Skip to main content

Social Interactions in Microbes

Final Report Summary - INTERACTINGMICROBES (Social Interactions in Microbes)

Microorganisms affect almost every aspect of our lives. They live on, in and around us and can affect us is both positive and negative ways. On the positive side, microbes live in our gut and help us to digest food, they break down our waste and they provide a wide range of industrial functions to produce foods like bread and yogurt. Where microbes live, they commonly live in dense communities that contain many genetically different species and strains. However, the typical methods in microbiology study a single genotype in isolation. The central hypothesis underlying our ERC grant is that genetic diversity in microbial groups has strong interactive effects on cells that cannot be understood by studying genotypes in isolation. The project had three aims that tests this hypothesis at the three different levels of genetic diversity found in natural cellular groups and communities.

Objective 1: The effect of mutational diversity on cellular groups. We combined evolutionary logic with computational models of microbial groups to investigate the effect of genetic diversity on microbial groups. This predicts that genetic diversity will generate competition among strains that affects many microbial traits. We established two highly-tractable empirical systems to test these predictions, polymer production in the bacterium Pseudomonas fluorescens, and aggregation behaviour in the yeast Saccharomyces cerevisiae.

Objective 2: The effect of strain diversity on cellular groups. In natural systems, including infections, microbes commonly mix with other strains of their species. However, the effects of this diversity are poorly understood. We developed a set of assays to investigate the effects of strain and species mixing centred upon Pseudomonas aeruginosa; a pathogenic bacterium that commonly infects people in hospitals, where it is associated with patient mortality. Our approach combines basic microbiology with genomics to characterize the mechanisms underlying the responses of P. aeruginosa strains to one another. We discovered a diverse range of strong responses of one strain to other strains, including increase biofilm formation, which are consistent with bacteria evolving to upregulate both attack and defence upon detection of other strains.

Objective 3: The effect of species diversity on cellular communities. At their most diverse, microbial groups can contain hundreds of different species that interact in a complex ecological network. Again, the effects of this diversity are currently very poorly understood. We have dissected this complexity in two ways. Firstly, we have published a new body of theory and a conceptual framework for understanding interactions between species. In addition, we have studied empirically how species interact with one another in laboratory experiments. This work revealed that ecological competition is the typical outcome of interactions between different microbial species and it offers new insights on how we might engineer microbial communities for our own advantage.