Abstract
The sequencing of the human genome has driven the study of human biology in a significant way and enabled the genome-wide study to elucidate the molecular basis of complex human diseases. Recently, the role of microbiota on human physiology and health has received much attention. The influence of gut microbiome (the collective genomes of the gut microbiota) in obesity has been demonstrated, which may pave the way for new prophylactic and therapeutic strategies such as bacteriotherapy. The significance and recent understandings in the area of “human microbiomics” are discussed here.
Keywords: Human microbiome, Metagenomics, Microbial diversity, 16S rRNA, Obesity, Bacteriotherapy
Full Text
The Full Text of this article is available as a PDF (137.6 KB).
References
- 1.Xu J., Mahowald M.A., Ley R.E., Lozupone C.A., Hamady M. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol. 2007;5:e156. doi: 10.1371/journal.pbio.0050156. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Li M., Wang B., Zhang M., Rantalainen M., Wang S. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci USA. 2008;105:2117–2122. doi: 10.1073/pnas.0712038105. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Xu J., Gordon J.I. Inaugural article: Honor thy symbionts. Proc Natl Acad Sci USA. 2003;100:10452–10459. doi: 10.1073/pnas.1734063100. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Gill S.R., Pop M., Deboy R.T., Eckburg P.B., Turnbaugh P.J. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355–1359. doi: 10.1126/science.1124234. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Turnbaugh P.J., Ley R.E., Hamady M., Fraser-Liggett C.M., Knight R., Gordon J.I. The human microbiome project. Nature. 2007;449:804–810. doi: 10.1038/nature06244. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Gao Z., Tseng C.H., Pei Z., Blaser M.J. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci USA. 2007;104:2927–2932. doi: 10.1073/pnas.0607077104. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Nasidze I., Li J., Quinque D., Tang K., Stoneking M. Global diversity in the human salivary microbiome. Genome Res. 2009;19:636–643. doi: 10.1101/gr.084616.108. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Bik E.M., Eckburg P.B., Gill S.R., Nelson K.E., Purdom E.A. Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci USA. 2006;103:732–737. doi: 10.1073/pnas.0506655103. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Eckburg P.B., Bik E.M., Bernstein C.N., Purdom E., Dethlefsen L. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–1638. doi: 10.1126/science.1110591. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Srinivasan S., Fredricks D.N. The human vaginal bacterial biota and bacterial vaginosis. Interdiscip Perspect Infect Dis. 2008;2008:750479. doi: 10.1155/2008/750479. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Sperandio V. Genome sequence of E. coli O157:H7. Trends Microbiol. 2001;9:159. doi: 10.1016/S0966-842X(01)02023-6. [DOI] [PubMed] [Google Scholar]
- 12.Turnbaugh P.J., Hamady M., Yatsunenko T., Cantarel B.L., Duncan A. A core gut microbiome in obese and lean twins. Nature. 2009;457:480–484. doi: 10.1038/nature07540. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Mahowald M.A., Rey F.E., Seedorf H., Turnbaugh P.J., Fulton R.S. Characterizing a model human gut microbiota composed of members of its two dominant bacterialphyla. Proc Natl Acad Sci USA. 2009;106:5859–5864. doi: 10.1073/pnas.0901529106. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Hutchison C.A., III, Venter J.C. Single-cell genomics. Nat Biotechnol. 2006;24:657–658. doi: 10.1038/nbt0606-657. [DOI] [PubMed] [Google Scholar]
- 15.Marcy Y., Ouverney C., Bik E.M., Losekann T., Ivanova N. Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA. 2007;104:11889–11894. doi: 10.1073/pnas.0704662104. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Huovinen P. Bacteriotherapy: the time has come. BMJ. 2001;323:353–354. doi: 10.1136/bmj.323.7309.353. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Corr S.C., Li Y., Riedel C.U., O’Toole P.W., Hill C., Gahan C.G. Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118. Proc Natl Acad Sci USA. 2007;104:7617–7621. doi: 10.1073/pnas.0700440104. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.Roos K., Holm S.E., Grahn Håkansson E., Lagergren L. Recolonization with selected alfa streptococci for prophylaxis of recurrent streptococcal pharyngotonsillitis- a randomised placebo controlled multicentre study. Scand J Infect Dis. 1996;28:459–62. doi: 10.3109/00365549609037940. [DOI] [PubMed] [Google Scholar]
- 19.Rembacken B.J., Snelling A.M., Hawkey P.M., Chalmers D.M., Axon A. Non pathogenic Escherichia coli versus mesalazine for the treatment of ulcerative colitis: a randomised trial. Lancet. 1999;354:635–639. doi: 10.1016/S0140-6736(98)06343-0. [DOI] [PubMed] [Google Scholar]
- 20.Gloux K., Leclerc M., Iliozer H., L’Haridon R., Manichanh C. Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth. Appl Environ Microbiol. 2007;73:3734–3727. doi: 10.1128/AEM.02204-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21.Ley R.E., Bäckhed F., Turnbaugh P., Lozupone C.A., Knight R.D., Gordon J.I. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA. 2005;102:11070–11075. doi: 10.1073/pnas.0504978102. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 22.Turnbaugh P.J., Ley R.E., Mahowald M.A., Magrini V., Mardis E.R., Gordon J.I. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027–1031. doi: 10.1038/nature05414. [DOI] [PubMed] [Google Scholar]