Skip to main content
SpringerLink
Log in
Book cover

Encyclopedia of Metagenomics pp 1–7Cite as

Subtractive Hybridization Magnetic Bead Capture: Molecular Technique for Recovery of Full-Length ORFs from Metagenomes

  • Living reference work entry
  • First Online:

  • 138 Accesses

Synonyms

Recovery of full-length ORFs from metagenomic DNA

Definition

Subtractive hybridization magnetic bead capture (SHBMC) is a sequence-based metagenomic technique for the recovery of full-length ORFs from heterogeneous metagenomic DNA samples.

Introduction

It is widely acknowledged that the vast majority (~99 %) of microorganisms present in the environment are resistant to culture using classical microbiological methods. Approximately half of the total estimated bacterial phyla (61) are still to be cultured (Vartoukian et al. 2010). However, environmental microbial communities constitute a valuable resource for biotechnology and are a valid target for identification of novel genes and/or biological compounds such as biocatalysts or secondary metabolites (Sharma et al. 2005). In order to bypass the limitations of microbial culturing and to discover new microbial genes and functions, two approaches have been implemented, either culture-based, through the development of innovative...

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

References

  • Cowan D, Meyer Q, Stafford W, Muyanga S, Rory Cameron R, Wittwer P. Metagenomics gene discovery: past, present and future. TRENDS Biotechnol. 2005;23:321–9.

    Article  CAS  PubMed  Google Scholar 

  • Harris RP, Groth DM, Ledger J, Lee CY. Identification of sex specific DNA regions in the snake genome using a subtractive hybridization technique. Proc Assoc Advmt Anim Breed Genet. 2009;18:572–5.

    Google Scholar 

  • Knauth S, Schmidt H, Tippkotter R. Comparison of commercial kits for the extraction of DNA from paddy soils. Lett Appl Microbiol. 2013;56:222–8.

    Article  CAS  PubMed  Google Scholar 

  • Latisnere-Barragan H, Lopez-Cortes A. Isolation of phaC gene from marine bacteria Paracoccus homiensis strain E33 by magnetic beads subtractive hybridization. Ann Microbiol. 2012;62:1691–5.

    Article  CAS  Google Scholar 

  • Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M. Comparison of next-generation sequencing systems. J Biomed Biotechnol. 2012. doi:10.1155/2012/251364.

    Google Scholar 

  • Meiring T, Mulako I, Tuffin MI, Meyer Q, Cowan DA. Retrieval of full-length functional genes using subtractive hybridization magnetic bead capture. Methods Mol Biol. 2010;668:287–97. Clifton, NJ.

    Article  CAS  PubMed  Google Scholar 

  • Meyer QC, Burton SG, Cowan DA. Subtractive hybridization magnetic bead capture: a new technique for the recovery of full-length ORFs from metagenome. Biotechnol J. 2007;2:36–40.

    Article  CAS  PubMed  Google Scholar 

  • Morales SE, Holben WE. Linking bacterial identities and ecosystem processes: can ‘omic’ analyses be more than the sum of their parts? FEMS Microbiol Ecol. 2011;75:2–16.

    Article  CAS  PubMed  Google Scholar 

  • Paszkiewicz K, Studholme DJ. De novo assembly of short sequence reads. Brief Bioinform. 2010;11:457–72.

    Article  CAS  PubMed  Google Scholar 

  • Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet. 2004;38:525–52.

    Article  CAS  PubMed  Google Scholar 

  • Roh C, Villatte F, Kim B-G, Schmid RD. Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples. Appl Biochem Biotechnol. 2006;134:97–112.

    Article  CAS  PubMed  Google Scholar 

  • Schmeisser C, Steele H, Streit WR. Metagenomics, biotechnology with non-culturable microbes. Appl Microbiol Biotechnol. 2007;75:955–62.

    Article  CAS  PubMed  Google Scholar 

  • Sharma R, Ranjan R, Kapardar RK, Grover A. ‘Unculturable’ bacterial diversity: an untapped resource. Curr Sci. 2005;89:72–7.

    CAS  Google Scholar 

  • Thomas T, Gilbert J, Meyer F. Metagenomics - a guide from sampling to data analysis. Microbiol Inform Exp. 2012;2:3–3.

    Article  Google Scholar 

  • Vartoukian SR, Palmer RM, Wade WG. Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol Lett. 2010;309:1–7.

    CAS  PubMed  Google Scholar 

  • Wang J, McCord B. The application of magnetic bead hybridization for the recovery and STR amplification of degraded and inhibited forensic DNA. Electrophoresis. 2011;32:1631–8.

    Article  CAS  PubMed  Google Scholar 

  • Wang HH, Zhao CY, Li F. Rapid identification of mycobacterium tuberculosis complex by a novel hybridization signal amplification method based on self-assembly of dna-streptavidin nanoparticles. Braz J Microbiol. 2011;42:964–72.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Waschkowitz T, Rockstroh S, Daniel R. Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries. Appl Environ Microbiol. 2009;75:2506–16.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhou JZ, Bruns MA, Tiedje JM. DNA recovery from soils of diverse composition. Appl Environ Microbiol. 1996;62:316–22.

    CAS  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Centre for Microbial Ecology and Genomics (CMEG), Genome Research Institute (GRI), University of Pretoria, Hatfield, 0028, Pretoria, South Africa

    Don Cowan, Sandra Ronca & Jean-Baptiste Ramond

Authors
  1. Don Cowan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sandra Ronca
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jean-Baptiste Ramond
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Don Cowan .

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

© 2013 Springer Science+Business Media New York

About this entry

Cite this entry

Cowan, D., Ronca, S., Ramond, JB. (2013). Subtractive Hybridization Magnetic Bead Capture: Molecular Technique for Recovery of Full-Length ORFs from Metagenomes. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_628-2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_628-2

  • 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