Anaerostipes rhamnosivorans sp. nov., a human intestinal, butyrate-forming bacterium

References

1. Allen-Vercoe E., Daigneault M., White A., Panaccione R., Duncan S. H., Flint H. J., O’Neal L., Lawson P. A. ( 2012 ). Anaerostipes hadrus comb. nov., a dominant species within the human colonic microbiota; reclassification of Eubacterium hadrum Moore et al. 1976. . Anaerobe 18, 523–529. [View Article] [PubMed]
   [Google Scholar]
2. Barcenilla A., Pryde S. E., Martin J. C., Duncan S. H., Stewart C. S., Henderson C., Flint H. J. ( 2000 ). Phylogenetic relationships of butyrate-producing bacteria from the human gut. . Appl Environ Microbiol 66, 1654–1661. [View Article] [PubMed]
   [Google Scholar]
3. Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B. K., Lim Y.-W. ( 2007 ). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. . Int J Syst Evol Microbiol 57, 2259–2261. [View Article] [PubMed]
   [Google Scholar]
4. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133–142. [View Article] [PubMed]
   [Google Scholar]
5. Duncan S. H., Louis P., Flint H. J. ( 2004 ). Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. . Appl Environ Microbiol 70, 5810–5817. [View Article] [PubMed]
   [Google Scholar]
6. Eeckhaut V., Van Immerseel F., Pasmans F., De Brandt E., Haesebrouck F., Ducatelle R., Vandamme P. ( 2010 ). Anaerostipes butyraticus sp. nov., an anaerobic, butyrate-producing bacterium from Clostridium cluster XIVa isolated from broiler chicken caecal content, and emended description of the genus Anaerostipes . . Int J Syst Evol Microbiol 60, 1108–1112. [View Article] [PubMed]
   [Google Scholar]
7. Felsenstein J. ( 1985 ). Confidence limits on phylogenies – an approach using the bootstrap. . Evolution 39, 783–791. [View Article]
   [Google Scholar]
8. Flint H. J., Scott K. P., Duncan S. H., Louis P., Forano E. ( 2012a ). Microbial degradation of complex carbohydrates in the gut. . Gut Microbes 3, 289–306. [View Article] [PubMed]
   [Google Scholar]
9. Flint H. J., Scott K. P., Louis P., Duncan S. H. ( 2012b ). The role of the gut microbiota in nutrition and health. . Nat Rev Gastroenterol Hepatol 9, 577–589. [View Article] [PubMed]
   [Google Scholar]
10. Hague A., Singh B., Paraskeva C. ( 1997 ). Butyrate acts as a survival factor for colonic epithelial cells: further fuel for the in vivo versus in vitro debate. . Gastroenterology 112, 1036–1040. [View Article] [PubMed]
    [Google Scholar]
11. Huss V. A. R., Festl H., Schleifer K. H. ( 1983 ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4, 184–192. [View Article] [PubMed]
    [Google Scholar]
12. Kämpfer P., Kroppenstedt R. M. ( 1996 ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. . Can J Microbiol 42, 989–1005. [View Article]
    [Google Scholar]
13. Kimura M. ( 1983 ). The Neutral Theory of Molecular Evolution. London:: Cambridge University Press;. [View Article]
    [Google Scholar]
14. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E., Goodfellow M. . Chichester:: Wiley;.
    [Google Scholar]
15. 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]
16. Louis P., Duncan S. H., McCrae S. I., Millar J., Jackson M. S., Flint H. J. ( 2004 ). Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. . J Bacteriol 186, 2099–2106. [View Article] [PubMed]
    [Google Scholar]
17. Louis P., Young P., Holtrop G., Flint H. J. ( 2010 ). Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA : acetate CoA-transferase gene. . Environ Microbiol 12, 304–314. [View Article] [PubMed]
    [Google Scholar]
18. Miller L. T. ( 1982 ). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. . J Clin Microbiol 16, 584–586. [PubMed]
    [Google Scholar]
19. Muñoz-Tamayo R., Laroche B., Walter É., Doré J., Duncan S. H., Flint H. J., Leclerc M. ( 2011 ). Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species. . FEMS Microbiol Ecol 76, 615–624. [View Article] [PubMed]
    [Google Scholar]
20. Nübel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R. I., Ludwig W., Backhaus H. ( 1996 ). Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. . J Bacteriol 178, 5636–5643. [PubMed]
    [Google Scholar]
21. Plugge C. M., Zoetendal E. G., Stams A. J. M. ( 2000 ). Caloramator coolhaasii sp. nov., a glutamate-degrading, moderately thermophilic anaerobe. . Int J Syst Evol Microbiol 50, 1155–1162. [View Article] [PubMed]
    [Google Scholar]
22. Pryde S. E., Duncan S. H., Hold G. L., Stewart C. S., Flint H. J. ( 2002 ). The microbiology of butyrate formation in the human colon. . FEMS Microbiol Lett 217, 133–139. [View Article] [PubMed]
    [Google Scholar]
23. 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]
24. Schwiertz A., Hold G. L., Duncan S. H., Gruhl B., Collins M. D., Lawson P. A., Flint H. J., Blaut M. ( 2002 ). Anaerostipes caccae gen. nov., sp. nov., a new saccharolytic, acetate-utilising, butyrate-producing bacterium from human faeces. . Syst Appl Microbiol 25, 46–51. [View Article] [PubMed]
    [Google Scholar]
25. Stams A. J. M., Van Dijk J. B., Dijkema C., Plugge C. M. ( 1993 ). Growth of syntrophic propionate-oxidizing bacteria with fumarate in the absence of methanogenic bacteria. . Appl Environ Microbiol 59, 1114–1119. [PubMed]
    [Google Scholar]
26. 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]
27. Thompson J. D., Higgins D. G., Gibson T. J. ( 1994 ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22, 4673–4680. [View Article] [PubMed]
    [Google Scholar]
28. van Gelder A. H., Aydin R., Alves M. M., Stams A. J. M. ( 2012 ). 1,3-Propanediol production from glycerol by a newly isolated Trichococcus strain. . Microb Biotechnol 5, 573–578. [View Article] [PubMed]
    [Google Scholar]
29. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. & other authors ( 1987 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463–464. [View Article]
    [Google Scholar]
30. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991 ). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173, 697–703. [PubMed]
    [Google Scholar]