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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.

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