Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults

Environmental Microbiology

Volumn 17, Issue 12, 2015, Pages 4954-4964

  Tap, Julien ^a   Furet, Jean Pierre ^a   Bensaada, Martine ^a   Philippe, Catherine ^a   Roth, Hubert ^b,c   Rabot, Sylvie ^a   Lakhdari, Omar ^a   Lombard, Vincent ^d   Henrissat, Bernard ^d   Corthier, Gérard ^a   Fontaine, Eric ^b,c   Doré, Joël ^a   Leclerc, Marion ^a  

^a UMR1319 MICALIS   (France)

^b GRENOBLE UNIVERSITY HOSPITAL   (France)

^c Univ Lyon   (France)

^d AIX MARSEILLE UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

FATTY ACID; RNA 16S;

ADMINISTRATION AND DOSAGE; ADULT; CLINICAL TRIAL; CLOSTRIDIALES; DIET; DIETARY FIBER; DIETARY SUPPLEMENT; FECES; FEMALE; GENETICS; HUMAN; INTESTINE FLORA; ISOLATION AND PURIFICATION; MALE; MICROBIOLOGY; PREVOTELLA; PROCEDURES; SYMBIOSIS; YOUNG ADULT;

ADULT; CLOSTRIDIALES; DIET; DIETARY FIBER; DIETARY SUPPLEMENTS; FATTY ACIDS; FECES; FEMALE; GASTROINTESTINAL MICROBIOME; HUMANS; MALE; PREVOTELLA; RNA, RIBOSOMAL, 16S; SYMBIOSIS; YOUNG ADULT;

EID: 84955709661     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.13006     Document Type: Article

References (51)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., etal. (2011) Enterotypes of the human gut microbiome. Nature 473: 174-180.
3. Burkitt, D.P., Walker, A.R., and Painter, N.S. (1972) Effect of dietary fibre on stools and the transit-times, and its role in the causation of disease. Lancet 2: 1408-1412.
4. Cantarel, B.L., Coutinho, P.M., Rancurel, C., Bernard, T., Lombard, V., and Henrissat, B. (2009) The Carbohydrate-Active EnZymes database (CAZy): An expert resource for Glycogenomics. Nucleic Acids Res 37: D233-D238.
5. Chassard, C., Goumy, V., Leclerc, M., Del'homme, C., and Bernalier-Donadille, A. (2007) Characterization of the xylan-degrading microbial community from human faeces. FEMS Microbiol Ecol 61: 121-131.
6. Chassard, C., Delmas, E., Robert, C., and Bernalier-Donadille, A. (2010) The cellulose-degrading microbial community of the human gut varies according to the presence or absence of methanogens. FEMS Microbiol Ecol 74: 205-213.
7. Chessel, D., Dufour, A.B., and Thioulouse, J. (2004) The ade4 package-I-One-table methods. R News 4: 5-10.
8. Cotillard, A., Kennedy, S.P., Kong, L.C., Prifti, E., Pons, N., Le Chatelier, E., etal. (2013) Dietary intervention impact on gut microbial gene richness. Nature 500: 585-588.
9. Cummings, J.H., Bingham, S.A., Heaton, K.W., and Eastwood, M.A. (1992) Fecal weight, colon cancer risk, and dietary intake of nonstarch polysaccharides (dietary fiber). Gastroenterology 103: 1783-1789.
10. David, L.A., Maurice, C.F., Carmody, R.N., Gootenberg, D.B., Button, J.E., Wolfe, B.E., etal. (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505: 559-563.
11. De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J.B., Massart, S., etal. (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 107: 14691-14696.
12. Dodd, D., Mackie, R.I., and Cann, I.K. (2011) Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes. Mol Microbiol 79: 292-304.
13. Finegold, S.M., Attebery, H.R., and Sutter, V.L. (1974) Effect of diet on human fecal flora: Comparison of Japanese and American diets. Am J Clin Nutr 27: 1456-1469.
14. Flint, H.J., Duncan, S.H., Scott, K.P., and Louis, P. (2007) Interactions and competition within the microbial community of the human colon: Links between diet and health. Environ Microbiol 9: 1101-1111.
15. Flint, H.J., Bayer, E.A., Rincon, M.T., Lamed, R., and White, B.A. (2008) Polysaccharide utilization by gut bacteria: Potential for new insights from genomic analysis. Nat Rev Microbiol 6: 121-131.
16. Furet, J.P., Firmesse, O., Gourmelon, M., Bridonneau, C., Tap, J., Mondot, S., etal. (2009) Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol Ecol 68: 351-362.
17. Gibson, G.R., and Roberfroid, M.B. (1995) Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 125: 1401-1412.
18. Gill, S.R., Pop, M., Deboy, R.T., Eckburg, P.B., Turnbaugh, P.J., Samuel, B.S., etal. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.
19. Gosalbes, M.J., Durban, A., Pignatelli, M., Abellan, J.J., Jimenez-Hernandez, N., Perez-Cobas, A.E., etal. (2011) Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS ONE 6: e17447.
20. Graf, D., Di Cagno, R., Fak, F., Flint, H.J., Nyman, M., Saarela, M., and Watzl, B. (2015) Contribution of diet to the composition of the human gut microbiota. Microb Ecol Health Dis 26: 26164-26175.
21. Hayashi, H., Shibata, K., Sakamoto, M., Tomita, S., and Benno, Y. (2007) Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 57: 941-946.
22. van Hijum, S.A., de Jong, A., Baerends, R.J., Karsens, H.A., Kramer, N.E., Larsen, R., etal. (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics 6: 77-87.
23. Hildebrand, F., Tadeo, R., Voigt, A.Y., Bork, P., and Raes, J. (2014) LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome 2: 30-37.
24. Hooper, L.V., and Gordon, J.I. (2001) Commensal host-bacterial relationships in the gut. Science 292: 1115-1118.
25. Huang, X., and Madan, A. (1999) CAP3: a DNA sequence assembly program. Genome Res 9: 868-877.
26. Huang, Y., Gilna, P., and Li, W. (2009) Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics 25: 1338-1340.
27. Huse, S.M., Huber, J.A., Morrison, H.G., Sogin, M.L., and Welch, D.M. (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
28. Kristiansson, E., Hugenholtz, P., and Dalevi, D. (2009) ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics 25: 2737-2738.
29. Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., etal. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14: 169-181.
30. Lan, A., Bruneau, A., Philippe, C., Rochet, V., Rouault, A., Herve, C., etal. (2007) Survival and metabolic activity of selected strains of Propionibacterium freudenreichii in the gastrointestinal tract of human microbiota-associated rats. Br J Nutr 97: 714-724.
31. Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., etal. (2013) Richness of human gut microbiome correlates with metabolic markers. Nature 500: 541-546.
32. Ley, R.E., Backhed, F., Turnbaugh, P., Lozupone, C.A., Knight, R.D., and Gordon, J.I. (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102: 11070-11075.
33. Looijer-van Langen, M.A., and Dieleman, L.A. (2009) Prebiotics in chronic intestinal inflammation. Inflamm Bowel Dis 15: 454-462.
34. Mazmanian, S.K., Liu, C.H., Tzianabos, A.O., and Kasper, D.L. (2005) An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122: 107-118.
35. Miller, T.L., and Wolin, M.J. (1982) Enumeration of Methanobrevibacter smithii in human feces. Arch Microbiol 131: 14-18.
36. Miron, J., Ben-Ghedalia, D., and Morrison, M. (2001) Invited review: adhesion mechanisms of rumen cellulolytic bacteria. J Dairy Sci 84: 1294-1309.
37. O'Keefe, S.J., Li, J.V., Lahti, L., Ou, J., Carbonero, F., Mohammed, K., etal. (2015) Fat, fibre and cancer risk in African Americans and rural Africans. Nat Commun 6: 6342.
38. Pochart, P., Lemann, F., Flourie, B., Pellier, P., Goderel, I., and Rambaud, J.C. (1993) Pyxigraphic sampling to enumerate methanogens and anaerobes in the right colon of healthy humans. Gastroenterology 105: 1281-1285.
39. Pryde, S.E., Duncan, S.H., Hold, G.L., Stewart, C.S., and Flint, H.J. (2002) The microbiology of butyrate formation in the human colon. FEMS Microbiol Lett 217: 133-139.
40. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., etal. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
41. Rampelli, S., Schnorr, S.L., Consolandi, C., Turroni, S., Severgnini, M., Peano, C., etal. (2015) Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota. Curr Biol 25: 1682-1693.
42. Robert, C., and Bernalier-Donadille, A. (2003) The cellulolytic microflora of the human colon: evidence of microcrystalline cellulose-degrading bacteria in methane-excreting subjects. FEMS Microbiol Ecol 46: 81-89.
43. Robert, P., and Escoufier, Y. (1976) A unifying tool for linear multivariate statistical methods: the RV-coefficient. Appl Stat 25: 257-265.
44. Salonen, A., Lahti, L., Salojarvi, J., Holtrop, G., Korpela, K., Duncan, S.H., etal. (2014) Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. ISME J 8: 2218-2230.
45. Salyers, A.A., Vercellotti, J.R., West, S.E., and Wilkins, T.D. (1977a) Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon. Appl Environ Microbiol 33: 319-322.
46. Salyers, A.A., West, S.E., Vercellotti, J.R., and Wilkins, T.D. (1977b) Fermentation of mucins and plant polysaccharides by anaerobic bacteria from the human colon. Appl Environ Microbiol 34: 529-533.
47. Tasse, L., Bercovici, J., Pizzut-Serin, S., Robe, P., Tap, J., Klopp, C., etal. (2010) Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 20: 1605-1612.
48. Topping, D.L., and Clifton, P.M. (2001) Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol Rev 81: 1031-1064.
49. Turnbaugh, P.J., Backhed, F., Fulton, L., and Gordon, J.I. (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3: 213-223.
50. Walker, A.W., Ince, J., Duncan, S.H., Webster, L.M., Holtrop, G., Ze, X., etal. (2011) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 5: 220-230.
51. Wu, G.D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.Y., Keilbaugh, S.A., etal. (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334: 105-108.