Biodiversity and functional genomics in the human microbiome

Trends in Genetics

Volumn 29, Issue 1, 2013, Pages 51-58

  Morgan, Xochitl C ^a   Segata, Nicola ^a   Huttenhower, Curtis ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

Human Microbiome Project; Metagenomics; Microbiota

Indexed keywords

ACTINOMYCES; ASTHMA; ATOPIC DERMATITIS; BIODIVERSITY; CLOSTRIDIALES; CLOSTRIDIUM DIFFICILE; COLORECTAL CANCER; DESULFOVIBRIO; DIET; ESCHERICHIA COLI; FUNCTIONAL GENOMICS; FUSOBACTERIUM; GENE SEQUENCE; GENETIC VARIABILITY; GNOTOBIOTICS; HABITAT; HAEMOPHILUS; HUMAN; INTESTINE FLORA; LACTOBACILLUS; METAGENOME; MICROBIAL COLONIZATION; MICROBIOME; NEPHROLITHIASIS; NONHUMAN; OBESITY; PERIODONTITIS; PRIORITY JOURNAL; PSORIASIS; REVIEW; STREPTOCOCCUS; VEILLONELLA;

BIODIVERSITY; COMPUTATIONAL BIOLOGY; GASTROINTESTINAL TRACT; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICROBIOTA; PHYLOGENY;

EID: 84871709986     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2012.09.005     Document Type: Review

References (76)

1. Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214. Human Microbiome Project Consortium.
2. Peterson J., et al. The NIH Human Microbiome Project. Genome Res. 2009, 19:2317-2323.
3. Reyes A., et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010, 466:334-338.
4. Qin J., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65.
5. Ley R.E. Obesity and the human microbiome. Curr. Opin. Gastroenterol. 2010, 26:5-11.
6. Turnbaugh P.J., et al. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484.
7. Sokol H., et al. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm. Bowel Dis. 2009, 15:1183-1189.
8. Joossens M., et al. Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut 2011, 60:631-637.
9. Kaufman D.W., et al. Oxalobacter formigenes may reduce the risk of calcium oxalate kidney stones. J. Am. Soc. Nephrol. 2008, 19:1197-1203.
10. Human Microbiome Project Consortium A framework for human microbiome research. Nature 2012, 486:215-221.
11. Tringe S.G., Hugenholtz P. A renaissance for the pioneering 16S rRNA gene. Curr. Opin. Microbiol. 2008, 11:442-446.
12. Lazarevic V., et al. Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J. Microbiol. Methods 2009, 79:266-271.
13. Tyson G.W., et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428:37-43.
14. Venter J.C., et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304:66-74.
15. Gill S.R., et al. Metagenomic analysis of the human distal gut microbiome. Science 2006, 312:1355-1359.
16. Ley R.E., et al. Microbial ecology: human gut microbes associated with obesity. Nature 2006, 444:1022-1023.
17. Eckburg P.B., et al. Diversity of the human intestinal microbial flora. Science 2005, 308:1635-1638.
18. Fodor A., Earl A. 'Most wanted' taxa from the human microbiome. PLoS ONE 2012, 7:e41294.
19. Li K., et al. Analyses of the microbial diversity across the human microbiome. PLoS ONE 2012, 7:e32118.
20. Huse S.M., et al. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 2012, 7:e34242.
21. Ratner A.J., et al. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS ONE 2012, 7:e36466.
22. Rivera A.J., et al. Differences between the normal vaginal bacterial community of baboons and that of humans. Am. J. Primatol. 2011, 73:119-126.
23. Gajer P., et al. Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 2012, 4:132ra52.
24. Ravel J., et al. Vaginal microbiome of reproductive-age women. Proc. Natl. Acad. Sci. U.S.A. 2011, 108(Suppl. 1):4680-4687.
25. Wylie K.M., et al. Novel bacterial taxa in the human microbiome. PLoS ONE 2012, 7:e35294.
26. Hajishengallis G., et al. Low-abundance biofilm species orchestrates inflammatory periodontal disease through the commensal microbiota and complement. Cell Host Microbe 2011, 10:497-506.
27. Koenig J.E., et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. U.S.A. 2011, 108(Suppl. 1):4578-4585.
28. Dominguez-Bello M.G., et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:11971-11975.
29. Claesson M.J., et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 2012, 488:178-184.
30. Yatsunenko T., et al. Human gut microbiome viewed across age and geography. Nature 2012, 486:222-227.
31. Ley R.E., et al. Evolution of mammals and their gut microbes. Science 2008, 320:1647-1651.
32. Burke C., et al. Bacterial community assembly based on functional genes rather than species. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:14288-14293.
33. Cantarel B.L., et al. Complex carbohydrate utilization by the healthy human microbiome. PLoS ONE 2012, 7:e28742.
34. Rahija R.J. Gnotobiotics. The Mouse in Biomedical Research 2007, 217-233. Academic Press. 2nd edn. G.F. James (Ed.).
35. Gaboriau-Routhiau V.R., et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 2009, 31:677-689.
36. Faith J.J., et al. Creating and characterizing communities of human gut microbes in gnotobiotic mice. ISME J. 2010, 4:1094-1098.
37. Heijtz R.D., et al. Normal gut microbiota modulates brain development and behavior. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:3047-3052.
38. Olszak T., et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science 2012, 336:489-493.
39. Ivanov I.I., et al. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 2008, 4:337-349.
40. H17 cell differentiation. Nature 2008, 455:808-812.
41. Garrett W.S., et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 2010, 8:292-300.
42. Turnbaugh P.J., et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 2009, 1:6ra14.
43. Wu G.D., et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011, 334:105-108.
44. McNulty N.P., et al. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci. Transl. Med. 2011, 3:106ra106.
45. Zhang H., et al. Human gut microbiota in obesity and after gastric bypass. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:2365-2370.
46. Samuel B.S., Gordon J.I. A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:10011-10016.
47. Mazmanian S.K., et al. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 2005, 122:107-118.
48. Macpherson A.J., et al. IgA responses in the intestinal mucosa against pathogenic and non-pathogenic microorganisms. Microbes Infect. 2001, 3:1021-1035.
49. Wu H-J., et al. Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity 2010, 32:815-827.
50. Khan K.J., et al. Antibiotic therapy in inflammatory bowel disease: a systematic review and meta-analysis. Am. J. Gastroenterol. 2011, 106:661-673.
51. Veiga P., et al. Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:18132-18137.
52. Jonkers D., et al. Probiotics in the management of inflammatory bowel disease: a systematic review of intervention studies in adult patients. Drugs 2012, 72:803-823.
53. Oh P.L., et al. Characterization of the ileal microbiota in rejecting and nonrejecting recipients of small bowel transplants. Am. J. Transplant. 2012, 12:753-762.
54. Farrell J.J., et al. Variations of oral microbiota are associated with pancreatic diseases including pancreatic cancer. Gut 2012, 61:582-588.
55. Louie T.J., et al. Fidaxomicin versus vancomycin for Clostridium difficile infection. N. Engl. J. Med. 2011, 364:422-431.
56. Okuda H., et al. A possible mechanism of eighteen patient deaths caused by interactions of sorivudine, a new antiviral drug, with oral 5-fluorouracil prodrugs. J. Pharmacol. Exp. Ther. 1998, 287:791-799.
57. Spencer M.D., et al. Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology 2011, 140:976-986.
58. Bentley D.R., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59.
59. Eid J., et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323:133-138.
60. Rothberg J.M., et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475:348-352.
61. Gilbert J.A., et al. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 2008, 3:e3042.
62. Booijink C.C., et al. Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl. Environ. Microbiol. 2010, 76:5533-5540.
63. Li X., et al. A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface. PLoS ONE 2011, 6:e26542.
64. Verberkmoes N.C., et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009, 3:179-189.
65. Wikoff W.R., et al. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:3698-3703.
66. Jansson J., et al. Metabolomics reveals metabolic biomarkers of Crohn's disease. PLoS ONE 2009, 4:e6386.
67. Raes J., Bork P. Molecular eco-systems biology: towards an understanding of community function. Nat. Rev. Microbiol. 2008, 6:693-699.
68. Arumugam M., et al. Enterotypes of the human gut microbiome. Nature 2011, 473:174-180.
69. Huang Y.J., et al. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J. Allergy Clin. Immunol. 2011, 127:372-381.
70. Kong H.H., et al. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res. 2012, 22:850-859.
71. Marchesi J.R., et al. Towards the human colorectal cancer microbiome. PLoS ONE 2011, 6:e20447.
72. Hoppe B., et al. Efficacy and safety of Oxalobacter formigenes to reduce urinary oxalate in primary hyperoxaluria. Nephrol. Dial. Transplant. 2011, 26:3609-3615.
73. Liu B., et al. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS ONE 2012, 7:e37919.
74. Fahlen A., et al. Comparison of bacterial microbiota in skin biopsies from normal and psoriatic skin. Arch. Dermatol. Res. 2012, 304:15-22.
75. Segata N., et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 2012, 9:811-814.
76. Stothard P., et al. BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res. 2005, 33:D317-D320.