Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine

References

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. ( 1990 ). Basic local alignment search tool. . J Mol Biol 215, 403–410.[PubMed] [CrossRef]
   [Google Scholar]
2. Bäckhed F., Ding H., Wang T., Hooper L. V., Koh G. Y., Nagy A., Semenkovich C. F., Gordon J. I. ( 2004 ). The gut microbiota as an environmental factor that regulates fat storage. . Proc Natl Acad Sci U S A 101, 15718–15723. [View Article] [PubMed]
   [Google Scholar]
3. Bokkenheuser V. D., Winter J., Dehazya P., Kelly W. G. ( 1977 ). Isolation and characterization of human fecal bacteria capable of 21-dehydroxylating corticoids. . Appl Environ Microbiol 34, 571–575.[PubMed]
   [Google Scholar]
4. Brill J. A., Wiegel J. ( 1997 ). Differentiation between spore-forming and asporogenic bacteria using a PCR and Southern hybridization based method. . J Microbiol Methods 31, 29–36. [View Article]
   [Google Scholar]
5. Carlier J. P., Bedora-Faure M., K’ouas G., Alauzet C., Mory F. ( 2010 ). Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.. Int J Syst Evol Microbiol 60, 585–590. [View Article] [PubMed]
   [Google Scholar]
6. Clavel T., Doré J., Blaut M. ( 2006a ). Bioavailability of lignans in human subjects. . Nutr Res Rev 19, 187–196. [View Article] [PubMed]
   [Google Scholar]
7. Clavel T., Henderson G., Engst W., Doré J., Blaut M. ( 2006b ). Phylogeny of human intestinal bacteria that activate the dietary lignan secoisolariciresinol diglucoside. . FEMS Microbiol Ecol 55, 471–478. [View Article] [PubMed]
   [Google Scholar]
8. Clavel T., Lippman R., Gavini F., Doré J., Blaut M. ( 2007 ). Clostridium saccharogumia sp. nov. and Lactonifactor longoviformis gen. nov., sp. nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside. . Syst Appl Microbiol 30, 16–26. [View Article] [PubMed]
   [Google Scholar]
9. Clavel T., Charrier C., Braune A., Wenning M., Blaut M., Haller D. ( 2009 ). Isolation of bacteria from the ileal mucosa of TNF^deltaARE mice and description of Enterorhabdus mucosicola gen. nov., sp. nov.. Int J Syst Evol Microbiol 59, 1805–1812. [View Article] [PubMed]
   [Google Scholar]
10. Clavel T., Saalfrank A., Charrier C., Haller D. ( 2010 ). Isolation of bacteria from mouse caecal samples and description of Bacteroides sartorii sp. nov.. Arch Microbiol 192, 427–435. [View Article] [PubMed]
    [Google Scholar]
11. Derrien M., Vaughan E. E., Plugge C. M., de Vos W. M. ( 2004 ). Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. . Int J Syst Evol Microbiol 54, 1469–1476. [View Article] [PubMed]
    [Google Scholar]
12. Hanske L., Loh G., Sczesny S., Blaut M., Braune A. ( 2010 ). Recovery and metabolism of xanthohumol in germ-free and human microbiota-associated rats. . Mol Nutr Food Res 54, 1405–1413. [View Article] [PubMed]
    [Google Scholar]
13. Hörmannsperger G., Clavel T., Haller D. ( 2012 ). Gut matters: microbe–host interactions in allergic diseases. . J Allergy Clin Immunol 129, 1452–1459. [View Article] [PubMed]
    [Google Scholar]
14. Kontoyiannis D., Pasparakis M., Pizarro T. T., Cominelli F., Kollias G. ( 1999 ). Impaired on/off regulation of TNF biosynthesis in mice lacking TNF AU-rich elements: implications for joint and gut-associated immunopathologies. . Immunity 10, 387–398. [View Article] [PubMed]
    [Google Scholar]
15. Leser T. D., Amenuvor J. Z., Jensen T. K., Lindecrona R. H., Boye M., Møller K. ( 2002 ). Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. . Appl Environ Microbiol 68, 673–690. [View Article] [PubMed]
    [Google Scholar]
16. Levine U. Y., Looft T., Allen H. K., Stanton T. B. ( 2013 ). Butyrate-producing bacteria, including mucin degraders, from the swine intestinal tract. . Appl Environ Microbiol 79, 3879–3881. [View Article] [PubMed]
    [Google Scholar]
17. Li E., Hamm C. M., Gulati A. S., Sartor R. B., Chen H., Wu X., Zhang T., Rohlf F. J., Zhu W. & other authors ( 2012 ). Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. . PLoS ONE 7, e26284. [View Article] [PubMed]
    [Google Scholar]
18. Manach C., Williamson G., Morand C., Scalbert A., Rémésy C. ( 2005 ). Bioavailability and bioefficacy of polyphenols in humans. I. Review of 97 bioavailability studies. . Am J Clin Nutr 81 (Suppl), 230S–242S.[PubMed]
    [Google Scholar]
19. Pfeiffer N., Desmarchelier C., Blaut M., Daniel H., Haller D., Clavel T. ( 2012 ). Acetatifactor muris gen. nov., sp. nov., a novel bacterium isolated from the intestine of an obese mouse. . Arch Microbiol 194, 901–907. [View Article] [PubMed]
    [Google Scholar]
20. Postgate J. R. ( 1963 ). Versatile medium for the enumeration of sulfate-reducing bacteria. . Appl Microbiol 11, 265–267.[PubMed]
    [Google Scholar]
21. Qin J., Li R., Raes J., Arumugam M., Burgdorf K. S., Manichanh C., Nielsen T., Pons N., Levenez F. & other authors ( 2010 ). A human gut microbial gene catalogue established by metagenomic sequencing. . Nature 464, 59–65. [View Article] [PubMed]
    [Google Scholar]
22. Ridlon J. M., Kang D. J., Hylemon P. B. ( 2006 ). Bile salt biotransformations by human intestinal bacteria. . J Lipid Res 47, 241–259. [View Article] [PubMed]
    [Google Scholar]
23. Roberfroid M. ( 2007 ). Prebiotics: the concept revisited. . J Nutr 137 (Suppl 2), 830S–837S.[PubMed]
    [Google Scholar]
24. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406–425.[PubMed]
    [Google Scholar]
25. Schneider H., Schwiertz A., Collins M. D., Blaut M. ( 1999 ). Anaerobic transformation of quercetin-3-glucoside by bacteria from the human intestinal tract. . Arch Microbiol 171, 81–91. [View Article] [PubMed]
    [Google Scholar]
26. Schoefer L., Mohan R., Schwiertz A., Braune A., Blaut M. ( 2003 ). Anaerobic degradation of flavonoids by Clostridium orbiscindens . . Appl Environ Microbiol 69, 5849–5854. [View Article] [PubMed]
    [Google Scholar]
27. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 2731–2739. [View Article] [PubMed]
    [Google Scholar]
28. Tissier H. ( 1908 ). Recherches sur la flore intestinale normale des enfants âgés d’un an à cinq ans. . Ann Inst Pasteur (Paris) 22, 189–208.
    [Google Scholar]
29. Turnbaugh P. J., Hamady M., Yatsunenko T., Cantarel B. L., Duncan A., Ley R. E., Sogin M. L., Jones W. J., Roe B. A. & other authors ( 2009 ). A core gut microbiome in obese and lean twins. . Nature 457, 480–484. [View Article] [PubMed]
    [Google Scholar]
30. Werner T., Wagner S. J., Martínez I., Walter J., Chang J. S., Clavel T., Kisling S., Schuemann K., Haller D. ( 2011 ). Depletion of luminal iron alters the gut microbiota and prevents Crohn’s disease-like ileitis. . Gut 60, 325–333. [View Article] [PubMed]
    [Google Scholar]
31. Winter J., Popoff M. R., Grimont P., Bokkenheuser V. D. ( 1991 ). Clostridium orbiscindens sp. nov., a human intestinal bacterium capable of cleaving the flavonoid C-ring. . Int J Syst Bacteriol 41, 355–357. [View Article] [PubMed]
    [Google Scholar]
32. Wright E. S., Yilmaz L. S., Noguera D. R. ( 2012 ). decipher, a search-based approach to chimera identification for 16S rRNA sequences. . Appl Environ Microbiol 78, 717–725. [View Article] [PubMed]
    [Google Scholar]