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In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis

Network analysis of large metagenomic datasets generated by current sequencing technologies can reveal significant co-occurrence patterns between microbial species of a biological community. These patterns can be analyzed in terms of pairwise combinations between all species comprising a community....

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Autores principales: Das, Promi, Ji, Boyang, Kovatcheva-Datchary, Petia, Bäckhed, Fredrik, Nielsen, Jens
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5877883/
https://www.ncbi.nlm.nih.gov/pubmed/29601608
http://dx.doi.org/10.1371/journal.pone.0195161
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author Das, Promi
Ji, Boyang
Kovatcheva-Datchary, Petia
Bäckhed, Fredrik
Nielsen, Jens
author_facet Das, Promi
Ji, Boyang
Kovatcheva-Datchary, Petia
Bäckhed, Fredrik
Nielsen, Jens
author_sort Das, Promi
collection PubMed
description Network analysis of large metagenomic datasets generated by current sequencing technologies can reveal significant co-occurrence patterns between microbial species of a biological community. These patterns can be analyzed in terms of pairwise combinations between all species comprising a community. Here, we construct a co-occurrence network for abundant microbial species encompassing the three dominant phyla found in human gut. This was followed by an in vitro evaluation of the predicted microbe-microbe co-occurrences, where we chose species pairs Bifidobacterium adolescentis and Bacteroides thetaiotaomicron, as well as Faecalibacterium prausnitzii and Roseburia inulinivorans as model organisms for our study. We then delineate the outcome of the co-cultures when equal distributions of resources were provided. The growth behavior of the co-culture was found to be dependent on the types of microbial species present, their specific metabolic activities, and resulting changes in the culture environment. Through this reductionist approach and using novel in vitro combinations of microbial species under anaerobic conditions, the results of this work will aid in the understanding and design of synthetic community formulations.
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spelling pubmed-58778832018-04-13 In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis Das, Promi Ji, Boyang Kovatcheva-Datchary, Petia Bäckhed, Fredrik Nielsen, Jens PLoS One Research Article Network analysis of large metagenomic datasets generated by current sequencing technologies can reveal significant co-occurrence patterns between microbial species of a biological community. These patterns can be analyzed in terms of pairwise combinations between all species comprising a community. Here, we construct a co-occurrence network for abundant microbial species encompassing the three dominant phyla found in human gut. This was followed by an in vitro evaluation of the predicted microbe-microbe co-occurrences, where we chose species pairs Bifidobacterium adolescentis and Bacteroides thetaiotaomicron, as well as Faecalibacterium prausnitzii and Roseburia inulinivorans as model organisms for our study. We then delineate the outcome of the co-cultures when equal distributions of resources were provided. The growth behavior of the co-culture was found to be dependent on the types of microbial species present, their specific metabolic activities, and resulting changes in the culture environment. Through this reductionist approach and using novel in vitro combinations of microbial species under anaerobic conditions, the results of this work will aid in the understanding and design of synthetic community formulations. Public Library of Science 2018-03-30 /pmc/articles/PMC5877883/ /pubmed/29601608 http://dx.doi.org/10.1371/journal.pone.0195161 Text en © 2018 Das 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
Das, Promi
Ji, Boyang
Kovatcheva-Datchary, Petia
Bäckhed, Fredrik
Nielsen, Jens
In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
title In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
title_full In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
title_fullStr In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
title_full_unstemmed In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
title_short In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
title_sort in vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5877883/
https://www.ncbi.nlm.nih.gov/pubmed/29601608
http://dx.doi.org/10.1371/journal.pone.0195161
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