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Rarity of microbial species: In search of reliable associations

The role of microbial interactions in defining the properties of microbiota is a topic of key interest in microbial ecology. Microbiota contain hundreds to thousands of operational taxonomic units (OTUs), most of them rare. This feature of community structure can lead to methodological difficulties:...

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Autores principales: Cougoul, Arnaud, Bailly, Xavier, Vourc’h, Gwenaël, Gasqui, Patrick
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420159/
https://www.ncbi.nlm.nih.gov/pubmed/30875367
http://dx.doi.org/10.1371/journal.pone.0200458
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author Cougoul, Arnaud
Bailly, Xavier
Vourc’h, Gwenaël
Gasqui, Patrick
author_facet Cougoul, Arnaud
Bailly, Xavier
Vourc’h, Gwenaël
Gasqui, Patrick
author_sort Cougoul, Arnaud
collection PubMed
description The role of microbial interactions in defining the properties of microbiota is a topic of key interest in microbial ecology. Microbiota contain hundreds to thousands of operational taxonomic units (OTUs), most of them rare. This feature of community structure can lead to methodological difficulties: simulations have shown that methods for detecting pairwise associations between OTUs, which presumably reflect interactions, yield problematic results. The performance of association detection tools is impaired when there is a high proportion of zeros in OTU tables. Our goal was to understand the impact of OTU rarity on the detection of associations. We explored the utility of common statistics for testing associations; the sensitivity of alternative association measures; and the performance of network inference tools. We found that a large proportion of pairwise associations, especially negative associations, cannot be reliably tested. This constraint could hamper the identification of candidate biological agents that could be used to control rare pathogens. Identifying testable associations could serve as an objective method for filtering datasets in lieu of current empirical approaches. This trimming strategy could significantly reduce the computational time needed to infer networks and network inference quality. Different possibilities for improving the analysis of associations within microbiota are discussed.
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spelling pubmed-64201592019-04-02 Rarity of microbial species: In search of reliable associations Cougoul, Arnaud Bailly, Xavier Vourc’h, Gwenaël Gasqui, Patrick PLoS One Research Article The role of microbial interactions in defining the properties of microbiota is a topic of key interest in microbial ecology. Microbiota contain hundreds to thousands of operational taxonomic units (OTUs), most of them rare. This feature of community structure can lead to methodological difficulties: simulations have shown that methods for detecting pairwise associations between OTUs, which presumably reflect interactions, yield problematic results. The performance of association detection tools is impaired when there is a high proportion of zeros in OTU tables. Our goal was to understand the impact of OTU rarity on the detection of associations. We explored the utility of common statistics for testing associations; the sensitivity of alternative association measures; and the performance of network inference tools. We found that a large proportion of pairwise associations, especially negative associations, cannot be reliably tested. This constraint could hamper the identification of candidate biological agents that could be used to control rare pathogens. Identifying testable associations could serve as an objective method for filtering datasets in lieu of current empirical approaches. This trimming strategy could significantly reduce the computational time needed to infer networks and network inference quality. Different possibilities for improving the analysis of associations within microbiota are discussed. Public Library of Science 2019-03-15 /pmc/articles/PMC6420159/ /pubmed/30875367 http://dx.doi.org/10.1371/journal.pone.0200458 Text en © 2019 Cougoul et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Cougoul, Arnaud
Bailly, Xavier
Vourc’h, Gwenaël
Gasqui, Patrick
Rarity of microbial species: In search of reliable associations
title Rarity of microbial species: In search of reliable associations
title_full Rarity of microbial species: In search of reliable associations
title_fullStr Rarity of microbial species: In search of reliable associations
title_full_unstemmed Rarity of microbial species: In search of reliable associations
title_short Rarity of microbial species: In search of reliable associations
title_sort rarity of microbial species: in search of reliable associations
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420159/
https://www.ncbi.nlm.nih.gov/pubmed/30875367
http://dx.doi.org/10.1371/journal.pone.0200458
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