Skip to main content
SpringerLink
Log in

Novel Approaches to Pathogen Discovery in Metagenomes

  • Living reference work entry
  • First Online:
Encyclopedia of Metagenomics

  • 166 Accesses

Synonyms

Community genomics; Metagenomics and pathogen identification; Microbiome and virome; Pathogenomics

Definitions

Pathogen discovery: identification of causative microbial or viral agent(s) for an illness or asymptomatic infection. The identification may refer to etiological diagnosis for individuals, epidemiology investigation on population scale, and animal or environmental surveillance on orphan pathogens.

Metagenomics: genomic study on a population of biologically or functionally close microorganisms as a whole community, without separation of components into pure culture isolates.

Introduction

The best-known statement on pathogen discovery probably is the so-called Koch’s postulates, in which isolation of disease causative microbe and determination of its etiological features are of the essence (Falkow 2004; Lipkin 2010). There are fascinating and tragic stories in medical history of human volunteers or doctors who sacrificed health or even their lives to test pathogens on...

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

References

  • Arumugam M, Raes J, et al. Enterotypes of the human gut microbiome. Nature. 2011;473(7346):174–80.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Djikeng A, Spiro D. Advancing full length genome sequencing for human RNA viral pathogens. Futur Virol. 2009;4(1):47–53.

    Article  CAS  Google Scholar 

  • Eisen JA, MacCallum CJ. Genomics of emerging infectious disease: a PLoS collection. PLoS Biol. 2009;7(10):e1000224.

    Article  PubMed Central  PubMed  Google Scholar 

  • Falkow S. Molecular Koch’s postulates applied to bacterial pathogenicity – a personal recollection 15 years later. Nat Rev Microbiol. 2004;2(1):67–72.

    Article  CAS  PubMed  Google Scholar 

  • Fournier PE, Raoult D. Prospects for the future using genomics and proteomics in clinical microbiology. Annu Rev Microbiol. 2011;65(65):169–88.

    Article  CAS  PubMed  Google Scholar 

  • Fredericks DN, Relman DA. Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clin Microbiol Rev. 1996;9(1):18–33.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gega A, Kozal MJ. New technology to detect low-level drug-resistant HIV variants. Futur Virol. 2011;6(1):17–26.

    Article  Google Scholar 

  • Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68(4):669–85.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Joseph SJ, Read TD. Bacterial population genomics and infectious disease diagnostics. Trends Biotechnol. 2010;28(12):611–8.

    Article  CAS  PubMed  Google Scholar 

  • Koser CU, Ellington MJ, et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog. 2012;8(8):e1002824.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kuczynski J, Lauber CL, et al. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet. 2012;13(1):47–58.

    Article  CAS  Google Scholar 

  • Lipkin WI. Microbe hunting. Microbiol Mol Biol Rev. 2010;74(3):363–77.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Loman NJ, Misra RV, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012;30(5):434–9.

    Article  CAS  PubMed  Google Scholar 

  • Mokili JL, Rohwer F, et al. Metagenomics and future perspectives in virus discovery. Curr Opin Virol. 2012;2(1):63–77.

    Article  CAS  PubMed  Google Scholar 

  • Olsen RJ, Long SW, et al. Bacterial genomics in infectious disease and the clinical pathology laboratory. Arch Pathol Lab Med. 2012;136(11):1414–22.

    Article  PubMed  Google Scholar 

  • Pallen MJ, Loman NJ, et al. High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Curr Opin Microbiol. 2010;13(5):625–31.

    Article  CAS  PubMed  Google Scholar 

  • Petrosino JF, Highlander S, et al. Metagenomic pyrosequencing and microbial identification. Clin Chem. 2009;55(5):856–66.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Qin J, Li R, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Relman DA. Microbial genomics and infectious diseases. N Engl J Med. 2011;365(4):347–57.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Thomas T, Gilbert J, et al. Metagenomics – a guide from sampling to data analysis. Microb Inform Exp. 2012;2(1):3.

    Article  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Viral Diseases Branch, WRAIR, 503 Robert Grant Ave., Bldg. 503, Rm 3A06, Silver Spring, MD, 20910, USA

    Jun Hang

Authors
  1. Jun Hang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jun Hang .

Editor information

Editors and Affiliations

  1. J. Craig Venter Institute (JCVI), Rockville, Maryland, USA

    Karen E. Nelson

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media New York

About this entry

Cite this entry

Hang, J. (2012). Novel Approaches to Pathogen Discovery in Metagenomes. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_732-2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_732-2

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-6418-1

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

Publish with us

Policies and ethics

Search

Navigation