Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

Metagenomic Research: Methods and Ecological Applications

  • Navneet Batra
  • Sonu Bhatia
  • Arvind Behal
  • Jagtar Singh
  • Amit Joshi
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_766-2



The aim of metagenomics is to investigate enormous diversity of taxonomically and phylogenetically relevant genes, individual catabolic genes, and whole operons by explicating the genomes of uncultured microbes. The concept of metagenomics was introduced by Handelsman which involves the extraction of genomic DNA from the microbial community inhabiting the environment. Either this DNA is cloned as libraries for functional screening, or PCR-based enrichment is performed with respect to gene of interest. Generally, DNA is considered as the most appropriate method for assessing environmental microbial community’s structure as any selection biasness is not involved. High-throughput methods can be employed for direct sequencing of the metagenome. The functional approach is used to explore genes that encode novel enzymes or drugs, but advancements are needed for function-based metagenomics by employing...


Microbial Community Bacterial Artificial Chromosome Terminal Restriction Fragment Length Polymorphism Multiple Displacement Amplification Metagenomic Approach 
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.
This is a preview of subscription content, log in to check access.


  1. Banik JJ, Brady SF. Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules. Curr Opin Microbiol. 2010;13:603–9.PubMedCentralPubMedCrossRefGoogle Scholar
  2. Chen IC, Lin WD, Hsu SK, et al. Isolation and characterization of a novel lysine racemase from a soil metagenomic library. Appl Environ Microbiol. 2009;75:5161–6.PubMedCentralPubMedCrossRefGoogle Scholar
  3. Cowan D, Meyer Q, Stafford W, et al. Metagenomic gene discovery: past, present and future. Trends Biotechnol. 2005;23:321–9.PubMedCrossRefGoogle Scholar
  4. Delmont TO, Robe P, Clark I, et al. Metagenomic comparison of direct and indirect soil DNA extraction approaches. J Microbiol Methods. 2011;86:397–400.PubMedCrossRefGoogle Scholar
  5. Ghazanfar S, Azim A, Ghazanfar MA, et al. Metagenomics and its application in soil microbial community studies: biotechnological prospects. J Anim Plant Sci. 2010;6:611–22.Google Scholar
  6. Guazzaroni ME, Beloqui A, Golyshin PN, et al. Metagenomics as a new technological tool to gain scientific knowledge. World J Microbiol Biotechnol. 2009;25:945–54.CrossRefGoogle Scholar
  7. Hirsch PR, Mauchline TH, Clark IM. Culture-independent molecular techniques for soil microbial ecology. Soil Biol Biochem. 2010;42:878–87.CrossRefGoogle Scholar
  8. Imfeld G, Vuilleumier S. Measuring the effects of pesticides on bacterial communities in soil: a critical review. Eur J Soil Biol. 2012;49:22–30.CrossRefGoogle Scholar
  9. Kakirde KS, Parsley LC, Liles MR. Size does matter: application-driven approaches for soil metagenomics. Soil Biol Biochem. 2010;42:1911–23.PubMedCentralPubMedCrossRefGoogle Scholar
  10. Keshri J, Mishra A, Jha B. Microbial population index and community structure in saline-alkaline soil using gene targeted metagenomics. Microbiol Res. 2013;168:165–73.PubMedCrossRefGoogle Scholar
  11. Larsen P, Hamada Y, Gilberta J. Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction. J Biotechnol. 2012;160:17–24.PubMedCrossRefGoogle Scholar
  12. Lewin A, Wentzel A, Valla S. Metagenomics of microbial life in extreme temperature environments. Curr Opin Biotechnol. 2012;24:1–10.CrossRefGoogle Scholar
  13. Logares R, Haverkamp THA, Kumar S, et al. Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches. J Microbiol Methods. 2012;91:106–13.PubMedCrossRefGoogle Scholar
  14. Mocali S, Benedetti A. Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res Microbiol. 2010;161:497–505.PubMedCrossRefGoogle Scholar
  15. Monier JM, Demaneche S, Delmont TO, et al. Metagenomic exploration of antibiotic resistance in soil. Curr Opin Microbiol. 2011;14:229–35.PubMedCrossRefGoogle Scholar
  16. Nelson KE, Weinstock GM, Highlander SK, et al. A catalog of reference genomes from the human microbiome. Science. 2010;328:994–9.PubMedCrossRefGoogle Scholar
  17. Sharma R, Ranjan R, Kapardar RK, et al. Unculturable bacterial diversity: an untapped resource. Curr Sci. 2005;89:72–7.Google Scholar
  18. Singh J, Behal A, Singla N, et al. Metagenomics: concept, methodology, ecological inference and recent advances. Biotechnol J. 2009;4:480–94.PubMedCrossRefGoogle Scholar
  19. Streit WR, Schmitz RA. Metagenomics - the key to the uncultured microbes. Curr Opin Microbiol. 2004;7:492–8.PubMedCrossRefGoogle Scholar
  20. Thomas T, Gilbert J, Meyer F. Metagenomics - a guide from sampling to data analysis. Microbiol Inform Exp. 2012;2:3.CrossRefGoogle Scholar
  21. Uhlik O, Leewis MC, Strejcek M, et al. Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv. 2013;31:154–65.PubMedCentralPubMedCrossRefGoogle Scholar
  22. Vasconcellos SP, Angolini CFF, García INS, et al. Screening for hydrocarbon biodegraders in a metagenomic clone library derived from Brazilian petroleum reservoirs. Org Geochem. 2010;41:675–81.CrossRefGoogle Scholar
  23. Willner D, Hugenholtz P. Metagenomics and community profiling: culture-independent techniques in the clinical laboratory. Clin Microbiol Newsl. 2013;35:1–9.CrossRefGoogle Scholar
  24. Xing MN, Zhang XZ, Huang H. Application of metagenomic techniques in mining enzymes from microbial communities for biofuel synthesis. Biotechnol Adv. 2012;30:920–9.PubMedCrossRefGoogle Scholar
  25. Yilmaz P, Kottmanna R, Pruesse E, et al. Analysis of 23S rRNA genes in metagenomes – a case study from the global ocean sampling expedition. Syst Appl Microbiol. 2011;34:462–9.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Navneet Batra
    • 1
  • Sonu Bhatia
    • 1
  • Arvind Behal
    • 1
  • Jagtar Singh
    • 2
  • Amit Joshi
    • 3
  1. 1.P G Department of BiotechnologyGGDSD CollegeChandigarhIndia
  2. 2.Department of BiotechnologyPanjab UniversityChandigarhIndia
  3. 3.Department of Biotechnology & BioinformaticsSGGS CollegeChandigarhIndia