Disturbances and Interactions in Microbial Communities

Abstract

Bacteria rarely exist in isolation in nature but instead form complex, multispecies communities in which interactions between members shape ecosystems and host health. Defined microbial communities, assembled from a known set of species, can be used to experimentally dissect these interactions while maintaining a controlled community context. The gastric microbiota provides a relevant system for studying microbial interactions, particularly in the context of Helicobacter pylori and its role in gastric disease. In this thesis, a defined gastric microbial community comprising H. pylori, Escherichia coli, Pseudomonas aeruginosa, Streptococcus salivarius, and Lactobacillus kalixensis was established under chemically defined conditions. Pairwise analyses revealed predominantly negative effects on H. pylori and strong support of L. kalixensis by co-culture (Paper I). A statistical framework subsequently revealed higher-order effects that could not be predicted from pairwise interactions, including mitigation of negative pairwise interactions targeting H. pylori (Paper II). The defined gastric community was further used to investigate responses to external perturbations. Exposure to non-antibiotic pharmaceuticals (Paper III) and antibiotics (Paper IV) showed that community context can alter bacterial responses to drug exposure, with the community providing greater protection against some treatments than what was observed in monoculture. For non-antibiotic pharmaceuticals, this protection was concentration-dependent and diminished above a threshold concentration. In complementary work, milk oligosaccharides were investigated for their effects on biofilm formation by individual bacterial species and found to have previously unknown anti-biofilm effects (Paper V). Together, these studies demonstrate that microbial interactions are shaped by community context and can influence responses to external perturbations, highlighting the value of defined communities for experimentally dissecting microbial ecology.