BEE_GEMS · Genetic factors Enabling Microbiome Symbioses: Bees as a natural model system

The gut microbiome is essential for the wellbeing of many animals including humans and bees. However, the genetic factors that enable stable, healthy microbiomes remain poorly understood. In particular, little is known about how different members of a gut microbial community communicate and interact with one another, both at the molecular level (which genes underlie the interactions) and the ecological level (how these genes are distributed across populations). Due to the complexity of most gut microbiomes, previous work in this field has largely been limited to in vitro studies using simplified, synthetic communities. In contrast, the core aim of this project is a systematic analysis of microbial interaction mechanisms at both the molecular and ecological levels. Unlike other systems, we can culture all members of the bee gut microbiome and have recently developed genetic tools for their manipulation. I will leverage these unique advantages, together with my expertise in social bees (honey bees, bumble bees) and microbial genetics, in an integrative approach to fulfil the project objectives. Work Package 1 will reveal the genes underlying pairwise intermicrobial interactions though unbiased in vitro and in vivo transcriptomics and proteomics. These genes, together with candidates I previously identified (secretion systems and toxin genes), will be investigated in detail using genetic and biochemical methods to uncover their mechanisms of action and novel functions. Work Package 2 will clarify how these interactions play out across populations by assessing variation of interaction genes with ecological factors (geography, host background), and by probing the evolutionary forces that lead to these variations. Our findings will contribute empirically to identifying the general principles behind microbiome assembly and function, which has broad implications across all fields where microbiomes play important roles including in agriculture, medicine, and biotechnology.