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 toward microorganisms that are likely to possess genes of relevance to a specific research objective. In this chapter, we discuss how combined DNA-SIP and metagenomic 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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