Periodic Reporting for period 3 - MicroBeeOme (Evolution of the honey bee gut microbiome through bacterial diversification )
Reporting period: 2020-03-01 to 2021-08-31
The current project addresses these questions by studying the gut microbiome of honey bees. We have recently found that the eight dominant bacterial lineages in the honey bee gut have substantially diversified, which is a striking parallelism to the evolution of the mammalian gut microbiome. Moreover, we have established experiments to colonize microbiota-free bees with cultured isolates of divergent bee gut bacteria. This provides us with unique opportunities to study bacterial evolution in the gut in a simple and experimentally amenable system. The project is divided into four work packages addressing interconnected research questions of current biology: We will (i) determine the population genomic landscape of divergent gut bacteria, (ii) investigate whether bacterial diversification has resulted in competition or cooperation, (iii) elucidate mechanisms of bacterial interactions, and (iv) reveal how bacterial diversification impacts the symbiosis with the host. To this end, we are using a multidisciplinary approach combining comparative metagenomics, transcriptomics, metabolomics, bee colonization experiments, microscopy, bacterial genetics, and automated bee tracking. This project situated at the forefront of microbial symbiosis will provide ground-breaking insights into microbial evolution and ecology, gut microbiology, and honey bee health and biology.
In another part of the project, we are using metabolomics studies to investigate functional differences between species and strains to obtain an understanding of the mechanism underlying coexistence. The first results of these experiments have revealed unprecedented insights into the metabolic activities of bacterial species in the honey bee gut. We could not only identify the major bacterial substrates derived from the pollen diet of the host, but also assign them to individual community members. These results have been published in PLoS Biology (Kesnerova et al 2017) and present the basis for strain-level analysis of metabolic activities of the bee gut microbiota and their impact on the host.
The shotgun metagenomics approach does not only allow to look at strain-level diversity across different host populations or honey bee species, but also to test hypothesis under experimental settings, such as in vitro culture or bee colonization experiments. Until the end of the project, we thus expect to obtain results that advance our understanding of the different factors that contribute to the generation and maintenance of strain-level diversity.
The combination of the shotgun metagenomics approaches with other omics methods, such as metabolomics and transcriptomics, and the fact that we can culture all strains in vitro and carry out bee colonizations will allow us to obtain a molecular understanding of the bacterial interactions and their impact on the host, providing unprecedented insights about strain-level diversity in natural microbial communities.