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High-Throughput Characterization and Comparison of Microbial Communities

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Computational Medicine

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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 next-generation 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.

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Authors and Affiliations

  1. Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria

    Bettina Halwachs

  2. Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria

    Bettina Halwachs

  3. Institute of Pathology, Medical University of Graz, Graz, Austria

    Gregor Gorkiewicz

  4. Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010, Graz, Austria

    Gerhard G. Thallinger

  5. Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010, Graz, Austria

    Gerhard G. Thallinger

Authors
  1. Bettina Halwachs
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  2. Gregor Gorkiewicz
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  3. Gerhard G. Thallinger
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Correspondence to Gerhard G. Thallinger .

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  1. , Section for Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, 6020, Austria

    Zlatko Trajanoski

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Halwachs, B., Gorkiewicz, G., Thallinger, G.G. (2012). High-Throughput Characterization and Comparison of Microbial Communities. In: Trajanoski, Z. (eds) Computational Medicine. Springer, Vienna. https://doi.org/10.1007/978-3-7091-0947-2_3

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