Analysis of the global genetic requirements and gene expression changes in E. coli in the presence of a simple microbiome revealed pairwise and higher-order interactions, and underlying molecular mechanisms.
Simulations and experiments on systems containing two different populations of microorganisms show that interactions that benefit at least one of the populations can lead to communities with stable compositions, and that strong cooperation between two populations can lead to communities in which both populations are mixed together.
A novel computation tool for microbial community modeling predicts the evolution and diversification of E. coli in laboratory evolution experiments and gives insight into the underlying metabolic processes.
Experiments in ex-germ-free mice establish a measurable effect of colonization history on gut microbiota assembly, illuminating a potential cause for the high levels of unexplained individuality in host-associated microbial communities.
Multistability and regime shifts are common and species diversity is high in microbial communities when nutrient supplies are balanced and competing species have different stoichiometries of essential nutrients.