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Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes
Senckenberg Biodivers & Climate Res Ctr, Senckenberganlage 25, D-60325 Frankfurt, Germany.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA; Univ Chicago, Dept Med, 5841 S Maryland Ave, Chicago, IL 60637 USA.
Katholieke Univ Leuven, Rega Inst, Ctr Biol Dis, B-3000 Leuven, Belgium.
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2016 (English)In: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 40, no 5, 686-700 p.Article in journal (Refereed) Published
Abstract [en]

With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.

Place, publisher, year, edition, pages
2016. Vol. 40, no 5, 686-700 p.
Keyword [en]
marker gene, community ecology, microbial ecology, microbial diversity, species interactions, statistical methods
National Category
Agricultural Sciences Microbiology
Identifiers
URN: urn:nbn:se:uu:diva-297240DOI: 10.1093/femsre/fuw017ISI: 000385138200007PubMedID: 27358393OAI: oai:DiVA.org:uu-297240DiVA: diva2:941409
Funder
German Research Foundation (DFG), BA 4843/2-1 UN 262/9-1EU, European Research Council, PUT171 9286 EMP265
Available from: 2016-06-22 Created: 2016-06-22 Last updated: 2016-12-05Bibliographically approved

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