Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes

Miklós Bálint; Mohammad Bahram; A Murat Eren; Karoline Faust; Jed A Fuhrman; Björn Lindahl; Robert B O'Hara; Maarja Öpik; Mitchell L Sogin; Martin Unterseher; Leho Tedersoo

doi:10.1093/femsre/fuw017

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes

FEMS Microbiol Rev. 2016 Sep;40(5):686-700. doi: 10.1093/femsre/fuw017. Epub 2016 Jun 29.

Authors

Affiliations

¹ Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt, Germany mbalint@senckenberg.de.
² Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., 51005 Tartu, Estonia Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.
³ Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
⁴ Center for the Biology of Disease, Rega Institute, KU Leuven, 3000, Belgium.
⁵ Department of Biological Sciences, University of Southern California, MC0371, Los Angeles, CA 90089, USA.
⁶ Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, SE-750 07, Uppsala, Sweden.
⁷ Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt, Germany.
⁸ Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., 51005 Tartu, Estonia.
⁹ Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
¹⁰ Institute of Botany and Landscape Ecology, Ernst-Moritz-Arndt University Greifswald, Soldmannstr. 15, Greifswald, D-17487, Germany.
¹¹ Natural History Museum, University of Tartu, 14a Ravila St., 50411 Tartu, Estonia.

PMID: 27358393
DOI: 10.1093/femsre/fuw017

Abstract

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.

Keywords: community ecology; marker gene; microbial diversity; microbial ecology; species interactions; statistical methods.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

Archaea / classification
Archaea / genetics*
Bacteria / classification
Bacteria / genetics*
Biodiversity
Data Interpretation, Statistical
Fungi / classification
Fungi / genetics*
Genetic Markers / genetics*
High-Throughput Nucleotide Sequencing / methods
Microbiota / genetics*
Sequence Analysis, DNA / methods

Substances

Genetic Markers