Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes
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...
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| Veröffentlicht in: | FEMS microbiology reviews 2016-09, Vol.40 (5), p.686-700 |
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| creator | Bálint, Miklós Bahram, Mohammad Eren, A. Murat Faust, Karoline Fuhrman, Jed A. Lindahl, Björn O'Hara, Robert B. Öpik, Maarja Sogin, Mitchell L. Unterseher, Martin Tedersoo, Leho |
| description | 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.
Graphical Abstract Figure.
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. |
| doi_str_mv | 10.1093/femsre/fuw017 |
| format | Article |
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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.
Graphical Abstract Figure.
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.</description><identifier>ISSN: 1574-6976</identifier><identifier>ISSN: 0168-6445</identifier><identifier>EISSN: 1574-6976</identifier><identifier>DOI: 10.1093/femsre/fuw017</identifier><identifier>PMID: 27358393</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Archaea - classification ; Archaea - genetics ; Bacteria - classification ; Bacteria - genetics ; Biodiversity ; community ecology ; Data Interpretation, Statistical ; Ecology ; Ekologi ; Fungi - classification ; Fungi - genetics ; Genetic Markers - genetics ; High-Throughput Nucleotide Sequencing - methods ; marker gene ; microbial diversity ; microbial ecology ; Microbiology ; Microbiota - genetics ; Mikrobiologi ; Sequence Analysis, DNA - methods ; species interactions ; statistical methods</subject><ispartof>FEMS microbiology reviews, 2016-09, Vol.40 (5), p.686-700</ispartof><rights>FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2016</rights><rights>FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c436t-c11ea9a218ab52057db69ad5dc3b896d248758745c60d87dd8b1c47e90bf307d3</citedby><cites>FETCH-LOGICAL-c436t-c11ea9a218ab52057db69ad5dc3b896d248758745c60d87dd8b1c47e90bf307d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,1598,27901,27902</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/femsre/fuw017$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27358393$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297240$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttps://res.slu.se/id/publ/79922$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Bálint, Miklós</creatorcontrib><creatorcontrib>Bahram, Mohammad</creatorcontrib><creatorcontrib>Eren, A. Murat</creatorcontrib><creatorcontrib>Faust, Karoline</creatorcontrib><creatorcontrib>Fuhrman, Jed A.</creatorcontrib><creatorcontrib>Lindahl, Björn</creatorcontrib><creatorcontrib>O'Hara, Robert B.</creatorcontrib><creatorcontrib>Öpik, Maarja</creatorcontrib><creatorcontrib>Sogin, Mitchell L.</creatorcontrib><creatorcontrib>Unterseher, Martin</creatorcontrib><creatorcontrib>Tedersoo, Leho</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><title>Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes</title><title>FEMS microbiology reviews</title><addtitle>FEMS Microbiol Rev</addtitle><description>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.
Graphical Abstract Figure.
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.</description><subject>Archaea - classification</subject><subject>Archaea - genetics</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Biodiversity</subject><subject>community ecology</subject><subject>Data Interpretation, Statistical</subject><subject>Ecology</subject><subject>Ekologi</subject><subject>Fungi - classification</subject><subject>Fungi - genetics</subject><subject>Genetic Markers - genetics</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>marker gene</subject><subject>microbial diversity</subject><subject>microbial ecology</subject><subject>Microbiology</subject><subject>Microbiota - genetics</subject><subject>Mikrobiologi</subject><subject>Sequence Analysis, DNA - methods</subject><subject>species interactions</subject><subject>statistical methods</subject><issn>1574-6976</issn><issn>0168-6445</issn><issn>1574-6976</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc1PFjEQhxuikQ89ciU9emCl3W63W28ERE0wXsBrM21nsbK7fW23wOtf78KL4MV4msnkyW8m8xCyz9k7zrQ46nHMCY_6csu42iI7XKqmarVqX_zVb5PdnH8wxqSW8hXZrpWQndBih0xfwjCEOGUae5oQfD6k8_dYMkz-YTbDHbynY3Ap2gADdXEcyxTmNc1zKm4uCenCUsg5ugDzQxZMMKx_oac3AegI6RoTvcIJ82vysoch45vHukcuzz5cnHyqzr9-_HxyfF65RrRz5ThH0FDzDqysmVTethq89E7YTre-bjolO9VI1zLfKe87y12jUDPbC6a82CPVJjff4qpYs0phOWNtIgSTh2Ih3ReT0Sit63rhD__Jn4ZvxyamK1OKqbWqG7bgbzf4KsWfBfNsxpAdDgNMuPzO8I63rRCM6-dLlgfmxVT_lM2ZuTdoNgbNxuDCHzxGFzuif6L_KHveHcvqP1m_AYWrqio</recordid><startdate>20160901</startdate><enddate>20160901</enddate><creator>Bálint, Miklós</creator><creator>Bahram, Mohammad</creator><creator>Eren, A. 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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.
Graphical Abstract Figure.
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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>27358393</pmid><doi>10.1093/femsre/fuw017</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | FEMS microbiology reviews, 2016-09, Vol.40 (5), p.686-700 |
| issn | 1574-6976 0168-6445 1574-6976 |
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| source | Oxford Journals Open Access Collection |
| subjects | Archaea - classification Archaea - genetics Bacteria - classification Bacteria - genetics Biodiversity community ecology Data Interpretation, Statistical Ecology Ekologi Fungi - classification Fungi - genetics Genetic Markers - genetics High-Throughput Nucleotide Sequencing - methods marker gene microbial diversity microbial ecology Microbiology Microbiota - genetics Mikrobiologi Sequence Analysis, DNA - methods species interactions statistical methods |
| title | Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes |
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