Microbiotes and metagenomics;Microbiotes et métagénomique

Medecine/Sciences

Volumn 32, Issue 11, 2016, Pages 937-943

  Weissenbach, Jean ^a,b   Sghir, Abdelghani ^b  

^a CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^b UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA;

ANIMAL; GENETICS; HUMAN; INTESTINE FLORA; METAGENOME; METAGENOMICS; MICROFLORA; PHYSIOLOGY; PROCEDURES;

ANIMALS; GASTROINTESTINAL MICROBIOME; HUMANS; METAGENOME; METAGENOMICS; MICROBIOTA; RNA, RIBOSOMAL;

EID: 85008319116     PISSN: 07670974     EISSN: 19585381     Source Type: Journal    
DOI: 10.1051/medsci/20163211008     Document Type: Review

References (49)

1. Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 1998; 95: 6578-83.
2. Iriberri J, Herndl GJ. Formation and microbial utilization of amorphous aggregates in the sea: Ecological significance. Microbiologia 1995; 11: 309-22.
3. Staley JT, Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 1985; 39: 321-46.
4. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: Proposal for the domains archaea, bacteria, and eucarya. Proc Natl Acad Sci USA 1990; 87: 4576-9.
5. Olsen GJ, Lane DJ, Giovannoni SJ, et al. Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 1986; 40: 337-65.
6. Romby P, Marzi S, Westhof E. La structure atomique du ribosome en pleine lumière. Prix Nobel de Chimie 2009 à Venkatraman Ramakrishnan, Thomas A. Steitz et Ada E. Yonath. Med Sci (Paris) 2009; 25: 977-81.
7. Dauga C, Doré J, Sghir A. La diversité insoupçonnée du monde microbien. Med Sci (Paris) 2005; 21: 290-6.
8. Amann RI, Ludwig W, Schleifer KH Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995; 59: 143-69.
9. Colwell RR Viable but nonculturable bacteria: a survival strategy. J Infect Chemother 2000; 6: 121-5.
10. Tanaka Y, Hanada S, Manome A, et al. Catellibacterium nectariphilum gen. Nov., sp. Nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth. Int J Syst Evol Microbiol 2004; 54: 955-9.
11. Lennon JT, Jones SE Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 2011; 9: 119-30.
12. Perna NT, Plunkett G, 3rd, Burland V, et al. Genome sequence of enterohaemorrhagic Escherichia coli O157: H7. Nature 2001; 409: 529-33.
13. Daubin V, Abby SS. Les transferts horizontaux de gènes et l'arbre de la vie. Med Sci (Paris) 2012; 28: 695-8.
14. Vernikos G, Medini D, Riley DR, Tettelin H. Ten years of pan-genome analyses. Curr Opin Microbiol 2015; 23: 148-54.
15. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004; 68: 669-85.
16. Burcelin R, Chabo C, Blasco-Baque V, et al. Le microbiote intestinal à l'origine de nouvelles perspectives thérapeutiques pour les maladies métaboliques? Med Sci (Paris) 2013; 29: 800-6.
17. Cani PD, Everard A. Akkermansia muciniphila: une nouvelle cible pour contrôler l'obésité, le diabète de type 2 et l'inflammation? Med Sci (Paris) 2014; 30: 125-7.
18. Andrejak C, Delhaes L. Le microbiome pulmonaire en 2015: une fenêtre ouverte sur les pathologies pulmonaires chroniques. Med Sci (Paris) 2015; 31: 971-8.
19. Audebert C, Hot D, Lemoine Y, Caboche S. Le séquençage haut-débit: vers un diagnostic basé sur la séquence complète du génome de l'agent infectieux. Med Sci (Paris) 2014; 30: 1144-51.
20. El Kaoutari A, Armougom F, Raoult D, Henrissat B. Le microbiote intestinal et la digestion des polysaccharides. Med Sci (Paris) 2014; 30: 259-65.
21. Sharpton TJ. An introduction to the analysis of shotgun metagenomic data. Front Plant Sci 2014; 5: 209.
22. Handelsman J, Rondon MR, Brady SF, et al. Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chem Biol 1998; 5: R245-9.
23. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 59-65.
24. Lozupone CA, Stombaugh JI, Gordon JI, et al. Diversity, stability and resilience of the human gut microbiota. Nature 2012; 489: 220-30.
25. Li J, Jia H, Cai X, et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 2014; 32: 834-41.
26. Sunagawa S, Coelho LP, Chaffron S, et al. Ocean plankton. Structure and function of the global ocean microbiome. Science 2015; 348: 1261359.
27. Yooseph S, Sutton G, Rusch DB, et al. The Sorcerer ii global ocean sampling expedition: expanding the universe of protein families. PLoS Biol 2007; 5: e16.
28. Jetten MS, Strous M, van de Pas-Schoonen KT, et al. The anaerobic oxidation of ammonium. FEMS Microbiol Rev 1998; 22: 421-37.
29. Ettwig KF, Butler MK, Le Paslier D, et al. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 2010; 464: 543-8.
30. Kyrpides NC Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat Biotechnol 2009; 27: 627-32.
31. Turroni F, Marchesi JR, Foroni E, et al. Microbiomic analysis of the bifidobacterial population in the human distal gut. Isme J 2009; 3: 745-51.
32. Aslam Z, Yasir M, Yoon HS, et al. Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices. J Microbiol 2013; 51: 747-56.
33. Nam YD, Chang HW, Kim KH, et al. Bacterial, archaeal, and eukaryal diversity in the intestines of korean people. J Microbiol 2008; 46: 491-501.
34. Bartram AK, Lynch MD, Stearns JC, et al. Generation of multimillionsequence 16s rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol 2011; 77: 3846-52.
35. Gloor GB, Hummelen R, Macklaim JM, et al. Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products. PLoS One 2010; 5: e15406.
36. Sogin ML, Morrison HG, Huber JA, et al. Microbial diversity in the deep sea and the underexplored rare biosphere. Proc Natl Acad Sci USA 2006; 103: 12115-20.
37. Gibson GR, Cummings JH, Macfarlane GT. Use of a three-stage continuous culture system to study the effect of mucin on dissimilatory sulfate reduction and methanogenesis by mixed populations of human gut bacteria. Appl Environ Microbiol 1988; 54: 2750-5.
38. Jarrell KF, Walters AD, Bochiwal C, et al. Major players on the microbial stage: why archaea are important. Microbiology 2011; 157: 919-36.
39. St-Pierre B, Wright AD Diversity of gut methanogens in herbivorous animals. Animal 2013; 1: 49-56.
40. Ohkuma M Symbioses of flagellates and prokaryotes in the gut of lower termites. Trends Microbiol 2008; 16: 345-52.
41. Smits LP, Bouter KE, de Vos WM, et al. Therapeutic potential of fecal microbiota transplantation. Gastroenterology 2013; 145: 946-53.
42. Agrawal M, Aroniadis OC, Brandt LJ, et al. The long-term efficacy and safety of fecal microbiota transplant for recurrent, severe, and complicated Clostridium difficile infection in 146 elderly individuals. J Clin Gastroenterol 2016; 50: 403-7.
43. Le Chatelier E, Nielsen T, Qin J, et al. Richness of human gut microbiome correlates with metabolic markers. Nature 2013; 500: 541-6.
44. Lederberg J, McCray AT Ome sweet omics: a genealogical treasury of words. Scientist 2001; 15: 8.
45. Burcelin R, Nicolas S, Blasco-Baque V. Microbiotes et maladies métaboliques: de nouveaux concepts pour de nouvelles stratégies thérapeutiques. Med Sci (Paris) 2016; 32: 952-60.
46. Lagier JC, Raoult D. Culturomics: une méthode d'étude du microbiote humain. Med Sci (Paris) 2016; 32: 923-5.
47. Lagier JC, Raoult D. Greffe de microbiote fécal et infections: mise au point, perspectives. Med Sci (Paris) 2016; 32: 991-7.
48. Gaboriau-Routhiau V, Cerf-Bensussan N. Microbiote intestinal et développement du système immunitaire. Med Sci (Paris) 2016; 32: 961-7.
49. Chassaing B. Le microbiote intestinal, un acteur de la réponse immunitaire adaptative antivirale? Med Sci (Paris) 2015; 31: 355-7.