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Enhancing functional metagenomics of complex microbial communities using stable isotopes

Enhancing functional metagenomics of complex microbial communities using stable isotopes
Enhancing functional metagenomics of complex microbial communities using stable isotopes
Exploring the function of genes encoded by uncultivated microorganisms is one of the major challenges facing microbiologists. Functions can be predicted by sequence comparisons to known genes and proteins, but proof of function requires the analysis of gene products by in vitro or in vivo expression, which is referred to as functional metagenomics. Using this approach, genetic material is retrieved from the environment, cloned, and expressed under laboratory conditions in order to screen for specific biochemical activities. Stable-isotope probing (SIP) is an approach for capturing genetic material of active microorganisms in environmental samples. This method facilitates functional metagenomics by directing the search towards microorganisms that are likely to possess genes of relevance to a specific research objective. In this chapter, we discuss how combined DNA-SIP and metagenomics research has been used for enhancing functional screening efforts. In addition, we highlight emerging methods, such as mRNA-SIP and Raman-microspectroscopy, that can help retrieve genetic material from targeted microbial groups for the discovery of novel functions.
Springer Verlag
Hernandez Garcia, Marcela
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Neufeld, Josh D.
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Dumont, Marc G.
ad1ad358-0ed9-4f15-b5eb-7c6f54547eb5
Hernandez Garcia, Marcela
e73477e7-cf3e-4f50-97c8-4494c5b05cd0
Neufeld, Josh D.
5e6989c6-ca4a-4311-a36d-3c2efbe08683
Dumont, Marc G.
ad1ad358-0ed9-4f15-b5eb-7c6f54547eb5

Hernandez Garcia, Marcela, Neufeld, Josh D. and Dumont, Marc G. (2016) Enhancing functional metagenomics of complex microbial communities using stable isotopes. In, Functional Metagenomics: Tools and Applications. Berlin, DE. Springer Verlag. (In Press)

Record type: Book Section

Abstract

Exploring the function of genes encoded by uncultivated microorganisms is one of the major challenges facing microbiologists. Functions can be predicted by sequence comparisons to known genes and proteins, but proof of function requires the analysis of gene products by in vitro or in vivo expression, which is referred to as functional metagenomics. Using this approach, genetic material is retrieved from the environment, cloned, and expressed under laboratory conditions in order to screen for specific biochemical activities. Stable-isotope probing (SIP) is an approach for capturing genetic material of active microorganisms in environmental samples. This method facilitates functional metagenomics by directing the search towards microorganisms that are likely to possess genes of relevance to a specific research objective. In this chapter, we discuss how combined DNA-SIP and metagenomics research has been used for enhancing functional screening efforts. In addition, we highlight emerging methods, such as mRNA-SIP and Raman-microspectroscopy, that can help retrieve genetic material from targeted microbial groups for the discovery of novel functions.

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Accepted/In Press date: 28 April 2016
Organisations: Centre for Biological Sciences

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Local EPrints ID: 396516
URI: http://eprints.soton.ac.uk/id/eprint/396516
PURE UUID: 0945b0a2-0152-406c-a2f9-307ca063b549

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Date deposited: 10 Jun 2016 10:23
Last modified: 17 Apr 2020 16:32

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Contributors

Author: Marcela Hernandez Garcia
Author: Josh D. Neufeld
Author: Marc G. Dumont

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