Bacterial Infection Ecology

HZI Campus

Microbial communities colonise many parts of our bodies, critically impacting our health such as by protecting against pathogens. But how the diverse microbes arrange and organise themselves to generate health effects is largely unknown. To tackle this challenge, we are developing methods to map the structure of the microbiome and resolve how this structure affects health benefits. In addition, we study how microbiota influence and manipulate us, aiming for real translational and clinical potential including the development of probiotic anti-infectives and microbiota-inspired immunotherapeutics.

Head

Dr Martin Jahn

Research Group Leader

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Our bodies are home to diverse microbial communities that protect us against pathogens, with the mucus-lined epithelia being a particularly dense area of colonisation. The Bacterial Infection Ecology Lab strives to identify the rules of engagement that govern the interaction between microbiota, pathogens and host cells within animals. Using a multidisciplinary approach that merges ecological theory, bioinformatics, and advanced imaging, our research focuses on three key themes:

Core Principles of Spatial Microbiome Organization

Overview of our key projects and approaches.

Microbial communities consist of many strains and species, and their spatial arrangement at the single-cell scale defines if they actually meet and interact. Current sequencing-based methods often fail to capture interactions in hosts at such fine scales, leaving us with a resolution gap where key ecological and evolutionary processes happen. Using new imaging technologies and defined spatial models, we are bridging this gap and resolve the spatial ecology of gut microbiomes at the cell level. Here, we systematically compare healthy and diseased states. These data will provide an important baseline on structural organisation principles of the gut microbiota and how they might be boosted to promote resilience to perturbations such as by antibiotics, inflammation and infection.

Mapping the impact of microbiota on infection outcomes

Dense microbiota (blue) from the human gut.

How do the microbiota prevent infection? In this line of research, we are investigating the spatial ecology of pathogen resistance, with a focus on gut infections and associated inflammation. To this end, we are mapping how microbiota-pathogen interactions alter infection outcomes. This will inform the identification of key microbiota for infection resistance and their underlying ecology in infection. It will also enable biogeography-guided reformulations of taxa and function to disentangle their precise role in infection. Ultimately, this hypothesis-driven research will provide new fundamental insights to guide the rational design of beneficial microbial communities to enhance infection resistance.

Host Manipulation & microbiome inspired therapeutics

How do gut microbiota manipulate their mammalian host? To this end, my lab screens the human gut microbiota using a combination of bioinformatics and cell assays. These insights into microbial community-mediated host manipulation have the potential to be of high translational value in identifying candidates for targeted immune therapies, as well as paves the way to symbiont-mediated immune modulation in the context of inflammation and infection.