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Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
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2016 (English)In: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976Article in journal (Refereed) Epub ahead of print
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.

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Keyword [en]
marker gene, community ecology, microbial ecology, microbial diversity, species interactions, statistical methods
National Category
Agricultural Sciences
URN: urn:nbn:se:uu:diva-297240DOI: 10.1093/femsre/fuw017OAI: oai:DiVA.org:uu-297240DiVA: diva2:941409
Available from: 2016-06-22 Created: 2016-06-22 Last updated: 2016-08-09Bibliographically approved

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Bahram, Mohammad
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Systematic Biology
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