High-Throughput Characterization and Comparison of Microbial Communities
The human microbiome plays an important role in health and disease, but the structure of the bacterial communities and their interaction with the human body are still poorly understood. The recent introduction of next-generation sequencing technologies al
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High-Throughput Characterization and Comparison of Microbial Communities Bettina Halwachs, Gregor Gorkiewicz, and Gerhard G. Thallinger
Abstract
The human microbiome plays an important role in health and disease, but the structure of the bacterial communities and their interaction with the human body are still poorly understood. The recent introduction of nextgeneration sequencing technologies allows for the first time an unbiased and in-depth characterization of a microbiome based on the sequence of certain marker genes. However, analysis of the huge amount of sequence data generated in microbiome studies poses a considerable challenge to the individual researcher. Here we provide an overview of the steps involved in the characterization and comparison of complex microbial communities starting with sequence preprocessing on to taxonomic classification ending in statistical evaluation and visualization of the analysis results. A selection of different tools and techniques of each working step is introduced and discussed. Additionally, different sequencing approaches ahead of the bioinformatics analysis are considered. Furthermore, the application of microbiome analysis in medical research is shown by selected medical studies. The chapter is addressed to microbial ecologists or medical researchers without or little bioinformatics background as well as to bioinformatics scientists who are interested in the overall microbiome workflow, and its tools and techniques.
3.1 G.G. Thallinger (*) Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010 Graz, Austria e-mail: [email protected]
Introduction
Humans inhabit an earth dominated by microorganisms. This is illustrated by the fact that the number of microorganisms exceeds the number of human beings by a factor of 1021 (Kyrpides 2009). Humans are not just surrounded by microorganisms, but microorganisms also live on and inside the human body. The relationship with these microbes colonizing different body habitats
Z. Trajanoski (ed.), Computational Medicine, DOI 10.1007/978-3-7091-0947-2_3, # Springer-Verlag Wien 2012
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is mostly beneficial to our health. For reasons which are still poorly understood, this mutualistic (“commensal”) relationship sometimes switches into a pathogenic one (Avila et al. 2009). Commensal bacteria occupy niches, which can then not be inhabited by pathogenic strains (“colonization resistance”). However, under certain environmental triggers (e.g., antibiotic treatment) the mutualistic balance is disturbed, commensal bacteria are depleted, and certain pathogenic taxa can proliferate and subsequently harm the body. Metagenomics enables the culture-independent study of the whole genetic information of complex microbial communities, providing information about structure, function, and interactions of the microbial community with its habitat (Eisen 2007). Comprehensiv
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