Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community

Abstract

A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.

Emergent survival and extinction of species within gut bacterial communities

“…The stabilisation in four transfers we observed under defined media is consistent with those observed in complex, undefined growth media 7–9,23 . However, stabilisation in taxonomic composition may not reflect functional stabilisation since composition does not capture potential shifts in metabolic activities of species and community.…”

“…While discerning between these two sources is difficult in in vivo settings where available nutrients reaching the community are hard to track, in vitro synthetic communities provide a tractable approach to delineate the contribution of the biotic supply. Previous work has shown that synthetic gut bacterial communities can be readily assembled through serial dilution and remain stable over multiple transfers 7–9 . However, these communities were assembled in undefined growth media obscuring the relation between specific nutrient components and community composition.…”

OneNet – One network to rule them all: consensus network inference from microbiome data

“…Most taxa from the the cirrhotic guild were either not present in the “healthy individuals”-network (as they didn’t pass the prevalence threshold in the healthy individuals dataset) or had much fewer interactions and were not included in a guild. Overall, this suggests that the interactions identified between the cirrhotic species are context-dependent, a finding that has already been documented in other contexts Weiss et al [2023] and K. Faust [2021].…”

Advances in Culturomics Research on the Human Gut Microbiome: Optimizing Medium Composition and Culture Techniques for Enhanced Microbial Discovery

“…Meeting the nutritional and environmental needs of microorganisms requires thoughtful selection of medium components such as carbohydrates, nitrogen compounds, vitamins, and minerals [ 29 , 30 ]. For example, carbohydrates act as energy sources, while nitrogen compounds are fundamental for protein metabolism.…”