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Chapter Two - Analytical approaches for microbiome research

Published online by Cambridge University Press:  07 March 2020

By
Xavier A. Harrison  and
Simon J. S. Cameron
Edited by
Rachael E. Antwis ,
Xavier A. Harrison  and
Michael J. Cox
Rachael E. Antwis
Affiliation:
University of Salford
Xavier A. Harrison
Affiliation:
University of Exeter
Michael J. Cox
Affiliation:
University of Birmingham
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Summary

Two major outstanding questions in microbiome research ask what microbes are present in a community and how they interact with each other and their hosts. Recent, rapid improvements in nucleic acid (DNA and RNA) sequencing allow us to study the composition and function of microbiomes in unprecedented detail, leading to a step change in our understanding of host–microbe interactions. This chapter gives a broad overview of the basic toolkit available to modern microbiologists and microbial ecologists, exploring their application to key questions about microbiome structure and function. We cover tools based on nucleic acid sequencing (e.g. amplicon sequencing, metagenomics, metatranscriptomics) as well as approaches targeting larger molecules such as metabolomics and proteomics. We discuss the use of microbial culture as a means of measuring functional capacity of individual microbes, or building artificial communities to understand emergent properties of consortia. We emphasise the advantages of combining multiple techniques alongside robust experimental design to garner powerful quantitative estimates of microbiome structure, and how this relates to host–microbe interactions.

Keywords

bioinformaticscompositionculturingfunctional diversitymetabarcodingmetabolomicsmetageneticsmetatranscriptomicsproteomicssequencing
Type
Chapter
Information
Microbiomes of Soils, Plants and Animals
An Integrated Approach
 , pp. 8 - 28
Publisher: Cambridge University Press
Print publication year: 2020

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