Table 1.
General features of Bifidobacteriaceae genomes
| Taxon number | Bifidobacteriaceae strains | Genome statusa | 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