We are interested in broad questions about the ecology, evolution, functioning of host-associated microbial communities. Our main focus is on the gut microbiota of social bees. Honey bees, bumble bees, and stingless bees harbor specialized gut microbial communities that are important for bee health and disease. These communities are of relatively low complexity and experimentally tractable. This allows us combining bioinformatics with experimental approaches to address standing questions in microbial ecology. We are also expanding into other microbial ecosystems like the human lung or Swiss cheese!

Read below for the highlights of our research projects and acquired fundings:

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

Microbial communities residing in animal guts are dominated by specialized 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.

Group members involved in this research project:
Kirsten Ellegaard
Silvia Brochet

Gilles Baud, PhD student
Théodora Steiner


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, RGY0077/2016)

In collaboration with Miyazaki Lab, AIST, Japan and Sanchez Lab, Yale University, USA

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. We are using different approaches to elucidate the impact of HGT on microbial communities using the bee as a model.

At the Engel lab, the project is spear-headed by Germàn Bonilla-Rosso

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 is 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).

Multiple projects on this topic rely on the concerted efforts of:
Olivier Emery
Lucie Kešnerová
Konstantin Schmidt

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

In a 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 Dr. Sudip Das.

Funding of our research:

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