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Chapter 2.4.3 : Functional Metagenomics: Procedures and Progress

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Abstract:

Using metagenomic approaches to interrogate microbial communities is commonly based on sequencing the total DNA extracted from biomass. However, while this approach predominates in the literature, it does not provide an insight into the novel functions within a system and does not provide physical DNA for manipulation. In order to obtain novel functions from a microbial community, functional metagenomics was developed. This approach, which preceded the advent of large-scale sequence based metagenomics coupled with next generation sequencing, revolves around hosting and expressing heterologous DNA in a suitable surrogate host. Coupled with phenotypic screens functional metagenomics provides an alternative approach to obtaining functionally active genes from a microbial system, without the need to culture any organisms.

Citation: Morris L, Marchesi J. 2016. Functional Metagenomics: Procedures and Progress, p 2.4.3-1-2.4.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.3
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Tables

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TABLE 1

Advantages and disadvantages of the two main types of metagenomic approaches

Citation: Morris L, Marchesi J. 2016. Functional Metagenomics: Procedures and Progress, p 2.4.3-1-2.4.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.3
Generic image for table
TABLE 2

List of common screens used in functional metagenomics

Citation: Morris L, Marchesi J. 2016. Functional Metagenomics: Procedures and Progress, p 2.4.3-1-2.4.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.3
Generic image for table
TABLE 3

List of screens used on a functional metagenomic fosmid library from the distal human gut and examples of hit rate

Citation: Morris L, Marchesi J. 2016. Functional Metagenomics: Procedures and Progress, p 2.4.3-1-2.4.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.3
Generic image for table
TABLE 4

Recent (2010-present) successful functional metagenomic studies summarizing host organism(s) for library construction, types of genes targeted, diverse environments DNA was isolated from for metagenomic screening, type of vector used (with average metagenomic insert size), hit rate, and type of screening method implemented

Citation: Morris L, Marchesi J. 2016. Functional Metagenomics: Procedures and Progress, p 2.4.3-1-2.4.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.3

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