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.This is an overview 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 high-throughput sequencing of marker genes.This is an overview 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 high-throughput sequencing of marker genes.

Keywords

marker gene; community ecology; microbial ecology; microbial diversity; species interactions; statistical methods

Published in

FEMS Microbiology Reviews
2016, Volume: 40, number: 5, pages: 686-700 Publisher: OXFORD UNIV PRESS

SLU Authors

• Lindahl, Björn

  • Department of Soil and Environment, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Microbiology
Ecology


Publication identifier

DOI: https://doi.org/10.1093/femsre/fuw017

Permanent link to this page (URI)

https://res.slu.se/id/publ/79922