Ann Clin Microbiol.  2013 Dec;16(4):162-167. 10.5145/ACM.2013.16.4.162.

The Human Microbiome Project: Beginning and Future Status

• Murray PR

• KMID: 1501978
• DOI: http://doi.org/10.5145/ACM.2013.16.4.162

Abstract

In 1884 Robert Koch and Friedrich Loeffler published Koch's Postulates defining our historical understanding of the relationship between an organism and infection: one organism: one disease. In the last decade with research on the microbial community living on and in humans, a new concept of microbial diseases has emerged; that is, alterations of the microbial community can lead to disease including an extension beyond traditional "infectious" diseases to include metabolic disorders such as type 2 diabetes and obesity. As we continue to gain knowledge about the functions of the normal microbiome and the effects of alterations of the microbial population on disease pathogenesis, a new era of diagnostics and therapeutics will evolve.

Keyword

History; Human Microbiome; Metagenome

Reference

1.Human Microbiome Project Consortium. A framework for human microbiome research. Nature. 2012. 486:215–21.

2.Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012. 486:207–14.

3.NIH HMP Working Group. Peterson J., Garges S., Giovanni M., McInnes P., Wang L, et al. The NIH Human Microbiome Project. Genome Res. 2009. 19:2317–23.

4.Lander ES., Linton LM., Birren B., Nusbaum C., Zody MC., Baldwin J, et al. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001. 409:860–921.

5.Venter JC., Adams MD., Myers EW., Li PW., Mural RJ., Sutton GG, et al. The sequence of the human genome. Science. 2001. 291:1304–51.

6.Lander ES. Initial impact of the sequencing of the human genome. Nature. 2011. 470:187–97.

7.Relman DA. Microbiology: Learning about who we are. Nature. 2012. 486:194–5.

8.Parfrey LW., Knight R. Spatial and temporal variability of the human microbiota. Clin Microbiol Infect. 2012. 18(Suppl 4):8–11.

9.Gevers D., Knight R., Petrosino JF., Huang K., McGuire AL., Birren BW, et al. The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol. 2012. 10:e1001377.

10.Huse SM., Ye Y., Zhou Y., Fodor AA. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One. 2012. 7:e34242.

11.Cho I., Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012. 13:260–70.

12.Grice EA., Segre JA. The skin microbiome. Nat Rev Microbiol. 2011. 9:244–53.

13.Morgan XC., Segata N., Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends Genet. 2013. 29:51–8.

14.Fettweis JM., Serrano MG., Girerd PH., Jefferson KK., Buck GA. A new era of the vaginal microbiome: advances using next-generation sequencing. Chem Biodivers. 2012. 9:965–76.

15.Srinivasan S., Hoffman NG., Morgan MT., Matsen FA., Fiedler TL., Hall RW, et al. Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relation-ships of microbiota to clinical criteria. PLoS One. 2012. 7:e37818.

16.Li E., Hamm CM., Gulati AS., Sartor RB., Chen H., Wu X, et al. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS One. 2012. 7:e26284.

17.Petrof EO., Claud EC., Gloor GB., Allen-Vercoe E. Microbial ecosystems therapeutics: a new paradigm in medicine? Benef Microbes. 2013. 4:53–65.

18.Petrof EO., Gloor GB., Vanner SJ., Weese SJ., Carter D., Daigneault MC, et al. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome. 2013. 1:3.

19.Allen-Vercoe E., Reid G., Viner N., Gloor GB., Hota S., Kim P, et al. A Canadian Working Group report on fecal microbial therapy: microbial ecosystems therapeutics. Can J Gastroenterol. 2012. 26:457–62.

20.Damman CJ., Miller SI., Surawicz CM., Zisman TL. The microbiome and inflammatory bowel disease: is there a therapeutic role for fecal microbiota transplantation? Am J Gastroenterol. 2012. 107:1452–9.

21.Vincent C., Stephens DA., Loo VG., Edens TJ., Behr MA., Dewar K, et al. Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection. Microbiome. 2013. 1:18.

22.Morrow AL., Lagomarcino AJ., Schibler KR., Taft DH., Yu Z., Wang B, et al. Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. Microbiome. 2013. 1:13.

23.Berry D., Reinisch W. Intestinal microbiota: a source of novel biomarkers in inflammatory bowel diseases? Best Pract Res Clin Gastroenterol. 2013. 27:47–58.

24.Elinav E., Strowig T., Kau AL., Henao-Mejia J., Thaiss CA., Booth CJ, et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell. 2011. 145:745–57.

25.Wu S., Rhee KJ., Albesiano E., Rabizadeh S., Wu X., Yen HR, et al. A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nat Med. 2009. 15:1016–22.

26.Hajishengallis G., Darveau RP., Curtis MA. The keystone-pathogen hypothesis. Nat Rev Microbiol. 2012. 10:717–25.