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

Miklós Bálint, Mohammad Bahram, A Murat Eren, Karoline Faust, JA. Fuhrman, Björn Lindahl, Robert B O'Hara, Maarja Öpik, Mitchell L Sogin, Martin Unterseher, Leho Tedersoo, K. Abarenkov, L. Tedersoo, RH. Nilsson, TD. Ainsworth, L. Krause, T. Bridge, J. Aitchison, AS. Amend, KA. SeifertTD. Bruns, MJ. Anderson, MJ. Anderson, MJ. Anderson, DCI. Walsh, A. Antoninka, JE. Wolf, M. Bowker, KE. Ashelford, NA. Chuzhanova, JC. Fry, M. Bálint, L. Bartha, RB. O'Hara, M. Bálint, P-A. Schmidt, R. Sharma, Y. Ban, L. An, H. Jiang, A. Baselga, A. Baselga, CDL. Orme, HM. Bik, D. Fournier, W. Sung, DY. Kim, J. Chang, S-H. Hong, J-C. Cho

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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.
Original languageEnglish
Pages (from-to)189-96
Number of pages8
JournalFEMS Microbiology Reviews
Volume6
Issue number24
DOIs
Publication statusPublished - 2016

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Bálint, M., Bahram, M., Eren, A. M., Faust, K., Fuhrman, JA., Lindahl, B., O'Hara, R. B., Öpik, M., Sogin, M. L., Unterseher, M., Tedersoo, L., Abarenkov, K., Tedersoo, L., Nilsson, RH., Ainsworth, TD., Krause, L., Bridge, T., Aitchison, J., Amend, AS., ... Cho, J-C. (2016). Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiology Reviews, 6(24), 189-96. https://doi.org/10.1093/femsre/fuw017