Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson


  • Sarah Highlander
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_1-1


Microbiome: The microbes (bacteria, archaea, fungi, protists, and viruses) that inhabit a specific environment or host, such as all the microbes that live in and on the human body.

Mesophile: An organism that grows and thrives within a moderate temperature range, usually between 20° and 45 °C.

Fastidious Organism: An organism that has very specific and usually complex growth requirements.

Microbial Commensalism: Interaction between two species where one benefits but does not harm or affect the other.

Microbial Mutualism: Interaction between two species where both organisms benefit.


Only about 1 % of all prokaryotic species in the biosphere are thought to be cultivatable (Handelsman 2004). A few thousand taxa are associated with the human microbiome. The taxa on the skin are mostly cultivatable (ca. 90 %) (Gao et al. 2007), about 50 % of the oral species are cultivable (Dewhirst et al. 2010), and about 50 % of the taxa of the gut microbiome may be cultivable...


Micrococcus Luteus Diffusion Chamber Human Microbiome Palladium Chloride Strict Anaerobe 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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  1. D’Onofrio A, Crawford JM, Stewart EJ, Witt K, Gavrish E, Epstein S, et al. Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem Biol. 2010;17:254–64.PubMedCentralPubMedCrossRefGoogle Scholar
  2. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, et al. The human oral microbiome. J Bacteriol. 2010;192:5002–17.PubMedCentralPubMedCrossRefGoogle Scholar
  3. Gao Z, Tseng CH, Pei Z, Blaser MJ. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A. 2007;104:2927–32.PubMedCentralPubMedCrossRefGoogle Scholar
  4. Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci U S A. 2011;108:6252–7.PubMedCentralPubMedCrossRefGoogle Scholar
  5. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68:669–85.PubMedCentralPubMedCrossRefGoogle Scholar
  6. Kaeberlein T, Lewis K, Epstein SS. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science. 2002;296:1127–9.PubMedCrossRefGoogle Scholar
  7. Nichols D, Cahoon N, Trakhtenberg EM, Pham L, Mehta A, Belanger A, et al. Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species. Appl Environ Microbiol. 2010;76:2445–50.PubMedCentralPubMedCrossRefGoogle Scholar
  8. Rappe MS, Connon SA, Vergin KL, Giovannoni SJ. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature. 2002;418:630–3.PubMedCrossRefGoogle Scholar
  9. Sizova MV, Hohmann T, Hazen A, Paster BJ, Halem SR, Murphy CM, et al. New approaches for isolation of previously uncultivated oral bacteria. Appl Environ Microbiol. 2012;78:194–203.PubMedCentralPubMedCrossRefGoogle Scholar
  10. Vartoukian SR, Palmer RM, Wade WG. Cultivation of a Synergistetes strain representing a previously uncultivated lineage. Environ Microbiol. 2010;12:916–28.PubMedCentralPubMedCrossRefGoogle Scholar
  11. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, et al. Cultivating the uncultured. Proc Natl Acad Sci U S A. 2002;99:15681–6.PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Genomic MedicineJ. Craig Venter InstituteLa JollaUSA