT00000000
53	B. thermophilum DSM 20212	Draft (50)	2,252,351	60.07	1756	3	49	58	0.0341	Bovine rumen	JHWM00000000
54	B. tissieri DSM 100201	Draft (38)	2,873,483	61.05	2260	2	60	79	0.0350	Faeces of baby common marmosets	MWWV00000000
55	B. tsurumiense JCM 13495	Draft (25)	2,164,426	52.84	1629	3	46	85	0.0522	Hamster dental plaque	JGZU00000000
56	Aeriscardovia aeriphila LMG 21773	Draft (12)	1,631,097	54.03	1288	3	47	53	0.0411	Pig caecum	MWWU00000000
57	Alloscardovia criceti DSM 17774	Draft (11)	1,884,654	50.06	1524	4	45	58	0.0381	Dental plaque, golden hamster	AQXR00000000
58	Alloscardovia macacae DSM 24762	Draft (20)	1,891,581	55.82	1552	4	48	50	0.0322	Milk of a female macaque bred	MWWT00000000
59	Alloscardovia omnicolens DSM 21503	Draft (43)	1,847,146	46.65	1564	3	47	56	0.0358	Human tonsil	ATVB00000000
60	Bombiscardovia coagulans DSM 22924	Draft (15)	1,741,326	47.33	1441	2	45	36	0.0250	Bumblebee digestive tract	MWWS00000000
61	Gardnerella vaginalis ATCC 14018	Complete	1,667,406	41.36	1271	2	45	41	0.0323	Vaginal secretions	AP012332
62	Neoscardovia arbecensis 1879	Draft (21)	1,971,875	54.25	1641	2	45	56	0.0341	Feces of rabbit	n.d.
63	Parascardovia denticolens DSM 10105	Complete	1,890,857	58.31	1528	2	45	56	0.0366	Human dental caries	AP012333
64	Pseudoscardovia radai DSM 24742	Draft (35)	2,436,770	65.03	1779	3	47	41	0.0230	Digestive tract of wild pig Sus scrofa	MWWR00000000
65	Pseudoscardovia suis DSM 24744	Draft (26)	2,270,618	60.57	1736	3	48	45	0.0259	Digestive tract of wild pig Sus scrofa	MWWQ00000000
66	Scardovia inopinata JCM 12537	Complete	1,797,862	48.63	1465	2	46	49	0.0334	Human dental caries	AP012334
67	Scardovia wiggsiae F0424	Complete	1,550,817	52.93	1244	2	45	32	0.0257	Human dental caries	AKCI00000000

^aNumbers in brackets indicate the numbers of assembled contigs

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com