Exploring the interaction network of a synthetic gut bacterial community

Abstract

A key challenge in microbiome research is to predict functionality from microbial community composition. 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 growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM12) synthetic bacterial community, which is increasingly used as 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. Metabolomics analysis of spent culture supernatant of individual strains in combination with genome-informed pathway reconstruction provided insights into the metabolic potential 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 particular, Enterococcus faecalis KB1 was identified as important driver of community composition by affecting the abundance of several other consortium members. Together, this study gives fundamental insight into key drivers and mechanistic basis of the OMM12 interaction network, which serves as knowledge base for future mechanistic studies.

Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions

“…Physical separation is useful to study uncharacterized isolates; however, it precludes the detection of contact-dependent interactions. In the second approach, a relative abundance estimate can be obtained by microbial community profiling methods such as high-throughput sequencing ( Pishchany et al, 2018 ; Blasche et al, 2021 ), combined to a compound measure of absolute abundance [Optical density ( Venturelli et al, 2018 ), quantitative polymerase chain reaction (qPCR; Medlock et al, 2018 ; Weiss et al, 2021 ), total plate counts ( Cosetta et al, 2020 ), etc.] or a spiked-in quantification standard ( Blasche et al, 2021 ).…”

Metabolic reconstitution by a gnotobiotic microbiota varies over the circadian cycle

“…A widely used example, the OligoMM12, is a gnotobiotic consortium of 12 cultivable mouse-derived strains representing the major five bacterial phyla in the murine gut (Brugiroux et al, 2016). It is reproducible between facilities (Eberl et al, 2020) and extensive data now exists on the metabolism of individual species and their interactions with each other and the host (Streidl et al, 2021;Weiss et al, 2021;Wotzka et al, 2019;Yilmaz et al, 2021). However, working with these mice involves hygiene conditions similar to those required to work with germfree mice, which poses a technical challenge for the long-term analysis of mouse metabolism.…”

Hierarchical control of microbial community assembly

“…Microbial communities mediate a staggering number of biological processes that contribute to the health of humans, animals 1 and the planet as a whole 2 . The metabolic activity of co-occurring species results in the formation and depletion of nutrients in shared resource pools, where different modes of competition and cooperation impact community composition and form a network of metabolic crossfeeding 3,4,[13][14][15][16][17][18][19][20][21][22]5,23,24,[6][7][8][9][10][11][12] . Individual species often provide specific metabolic functions that influence the growth of a broader community, including use of terminal electron acceptors 14,25,26 , degradation of complex carbon sources [27][28][29][30] , removal of toxic byproducts [31][32][33] , or assimilation of nitrogen and sulfur 18,[34][35][36] .…”