Characterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov.

References

1. Bergey DG, WB W, Parte AC. The actinobacteria. Bergey’s Manual of Systematic Bacteriology 2012
   [Google Scholar]
2. Milani C, Lugli GA, Duranti S, Turroni F, Bottacini F et al. Genomic encyclopedia of type strains of the genus Bifidobacterium . Appl Environ Microbiol 2014; 80:6290–6302 [View Article]
   [Google Scholar]
3. Zhang G, Gao B, Adeolu M, Khadka B, Gupta RS. Phylogenomic analyses and comparative studies on genomes of the Bifidobacteriales: identification of molecular signatures specific for the order Bifidobacteriales and its different Subclades. Front Microbiol 2016; 7:978 [View Article]
   [Google Scholar]
4. Michelini S, Modesto M, Filippini G, Spiezio C, Sandri C et al. Corrigendum to "Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: Three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.)" [Syst. Appl. Microbiol. 39 (2016) 229-236]. Syst Appl Microbiol 2018
   [Google Scholar]
5. Lugli GA, Mangifesta M, Duranti S, Anzalone R, Milani C et al. Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov. Syst Appl Microbiol 2018; 41:173–183 [View Article]
   [Google Scholar]
6. Modesto M, Michelini S, Oki K, Biavati B, Watanabe K et al. Bifidobacterium catulorum sp. nov., a novel taxon from the faeces of the baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 2018; 68:575–581 [View Article]
   [Google Scholar]
7. Modesto M, Michelini S, Sansosti MC, De Filippo C, Cavalieri D et al. Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol 2018; 68:141–148 [View Article]
   [Google Scholar]
8. Duranti S, Mangifesta M, Lugli GA, Turroni F, Anzalone R et al. Bifidobacterium vansinderenii sp. nov., isolated from faeces of emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol 2017; 67:3987–3995 [View Article]
   [Google Scholar]
9. Pechar R, Killer J, Salmonová H, Geigerová M, Švejstil R et al. Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa). Int J Syst Evol Microbiol 2017; 67:2349–2356 [View Article]
   [Google Scholar]
10. Michelini S, Modesto M, Filippini G, Spiezio C, Sandri C et al. Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.). Syst Appl Microbiol 2016; 39:229–236 [View Article]
    [Google Scholar]
11. Michelini S, Modesto M, Pisi AM, Filippini G, Sandri C et al. Bifidobacterium eulemuris sp. nov., isolated from faeces of black lemurs (Eulemur macaco). Int J Syst Evol Microbiol 2016; 66:1567–1576 [View Article]
    [Google Scholar]
12. Laureys D, Cnockaert M, De Vuyst L, Vandamme P. Bifidobacterium aquikefiri sp. nov., isolated from water kefir. Int J Syst Evol Microbiol 2016; 66:1281–1286 [View Article]
    [Google Scholar]
13. Michelini S, Oki K, Yanokura E, Shimakawa Y, Modesto M et al. Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.). Int J Syst Evol Microbiol 2016; 66:255–265 [View Article]
    [Google Scholar]
14. Lugli GA, Milani C, Turroni F, Duranti S, Ferrario C et al. Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics. Appl Environ Microbiol 2014; 80:6383–6394 [View Article]
    [Google Scholar]
15. Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L et al. Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. BMC Genomics 2017; 18:568 [View Article]
    [Google Scholar]
16. Duranti S, Lugli GA, Napoli S, Anzalone R, Milani C et al. Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov. Int J Syst Evol Microbiol 2019; 69:1288–1298 [View Article]
    [Google Scholar]
17. Ventura M, van Sinderen D, Fitzgerald GF, Zink R. Insights into the taxonomy, genetics and physiology of bifidobacteria. Antonie van Leeuwenhoek 2004; 86:205–223 [View Article]
    [Google Scholar]
18. Turroni F, van Sinderen D, Ventura M. Genomics and ecological overview of the genus Bifidobacterium . Int J Food Microbiol 2011; 149:37–44 [View Article]
    [Google Scholar]
19. Ventura M, Turroni F, Lugli GA, van Sinderen D. Bifidobacteria and humans: our special friends, from ecological to genomics perspectives. J Sci Food Agric 2014; 94:163–168 [View Article]
    [Google Scholar]
20. Alberoni D, Gaggìa F, Baffoni L, Modesto MM, Biavati B et al. Bifidobacterium xylocopae sp. nov. and Bifidobacterium aemilianum sp. nov., from the carpenter bee (Xylocopa violacea) digestive tract. Syst Appl Microbiol 2019; 42:205–216 [View Article]
    [Google Scholar]
21. Modesto M, Watanabe K, Arita M, Satti M, Oki K et al. Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 2019; 69:2477–2485 [View Article]
    [Google Scholar]
22. Milani C, Mangifesta M, Mancabelli L, Lugli GA, James K et al. Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life. Isme J 2017; 11:2834–2847 [View Article]
    [Google Scholar]
23. Duranti S, Lugli GA, Mancabelli L, Armanini F, Turroni F et al. Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. Microbiome 2017; 5:66 [View Article]
    [Google Scholar]
24. Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA et al. Bifidobacteria and the infant gut: an example of co-evolution and natural selection. Cell Mol Life Sci 2018; 75:103–118 [View Article]
    [Google Scholar]
25. Turroni F, Foroni E, Pizzetti P, Giubellini V, Ribbera A et al. Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl Environ Microbiol 2009; 75:1534–1545 [View Article]
    [Google Scholar]
26. Ventura M, Zink R. Rapid identification, differentiation, and proposed new taxonomic classification of Bifidobacterium lactis . Appl Environ Microbiol 2002; 68:6429–6434 [View Article]
    [Google Scholar]
27. Milani C, Lugli GA, Duranti S, Turroni F, Bottacini F et al. Genomic encyclopedia of type strains of the genus Bifidobacterium . Appl Environ Microbiol 2014; 80:6290–6302 [View Article]
    [Google Scholar]
28. Milani C, Lugli GA, Duranti S, Turroni F, Mancabelli L et al. Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. Sci Rep 2015; 5:15782 [View Article]
    [Google Scholar]
29. Duranti S, Milani C, Lugli GA, Mancabelli L, Turroni F et al. Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis . Sci Rep 2016; 6:23971 [View Article]
    [Google Scholar]
30. Lugli GA, Milani C, Mancabelli L, van Sinderen D, Ventura M. MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation. FEMS Microbiol Lett 2016; 363:fnw049 [View Article]
    [Google Scholar]
31. Duranti S, Milani C, Lugli GA, Turroni F, Mancabelli L et al. Insights from genomes of representatives of the human gut commensal B ifidobacterium bifidum . Environ Microbiol 2015; 17:2515–2531 [View Article]
    [Google Scholar]
32. Lugli GA, Milani C, Duranti S, Mancabelli L, Mangifesta M et al. Tracking the taxonomy of the genus Bifidobacterium based on a phylogenomic approach. Appl Environ Microbiol 2018; 84:
    [Google Scholar]
33. Ventura M, Canchaya C, Del Casale A, Dellaglio F, Neviani E et al. Analysis of bifidobacterial evolution using a multilocus approach. Int J Syst Evol Microbiol 2006; 56:2783–2792 [View Article]
    [Google Scholar]
34. Zhao J, Zhang S, Wu L-Y, Zhang X-S. Efficient methods for identifying mutated driver pathways in cancer. Bioinformatics 2012; 28:2940–2947 [View Article]
    [Google Scholar]
35. Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002; 30:1575–1584 [View Article]
    [Google Scholar]
36. Lugli GA, Milani C, Duranti S, Alessandri G, Turroni F et al. Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches. Genome Biol 2019; 20:96 [View Article]
    [Google Scholar]
37. Glaeser SP, Kämpfer P. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 2015; 38:237–245 [View Article]
    [Google Scholar]
38. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T et al. Re-evaluating prokaryotic species. Nat Rev Microbiol 2005; 3:733–739 [View Article]
    [Google Scholar]
39. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article]
    [Google Scholar]
40. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article]
    [Google Scholar]
41. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
    [Google Scholar]
42. Pineiro M, Stanton C. Probiotic bacteria: legislative framework-- requirements to evidence basis. J Nutr 2007; 137:850S–853 [View Article]
    [Google Scholar]
43. Modesto M, Michelini S, Stefanini I, Sandri C, Spiezio C et al. Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta). Int J Syst Evol Microbiol 2015; 65:1726–1734 [View Article]
    [Google Scholar]
44. Schumann P. Peptidoglycan structure. Methods in Microbiology Elsevier; 2011 pp 101–129
    [Google Scholar]
45. Killer J, Kopečný J, Mrázek J, Havlík J, Koppová I et al. Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees. Syst Appl Microbiol 2010; 33:359–366 [View Article]
    [Google Scholar]
46. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article]
    [Google Scholar]
47. Biavati B, Mattarelli P. Genus Bifidobacterium. Bergey’s Manual of Systematic Bacteriology Springer-Verlag: New York Inc; 2012 pp 171–206
    [Google Scholar]
48. Karp PD, Paley S, Romero P. The pathway tools software. Bioinformatics 2002; 18:S225–S232 [View Article]
    [Google Scholar]