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Molecular Microbiome Analysis

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The Gut Microbiome in Health and Disease

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Abstract

Traditional microbiological research largely depends on the cultivation and characterization of microorganisms under laboratory conditions. However, with the establishment of new sequencing-based methods over the last two decades that expanded the accessible fraction of the microbiota to non-cultivable members, microbiome research has gained significant momentum and popularity. Today, next-generation sequencing allows even smaller research groups to carry out massively parallel sequencing at affordable costs. Selective amplification and sequencing of universal phylogenetic marker genes such as those of the small subunit ribosomal RNA still represent a cornerstone of the taxonomic composition analysis that is typically used to describe and compare microbiome samples. At the same time, shotgun sequencing of metagenomes that represent all members of a microbial community is becoming increasingly popular as a more expensive but also more comprehensive alternative to amplicon sequencing. Both approaches generate large amounts of sequence data, which require bioinformatic support for processing, analysis, and visualization. The following chapter provides an overview of the typical steps involved in microbiome projects, starting from sample collection and storage, over 16S rRNA and other marker gene amplification, amplicon, and metagenome sequencing to bioinformatic sequence analysis.

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  1. University of Hohenheim, Stuttgart, Germany

    Amélia Camarinha-Silva & W. Florian Fricke

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  1. Amélia Camarinha-Silva
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Correspondence to W. Florian Fricke .

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  1. Chair of Nutrition and Immunology, Technical University Munich, Freising, Germany

    Dirk Haller

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Camarinha-Silva, A., Fricke, W.F. (2018). Molecular Microbiome Analysis. In: Haller, D. (eds) The Gut Microbiome in Health and Disease. Springer, Cham. https://doi.org/10.1007/978-3-319-90545-7_4

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