Untangling the genetic basis of fibrolytic specialization by lachnospiraceae and ruminococcaceae in diverse gut communities

Diversity

Volumn 5, Issue 3, 2013, Pages 627-640

  Biddle, Amy ^a   Stewart, Lucy ^a   Blanchard, Jeffrey ^a   Leschine, Susan ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

Carbohydrate active enzymes comparative genomics; Clostridiales; Lachnospiraceae; Plant degradation; Ruminococcaceae

Indexed keywords

BACTERIUM; ENZYME; GENETICS; GENOME; MAMMAL; PLANT; SPECIALIZATION; SUGAR;

EID: 84886299775     PISSN: None     EISSN: 14242818     Source Type: Journal    
DOI: 10.3390/d5030627     Document Type: Article

References (41)

1. Collins, M.D.; Lawson, P.A.; Willems, A.; Cordoba, J.J.; Fernandez-Garayzabal, J.; Garcia, P.; Cai, J.; Hippe, H.; Farrow, J.A.E. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 1994, 44, 812-826.
2. Stackebrandt, E.; Rainey, F.A. Phylogenic relationships. In The Clostridia: Molecular Biology and Pathogenesis; Rood, J.I., McClane, B.A., Songer, J.G., Titball, R.W., Eds.; Academic Press: New York, NY, USA, 1997.
3. Garrity, G.M.; Bell, J.A.; Lilburn, T. The Proteobacteria, Part A, Introductory Essays: The Revised Road Map to the Manual. In Bergey's Manual® of Systematic Bacteriology; Brenner, D.J., Krieg, N.R., Staley, J.T., Garrity, G.M., Eds.; Springer: New York, NY, USA, 2005.
4. Ludwig, W.; Schleifer, K.-H.; Whitman, W.B. Revised road map to the phylum Firmicutes. In Bergey's Manual® of Systematic Bacteriology; Vos, P., Garrity, G.M., Jones, D., Krieg, N.R., Ludwig, W., Rainey, F.A., Schleifer, K-H., Whitman, W.B., Eds.; Springer: New York, NY, USA, 2009.
5. De Long, E.F. The microbial ocean from genomes to biomes. Nature 2009, 459, 200-206.
6. Jalanka-Tuovinen, J.; Salonen, A.; Nikkila, J.; Immonen, O.; Kekkonen, R.; Lahti, L.; Palva, A.; de Vos, W.M. Intestinal Microbiota in Healthy Adults: Temporal Analysis Reveals Individual and Common Core and Relation to Intestinal Symptoms. PLoS One 2011, 6, e23035.
7. Turnbaugh, P.J.; Hamady, M.; Yatsunenko, T.; Cantarel, B.L.; Duncan, A.; Ley, R.E.; Sogin, M.L.; Jones, W.J.; Roe, B.A.; Affourtit, J.P. A core gut microbiome in obese and lean twins. Nature 2008, 457, 480-484.
8. Peris-Bondia, F.; Latorre, A.; Artacho, A.; Moya, A.; D'Auria, G. The Active Human Gut Microbiota Differs from the Total Microbiota. PLoS One 2011, 6, e22448.
9. Tap, J.; Mondot, S.; Levenez, F.; Pelletier, E.; Caron, C.; Furet, J.; Ugarte, E.; Muñoz-Tamayo, R.; Paslier, D.L.E; Nalin, R. Towards the human intestinal microbiota phylogenetic core. Environ. Microbiol. 2009, 11, 2574-2584.
10. Barcenilla, A.; Pryde, S.E.; Martin, J.C.; Duncan, S.H.; Stewart, C.S.; Henderson, C.; Flint, H.J. Phylogenetic Relationships of Butyrate-Producing Bacteria from the Human Gut. Appl. Environ. Microbiol. 2000, 66, 1654-1661.
11. Duncan, S.H.; Barcenilla, A.; Stewart, C.S.; Pryde, S.E.; Flint, H.J. Acetate utilization and butyryl coenzyme A (CoA): acetate-CoA transferase in butyrate-producing bacteria from the human large intestine. Appl. Environ. Microbiol. 2002, 68, 5186-5190.
12. Frank, D.N.; Amand, A.L.S.; Feldman, R.A.; Boedeker, E.C.; Harpaz, N.; Pace, N.R. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. USA 2007, 104, 13780-13785.
13. Flint, H.J.; Bayer, E.A.; Rincon, M.T.; Lamed, R.; White, B.A. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat. Rev. Microbiol. 2008, 6, 121-131.
14. Ding, S.-Y.; Rincon, M.T.; Lamed, R.; Martin, J.C.; McCrae, S.I.; Aurilia, V.; Shoham, Y.; Bayer, E.A.; Flint, H.J. Cellulosomal Scaffoldin-Like Proteins from Ruminococcus. flavefaciens. J. Bacteriol. 2001, 183, 1945-1953.
15. Fujimoto, T.; Imaeda, H.; Takahashi, K.; Kasumi, E.; Bamba, S.; Fujiyama, Y.; Andoh, A. Decreased abundance of Faecalibacterium prausnitzii in the gut microbiota of Crohn's disease. J. Gastroen. Hepatol. 2013, 28, 613-619.
16. Leschine, S. Cellulose Degradation in Anaerobic Environments. Annu. Rev. Microbiol. 1995, 49, 399-426.
17. Lynd, L.R.; Weimer, P.J.; van Zyl, W.H.; Pretorius, I.S. Microbial Cellulose Utilization: Fundamentals and Biotechnology. Microbiol. Mol. Biol. Rev. 2002, 66, 506-577.
18. Brulc, J.M.; Antonopoulosb, D.A.; Millera, M.E.B.; Wilsona, M.K.; Yannarella, A.C.; Dinsdaled, E.A.; Edwardsd, R.E.; Frankh, E.D.; Emersoni, J.B.; Wacklini, P.; et al. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc. Natl. Acad. Sci. USA 2009, 106, 1948-1953.
19. Macfarlane, S.; Macfarlane, G.T. Composition and Metabolic Activities of Bacterial Biofilms Colonizing Food Residues in the Human Gut. Appl. Environ. Microbiol. 2006, 72, 6204-6211.
20. Cameron, E.A.; Maynard, M.A.; Smith, C.J.; Smith, T.J.; Koropatkin, N.M.; Martens, E.C. Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism. J. Biol. Chem. 2012, 287, 34614-34625.
21. Proctor, L.M. The Human Microbiome Project in 2011 and Beyond. Cell Host Microbe 2011, 10, 287-291.
22. Cole, J.R. The Ribosomal Database Project (RDP-II): Sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 2004, 33, D294-D296.
23. Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32, 1792-1797.
24. Tamura, K.; Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 1993, 10, 512-526.
25. Tamura, K.; Peterson, D.; Peterson, N.; Stecher, G.; Nei, M.; Kumar, S. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 2011, 28, 2731-2739.
26. FigTree, version 1.3.1. Available online: http://tree.bio.ed.ac.uk/software/figtree/ (accessed on 17 May 2013).
27. Markowitz, V.M.; Chen, I.M.A.; Palaniappan, K.; Chu, K.; Szeto, E.; Gretchkin, Y. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2011, 40, D115-D122.
28. Cantarel, B.L.; Coutinho, P.M.; Rancurel, C.; Bernard, T.; Lombard, V.; Henrissat, B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009, 37, D233-D238.
29. R Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2012; Version 2.15.1.
30. Venables, W.N.; Ripley, B.D. Modern Applied Statistics with S. Available online: http://www.stats.ox.ac.uk/pub/MASS4 (accessed on 17 May 2013).
31. Shapiro, S.S.; Wilk, M.B. An analysis of variance test for normality (complete samples). Biometrika 1965, 52, 591-611.
32. O'Hara, R.B.; Kotze, D.J. Do not log-transform count data. Methods Ecol. Evol. 2010, 1, 118-122.
33. The UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2011, 40, D71-D75.
34. Kanehisa, M.; Goto, S.; Sato, Y.; Furumichi, M.; Tanabe, M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2011, 40, D109-D114.
35. Keseler, I.M.; Mackie, A.; Peralta-Gil, M.; Santos-Zavaleta, A.; Gama-Castro, S.; Bonavides-Martinez, C.; Fulcher, C.; Huerta, A.M.; Kothari, A.; Krummenacker, M. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 2012, 41, D605-D612.
36. Karp, P.D. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 2005, 33, 6083-6089.
37. Saier, M.H. Families of transmembrane sugar transport proteins. Mol. Microbiol. 2000, 35, 699-710.
38. Brückner, R.; Titgemeyer, F. Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. FEMS Microbiol. Lett. 2002, 209, 141-148.
39. Jojima, T.; Omumasaba, C.A.; Inui, M.; Yukawa, H. Sugar transporters in efficient utilization of mixed sugar substrates: current knowledge and outlook. Appl. Microbiol. Biotechnol. 2009, 85, 471-480.
40. Stülke, J.; Hillen, W. Regulation of carbon catabolism in Bacillus species. Annu. Rev. Microbiol. 2000, 54, 849-880.
41. Rees, D.C.; Johnson, E.; Lewinson, O. ABC transporters: the power to change. Nat. Rev. Mol. Cell Biol. 2009, 10, 218-227