WP1: To test the ability of microbes to evolve more rapidly than host-encoded resistance against parasites
Defensive microbial symbionts provide hosts with evolvable protection against pathogens. In these networks, hosts and defensive symbionts can encounter a diversity of eco-evolutionary contexts imposed by pathogens. When under attack from coevolving pathogens, will hosts rely on symbionts or in their own defence mechanisms? In turn, how will coevolving pathogens shape the evolutionary trajectories of defensive symbiont populations? After evolving worm hosts (Caenorhabditis elegans) and and their good/bad microbes altogether, we found evidence of host dependence and pathogen virulence emerging under network evolution. The study provides the first insight into how eco-evolutionary complexity shapes fitness and diversity in a community of hosts, defensive symbionts & pathogens. This research is currently still in the publication pipeline. A related computational meta-analysis across the tree of symbiotic life has shown that the degree of both protection and cost scales positively with symbiont density, suggesting there is selection for hosts to regulate symbiont densities (published in American Naturalist in 2022).
WP2: To uncover the impacts of evolving protective microbes on host-parasite coevolution
We conducted an evolution experiment involving co-passaged populations of nematode hosts and pathogens when hosts were colonized (or not) by defensive bacteria. As published in Current Biology in 2022, we found that microbial protection during coevolution drove patterns of host tolerance and in parasites adapting to microbial defenses. At the genomic level, we found parasite populations had diverged between protected and unprotected hosts.
WP3: To test whether and how parasite heterogeneity affects host-protective microbe coevolution
We experimentally coevolved populations of worm hosts with protective bacteria in treatments varying the infection frequency with pathogens. In a study published in Ecology and Evolution in 2020, we found that when nfection varied every host generation, alternating host generations, every fifth host generation, or never. Our results showed that enhanced microbe-mediated protection evolved under all conditions when the pathogen was present, even rarely. Our results suggest that resident microbes can be a form of transgenerational immunity against rare pathogen infection.
WP4: To test whether and how host microbiota shapes host-protective microbe coevolution
Pathogens newly invading a host must compete with resident microbiota. Within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. In a study published in ISME J in 2025, we experimentally evolved pathogens and a native microbiota community in worm hosts to show that a competitively superior pathogen displaced microbiota and reduced species richness. However, its virulence was maintained across generations. Whole genome sequencing revealed shifts in the mode of selection with competitive interactions driving early diversification among pathogen populations. This work reveals how microbial competition during emerging infection determines the patterns and processes of evolution with major consequences for host health. As an extension of this research, we conducted transcriptomic analyses of worms colonised by its native microbiota and pathogens (pub in Molecular Ecology in 2025) exploring the impact of 're-wilding' a model animal with native microbiome on immunological patterns.
