Abstract
A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM12) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM12 interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM12 interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.
Highlights
The mammalian gastrointestinal tract harbors hundreds of bacterial species that occupy distinct ecological niches [1, 2]
Strains were grouped by growth rate (GR) into fast growing strains (GR > 1.5 h–1, E. faecalis KB1, B. animalis YL2, C. innocuum I46 and B. coccoides YL58), strains with intermediate growth rate
To probe overlap in substrate requirements and interactions between the individual OMM12 members mediated by waste products or bacteriocins, sterile spent culture medium (SM) after growth to late stationary phase of all strains was obtained
Summary
The mammalian gastrointestinal tract harbors hundreds of bacterial species that occupy distinct ecological niches [1, 2]. Diversity and stable coexistence of community members after initial assembly result in the exclusion of invaders [3, 4]. Community assembly and stability are inherently driven by commensal or cooperative trophic interactions, in which metabolic by- or end products of one species are the resources for another one [5,6,7]. Bacteria compete for substrates by employing diverse predatory mechanisms, like the production of bacteriocins [8]. These interaction patterns form complex ecological networks and determine community-level functions of the microbiota including dietary breakdown, metabolite production, and colonization resistance [9,10,11]. To be able to predict, preserve and manipulate microbial community function, it is important to identify functionally important members and understand relevant interaction mechanisms between individual bacteria
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