Impact of newly developed metagenomic tools on our knowledge of the gut microbiota and its role in human health: Diagnostic and therapeutic issues;Impact des nouveaux outils de métagénomique sur notre connaissance du microbiote intestinal et de son rôle en santé humaine

Medecine/Sciences

Volumn 32, Issue 11, 2016, Pages 944-951

  Blottière, Hervé M ^a   Doré, Joël ^a  

^a UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; DYSBIOSIS; HEALTH; HUMAN; INTESTINE FLORA; METAGENOMICS; PHYSIOLOGY; PROCEDURES; TRENDS;

ANIMALS; DYSBIOSIS; GASTROINTESTINAL MICROBIOME; HEALTH; HUMANS; METAGENOMICS;

EID: 85008325130     PISSN: 07670974     EISSN: 19585381     Source Type: Journal    
DOI: 10.1051/medsci/20163211009     Document Type: Review

References (59)

1. Blottière HM, de Vos WM, Ehrlich SD, Doré J. Human intestinal metagenomics: state of the art and future. Curr Opin Microbiol 2013; 16: 232-9.
2. Nicholson JK, Holmes E, Kinross J, et al. Host-gut microbiota metabolic interactions. Science 2012; 336: 1262-7.
3. Van Nood E, Vrieze A, Nieuwdorp M, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 2013; 368: 407-15.
4. Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 1977; 31: 107-33.
5. Sender R, Fuchs S, Milo R. Are we really vastly out numbered? Revisiting the ratio of bacterial to host cells in humans. Cell 2016; 164: 337-40.
6. Cultrone A, Tap J, Lapaque N, Doré J, Blottière HM. Metagenomics of the human intestinal tract: from who is there to what is done there. Curr Opin Food Sci 2015; 4: 64-8.
7. Suau A, Bonnet R, Sutren M, et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 1999; 65: 4799-4-807.
8. 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.
9. Clooney AG, Fouhy F, Sleator RD, et al. Comparing apples and oranges? Next generation sequencing and its impact on microbiome analysis. PLoS One 2016; 11: e0148028.
10. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 59-65.
11. Weinstock GM. Genomic approaches to studying the human microbiota. Nature 2012; 489: 250-6.
12. 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.
13. Xiao L, Feng Q, Liang S, et al. A catalog of the mouse gut metagenome. Nat Biotechnol 2015; 33: 1103-8.
14. Nielsen HB, Almeida M, Juncker AS, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol 2014; 32: 822-8.
15. Almeida M, Pop M, Le Chatelier E, et al. Capturing the most wanted taxa through cross-sample correlations. ISME J 2016; 10: 2459-67.
16. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature 2011; 473: 174-80.
17. Jeffery IB, Claesson MJ, O'Toole PW, Shanahan F. Categorization of the gut microbiota: enterotypes or gradients? Nat Rev Microbiol 2012; 10: 591-2.
18. Knights D, Ward TL, McKinlay CE, et al. Rethinking enterotypes. Cell Host Microbe 2014; 16: 433-7.
19. Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature 2014; 509: 357-60.
20. Wu GD, Chen J, Hoffmann C, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011; 334: 105-8.
21. Doré J, Blottière HM. The influence of diet on the gut microbiota and its consequences for health. Curr Opin Biotechnol 2015; 32: 195-9.
22. Vandeputte D, Falony G, Vieira-Silva S, et al. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut 2016; 65: 57-62.
23. Le Chatelier E, Nielsen T, Qin J, et al. Richness of human gut microbiome correlates with metabolic markers. Nature 2013; 500: 541-6.
24. Kong LC, Holmes BA, Cotillard A, et al. Dietary patterns differently associate with inflammation and gut microbiota in overweight and obese subjects. PLoS One 2014; 9: e109434.
25. Cotillard A, Kennedy SP, Kong LC, et al. Dietary intervention impact on gut microbial gene richness. Nature 2013; 500: 585-8.
26. Manichanh C, Rigottier-Gois L, Bonnaud E, et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 2006; 55: 205-11.
27. Sokol H, Pigneur B, Watterlot L, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA 2008; 105: 16731-6.
28. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006; 444: 1022-3.
29. Duncan SH, Lobley GE, Holtrop G, et al. Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 2008; 32: 1720-4.
30. Schwiertz A, Taras D, Schäfer K, et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity 2010; 18: 190-5.
31. Qin N, Yang, Li A, et al. Human gut microbiome alterations in liver cirrhosis. Nature 2014; 513: 59-64.
32. Forslund K, Hildebrand F, Nielsen T, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 2015; 528: 262-6.
33. Browne HP, Forster SC, Anonye BO, et al. Culturing of unculturable human microbiota reveals novel taxa and extensive sporulation. Nature 2016; 533: 543-6.
34. Larraufie P, de Wouters T, Veronese G, Blottière HM, Doré J. Functional metagenomics to decipher food-microbe-host crosstalk. Proc Nutr Soc 2015; 74: 1-4.
35. Lakhdari O, Cultrone A, Tap J, et al. Functional metagenomics: a high throughput screening method to study microbiota-driven cell signaling modulation in the human gut. PLoS One 2010; 5: e13092.
36. De Wouters T, Ledue F, Nepelska M, et al. A robust and adaptable high throughput screening method to study host-microbiota interactions in the human intestine. PLoS One 2014; 9: e105598.
37. Cohen LJ, Kang HS, Chu J, et al. Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist. Proc Natl Acad Sci USA 2015; 112: E4825-34.
38. Gaboriau-Routhiau V, Cerf-Bensussan N. Microbiote intestinal et développement du système immunitaire. Med Sci (Paris) 2016; 32: 961-7.
39. Lagier JC, Raoult D. Greffe de microbiote fécal et infections: mise au point, perspectives. Med Sci (Paris) 2016; 32: 991-7.
40. Gilgenkrantz H. La révolution des CRISPR est en marche. Med Sci (Paris) 2014; 30: 1066-9.
41. 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.
42. Lamas B, Richard ML, Sokol H. CARD9 et colite: un pont entre dysbiose et immunité. Med Sci (Paris) 2016; 32: 933-6.
43. Rahmouni O, Dubuquoy L, Desreumaux P, Neut C. Microbiote intestinal et développement des maladies inflammatoires chroniques de l'intestin. Med Sci (Paris) 2016; 32: 968-73.
44. Gevers D, Kugathasan S, Denson LA, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 2014; 15: 382-92.
45. Lepage P, Häsler R, Spehlmann ME, et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011; 141: 227-36.
46. D'Argenio V, Casaburi G, Precone V, et al. Metagenomics reveals dysbiosis and a potentially pathogenic N. flavescens strain in duodenum of adult celiac patients. Am J Gastroenterol 2016; 111: 879-90.
47. Saulnier DM, Riehle K, Mistretta TA, et al. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology 2011; 141: 1782-91.
48. Rajilic-Stojanovic M, Biagi E, Heilig HG, et al. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome. Gastroenterology 2011; 141: 1792-801.
49. Zeller G, Tap J, Voigt AY, et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol 2014; 10: 766.
50. Sobhani I, Tap J, Roudot-Thoraval F, et al. Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS One 2011; 6: e16393.
51. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006; 444: 1022-3.
52. Kostic AD, Gevers D, Siljander H, et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe 2015; 17: 260-73.
53. Murri M, Leiva I, Gomez-Zumaquero JM, et al. Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study. BMC Med 2013; 11: 46.
54. Claesson MJ, Jeffery IB, Conde S, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 2012; 488: 178-84.
55. Taur Y, Jenq RR, Perales MA, et al. The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood 2014; 124: 1174-82.
56. Abrahamsson TR, Jakobsson HE, Andersson AF, et al. Low diversity of the gut microbiota in infants with atopic eczema. J Allergy Clin Immunol 2012; 129: 434-40.
57. Karlsson FH, Fåk F, Nookaew I, et al. Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun 2012; 3: 1245.
58. Finegold SM, Dowd SE, Gontcharova V, et al. Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 2010; 16: 444-53.
59. Naseribafrouei A, Hestad K, Avershina E, et al. Correlation between the human fecal microbiota and depression. Neurogastroenterol Motil 2014; 26: 1155-62.