The human gut microbiome harbors astronomical quantities of genetic diversity across evolutionarily distant species. However, it is becoming increasingly apparent that not all contributors towards said diversity are subject to evolutionary dynamics. Rather, genetic variants can be present in a host due to the co-occurrence of multiple genetically diverged lineages of a given species, a form of...
How ecological interactions can shape community assembly and maintenance is of particular interest for microbial communities, which are generically highly diverse, and where even closely related strains can have distinct ecologies. Statistical physics offers mathematical tools to deal with the complexity of diverse communities. In recent years, considerable progress has been made in the study...
Microbiomes provide key ecological functions to their host; however, most host-associated microbiomes are too complicated to allow a model of essential host-microbe-microbe interactions. The intestinal microbiota of salmonids may offer a solution since it is often characterized by few dominating species. Healthy fish coexist with a mutualistic Mycoplasma sp. species, while stress allows the...
The immense diversity observed in natural microbial communities is surprising in light of the competitive exclusion principle and the numerous weapons microbes have evolved to inhibit each other's growth. In this work, we study patterns of antibiotic-mediated interactions between microbes using classical models from theoretical ecology. Building on previous work, we analyse the ecological...
The existence of an Evolutionarily Stable State (ESS) in a host-symbiont interaction at ecologically stable coexistence is studied in the framework of eco-evolutionary dynamics. Our basic objective is to obtain an evolutionary insight into the transmission behaviour of symbionts (which can be either parasitic or mutualistic depending on effects on mortality and fecundity) which are obligate...
Marine phytoplankton is composed of unicellular algae and their associated bacteria. These algal communities are highly variable in species composition, but their patterns tend to recur seasonally. This diversity suggests the existence of ecological niches for the associated bacteria. To clarify the role of the bacterial community on the phytoplankton, we co-cultured several bacterial species...
Commensal bacteria are also often major opportunistic pathogens with important public health consequences. For example, Escherichia coli colonises the gut of all humans and occasionally causes intestinal and extra-intestinal infections responsible for ~1M deaths worldwide each year. The colonization of hosts by E. coli is a highly dynamical process with strain turnover in the gut over...
Habitat degradation, including the change of natural habitats into agricultural areas, alters natural communities all over the world. Land-use change may affect the host and its microbiome composition and structure, thus influencing the host's function and health, and the potential transmission and spread of microbes and disease. However, the relative effect of land-use change in shaping the...
