Our lab studies functional and evolutionary aspects of microbial symbiosis focusing on the gut microbiota of honey bees and related social bee species. We address general questions of gut microbiology and aim to understand the role of the microbiota for bee health. Recently, we have also started to work on the human microbiota in collaboration with other groups.

Evolutionary and functional basis of coexistence in the gut microbiota (ERC-StG ‘MicroBeeOme’)

Microbial communities residing in animal guts are dominated by specialist bacteria that have adapted to live in these environment for millions of years (Moeller et al. 2016, Kwong et al. 2017, Ley et al. 2008). Yet, gut communities harbor an immense microbial diversity with closely related strains being able to coexist. We want to understand how gut communities are structured at the level of individual strains, which type of symbiotic interactions govern their coexistence and what are the underlying mechanisms. Focusing on the bee gut microbiota allows us to study a small number of bacterial lineages that have co-evolved with each other for >80 million years in the context of a relevant host organism. We use comparative genomics and metagenomics to understand how individual strains and specific functions are distributed in the host population. This allow us to understand diversification process in gut communities and identify the evolutionary driving forces. Findings from these analyses present the basis for experimental investigations. Our research profits from the fact that the bee microbiota is experimentally tractable: All community members can be cultured and gnotobiotic bee models have been established. We use these experimental tools in conjunction with transcriptomics, metabolomics, and bacterial genetics to study mechanisms underlying microbial symbiosis and coexistence in the bee gut. This research is currently funded by an ERC-StG called “MicroBeeOme”. Currently, Kirsten Ellegaard (Postdoc), Silvia Brochet (PhD student) and Théodora Steiner (technician) are working on this project.

Genome_circle_v1Partial representation of the genome map of a honey bee gut symbiont and comparison to genomes of related bacteria. Such analyses allow us to identify gene sets specific to honey bee gut symbionts hinting towards functions involved in adaptation in the gut.


Role of HGT and viruses for bacterial community ecology and evolution (HFSP grant together with Myiazaki and Sanchez labs in Japan/United States)

While horizontal gene transfer and viruses are known to be omnipresent in microbial communities, their role for community functioning, resilience and evolution are not well understood. We aim to study these questions in the bee gut microbiota model profiting from its simple composition, its experimental amenability, and the plenty of genomic data available. Our hypothesis is that both HGT and viruses contribute to intra-species diversity. HGT may facilitate dispersing functional redundancy across strains or distribute the burden of metabolically costly functions as common goods. Phages may play a role following “kill-the-winner” dynamics. This project is in part carried out in collaboration with two other groups (Miyazaki lab, AIST Japan; Sanchez lab, Yale University). We are using different approaches to elucidate the impact of HGT on microbial communities using the bee as a model. In my lab, the project is spear-headed by German Bonilla-Rosso, a postdoctoral researcher.


Symbiotic functions of bee gut bacteria (SNSF grant)

Little is known about the genetic basis of gut bacteria to interact among each other and with the host. We aim to reveal novel genetic determinants and mechanisms with key roles for symbiosis in the gut. The honey bee is an ideal model to discover and study such determinants because of its experimental amenability, the longstanding coevolution of the microbiota with the host and the fact that we know which bacterium resides where in the gut. This allows us to study a well-defined symbiotic system with a limited number of interactions. Among others, we are using genetic tools and transcriptomics to identify the genetic basis of particular functions of bee gut bacteria. Metabolomics experiments allow us to identify the exchange of metabolites between microbes and the host. This research ins not only important to understand fundamental aspects of gut bacteria-host interaction but also has implications for bee health .As pollinators, the honey bee represents a key species in nearly all terrestrial ecosystems, and plays a central role for the human food supply. Its global economical value has been estimated to account for €150 billions annually (Gallai et al. 2009; Bauer & Wing 2010). Therefore, recent reports on bee population declines have alerted scientists and bee keeping industries around the world, and a better understanding of factors influencing the health status of this important pollinator is of broad interest and urgent need (Genersch et al. 2010; Evans & Schwarz 2011). The gut microbiota is likely a vital contributor to the health of the honey bee and previous findings provide strong evidence for the presence of intimate and highly specific interactions with the host (Engel et al. 2012; Kwong et al. 2014). Three PhD students, Konstantin Schmidt, Lucie Kesnerova and Olivier Emery work on these topics.



Bee_GutFluorescence in situ hybridization (FISH) experiment visualizing two gut bacteria colonizing the epithelial cell surface of the honey bee gut. The gammaproteobacterial gut symbiont G. apicola is shown in magenta, the betaproteobacterial gut symbiont S. alvi is shown in green. Counterstain with DAPI in blue shows DNA of bacteria and host nuclei.


Microbial ecology and bacteria-host interactions in the human lung (FBM Interdisciplinary grant

I an quite different project and in collaboration with researchers at the University hospital of Lausanne (CHUV, Eric Bernasconi, Benjamin Marsland), we aim to further our understanding of the human lug microbiota. Health lungs have for a long time be thought to be sterile. But this is not true. Low number of commensal bacteria reside in our lungs. How they interact and impact the humna immune system and contribute to health and disease is not known. We are using samples from transplanted lungs and cell culture models to understand the cross-talk between bacteria and lung immune cells and also identify interactions among the bacteria themselves. This project is led by a postdoctoral researcher in my lab: Dr. Sudip Das.

Funding of our research:

Go here to find out about our publications regarding these research topics…