title: Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.
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.
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt, Germany mbalint@senckenberg.de.
authors.forename: Miklós
authors.initials: M
authors.lastname: Bálint
authors.affiliation: 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.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Bahram
authors.affiliation: 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.
authors.forename: A Murat
authors.initials: AM
authors.lastname: Eren
authors.affiliation: Center for the Biology of Disease, Rega Institute, KU Leuven, 3000, Belgium.
authors.forename: Karoline
authors.initials: K
authors.lastname: Faust
authors.affiliation: Department of Biological Sciences, University of Southern California, MC0371, Los Angeles, CA 90089, USA.
authors.forename: Jed A
authors.initials: JA
authors.lastname: Fuhrman
authors.affiliation: Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, SE-750 07, Uppsala, Sweden.
authors.forename: Björn
authors.initials: B
authors.lastname: Lindahl
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt, Germany.
authors.forename: Robert B
authors.initials: RB
authors.lastname: O'Hara
authors.affiliation: Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., 51005 Tartu, Estonia.
authors.forename: Maarja
authors.initials: M
authors.lastname: Öpik
authors.affiliation: Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
authors.forename: Mitchell L
authors.initials: ML
authors.lastname: Sogin
authors.affiliation: Institute of Botany and Landscape Ecology, Ernst-Moritz-Arndt University Greifswald, Soldmannstr. 15, Greifswald, D-17487, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Unterseher
authors.affiliation: Natural History Museum, University of Tartu, 14a Ravila St., 50411 Tartu, Estonia.
authors.forename: Leho
authors.initials: L
authors.lastname: Tedersoo
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics*; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D044822:Biodiversity; D003627:Data Interpretation, Statistical; D005658:Fungi / Q000145:classification / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D064307:Microbiota / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D005819:Genetic Markers
keywords: community ecology; marker gene; microbial diversity; microbial ecology; species interactions; statistical methods