In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
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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.
In: PLOS ONE, Vol. 13, No. 3, e0195161, 2018, p. 1-14.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
AU - Das, Promi
AU - Ji, Boyang
AU - Kovatcheva-Datchary, Petia
AU - Bäckhed, Fredrik
AU - Nielsen, Jens
PY - 2018
Y1 - 2018
N2 - 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.
AB - 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.
KW - Bacteria/genetics
KW - Coculture Techniques
KW - Gastrointestinal Microbiome
KW - Humans
U2 - 10.1371/journal.pone.0195161
DO - 10.1371/journal.pone.0195161
M3 - Journal article
C2 - 29601608
VL - 13
SP - 1
EP - 14
JO - PLoS ONE
JF - PLoS ONE
SN - 1932-6203
IS - 3
M1 - e0195161
ER -
ID: 209358170