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, Miklós ; Bahram, Mohammad ; Eren, A Murat ; Faust, Karoline ; Fuhrman, JA. ; Lindahl, Björn ; O'Hara, Robert B ; Öpik, Maarja ; Sogin, Mitchell L ; Unterseher, Martin ; Tedersoo, Leho ; Abarenkov, K. ; Tedersoo, L. ; Nilsson, RH. ; Ainsworth, TD. ; Krause, L. ; Bridge, T. ; Aitchison, J. ; Amend, AS. ; Seifert, KA. ; Bruns, TD. ; Anderson, MJ. ; Anderson, MJ. ; Anderson, MJ. ; Walsh, DCI. ; Antoninka, A. ; Wolf, JE. ; Bowker, M. ; Ashelford, KE. ; Chuzhanova, NA. ; Fry, JC. ; Bálint, M. ; Bartha, L. ; O'Hara, RB. ; Bálint, M. ; Schmidt, P-A. ; Sharma, R. ; Ban, Y. ; An, L. ; Jiang, H. ; Baselga, A. ; Baselga, A. ; Orme, CDL. ; Bik, HM. ; Fournier, D. ; Sung, W. ; Kim, DY. ; Chang, J. ; Hong, S-H. ; Cho, J-C. / Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. In: FEMS Microbiology Reviews. 2016 ; Vol. 6, No. 24. pp. 189-96.
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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.",
author = "Mikl{\'o}s B{\'a}lint and Mohammad Bahram and Eren, {A Murat} and Karoline Faust and JA. Fuhrman and Bj{\"o}rn Lindahl and O'Hara, {Robert B} and Maarja {\"O}pik and Sogin, {Mitchell L} and Martin Unterseher and Leho Tedersoo and K. Abarenkov and L. Tedersoo and RH. Nilsson and TD. Ainsworth and L. Krause and T. Bridge and J. Aitchison and AS. Amend and KA. Seifert and TD. Bruns and MJ. Anderson and MJ. Anderson and MJ. Anderson and DCI. Walsh and A. Antoninka and JE. Wolf and M. Bowker and KE. Ashelford and NA. Chuzhanova and JC. Fry and M. B{\'a}lint and L. Bartha and RB. O'Hara and M. B{\'a}lint and P-A. Schmidt and R. Sharma and Y. Ban and L. An and H. Jiang and A. Baselga and A. Baselga and CDL. Orme and HM. Bik and D. Fournier and W. Sung and DY. Kim and J. Chang and S-H. Hong and J-C. Cho",
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Bálint, M, Bahram, M, Eren, AM, Faust, K, Fuhrman, JA, Lindahl, B, O'Hara, RB, Öpik, M, Sogin, ML, Unterseher, M, Tedersoo, L, Abarenkov, K, Tedersoo, L, Nilsson, RH, Ainsworth, TD, Krause, L, Bridge, T, Aitchison, J, Amend, AS, Seifert, KA, Bruns, TD, Anderson, MJ, Anderson, MJ, Anderson, MJ, Walsh, DCI, Antoninka, A, Wolf, JE, Bowker, M, Ashelford, KE, Chuzhanova, NA, Fry, JC, Bálint, M, Bartha, L, O'Hara, RB, Bálint, M, Schmidt, P-A, Sharma, R, Ban, Y, An, L, Jiang, H, Baselga, A, Baselga, A, Orme, CDL, Bik, HM, Fournier, D, Sung, W, Kim, DY, Chang, J, Hong, S-H & Cho, J-C 2016, 'Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.', FEMS Microbiology Reviews, vol. 6, no. 24, pp. 189-96. https://doi.org/10.1093/femsre/fuw017

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

In: FEMS Microbiology Reviews, Vol. 6, No. 24, 2016, p. 189-96.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.

AU - Bálint, Miklós

AU - Bahram, Mohammad

AU - Eren, A Murat

AU - Faust, Karoline

AU - Fuhrman, JA.

AU - Lindahl, Björn

AU - O'Hara, Robert B

AU - Öpik, Maarja

AU - Sogin, Mitchell L

AU - Unterseher, Martin

AU - Tedersoo, Leho

AU - Abarenkov, K.

AU - Tedersoo, L.

AU - Nilsson, RH.

AU - Ainsworth, TD.

AU - Krause, L.

AU - Bridge, T.

AU - Aitchison, J.

AU - Amend, AS.

AU - Seifert, KA.

AU - Bruns, TD.

AU - Anderson, MJ.

AU - Anderson, MJ.

AU - Anderson, MJ.

AU - Walsh, DCI.

AU - Antoninka, A.

AU - Wolf, JE.

AU - Bowker, M.

AU - Ashelford, KE.

AU - Chuzhanova, NA.

AU - Fry, JC.

AU - Bálint, M.

AU - Bartha, L.

AU - O'Hara, RB.

AU - Bálint, M.

AU - Schmidt, P-A.

AU - Sharma, R.

AU - Ban, Y.

AU - An, L.

AU - Jiang, H.

AU - Baselga, A.

AU - Baselga, A.

AU - Orme, CDL.

AU - Bik, HM.

AU - Fournier, D.

AU - Sung, W.

AU - Kim, DY.

AU - Chang, J.

AU - Hong, S-H.

AU - Cho, J-C.

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

U2 - 10.1093/femsre/fuw017

DO - 10.1093/femsre/fuw017

M3 - Article

C2 - 27358393

VL - 6

SP - 189

EP - 196

JO - FEMS Microbiology Reviews

JF - FEMS Microbiology Reviews

SN - 0168-6445

IS - 24

ER -