Annika Hausmann Lab

Mucosal
Crosstalk

laboratory

Laboratory for Mucosal Crosstalk

We are the laboratory for Mucosal Crosstalk. Our research is dedicated to understanding how the interactions between our microbiota, the intestinal epithelium, and immune cells in the intestinal mucosa maintain intestinal homeostasis, and how these interactions derail in disease. To achieve this, we employ interdisciplinary approaches at the interface of epithelial cell biology, microbiology and mucosal immunology in combination with versatile in vivo and in vitro models.

The intestinal mucosa forms an integral barrier between our bodies and the outside world. Being exposed to a huge variety of metabolites and microbes taken up with our food or stably colonizing the intestine, it is permeable for essential nutrients while serving as a protective barrier to prevent microbial translocation. A tight balance between the intestinal epithelium, immune cells in the underlying tissue and the intestinal microbiota present in the lumen maintains intestinal homeostasis. The impairment of this balance can trigger disease, such as infection, metabolic disorders, and chronic inflammation (e.g. inflammatory bowel disease). Our work focuses on understanding how these key players interact to maintain intestinal homeostasis, with a special interest in the intestinal epithelium. The intestinal epithelium is in direct contact with the microbiota colonizing the intestinal lumen (e.g. sensing via pattern recognition receptors, uptake of metabolites), yet we know little about the molecular basis of how the epithelium integrates luminal and mucosal stimuli. We make use of state-of-the-art in vivo and advanced organoid-based in vitro models, (single cell) omics techniques and bioengineering approaches, to map mucosal cellular crosstalk and dissect the underlying molecular mechanisms in mouse and human.

Our Research

Characterization of microbiota impact on epithelial phenotypes

Using state-of-the-art in vivo and in vitro models, we characterize the impact of commensal bacteria on epithelial phenotypes using (sc) omics, microscopy and flow cytometry.

In vivo models

We employ gnotobiotic mice associated with microbial consortia of varying complexity to mechanistically dissect the impact of commensal bacteria on the intestinal epithelium. Using orthotopic transplantation, we can transplant genetically modified organoids into the murine colon.

In vitro models

We use human and murine organoids in combination with cultivation of bacterial consortia and bioengineering approaches to develop novel in vitro model systems for the molecular dissection of epithelium-microbiota interactions.

Meet the Team

Dr. Annika Hausmann
SNSF Ambizione Group Leader
Annika studied Molecular Medicine in Bonn and Freiburg (DE). She trained in Zurich (CH) and Copenhagen (DK) in mucosal immunology, host-microbe interactions and epithelial repair mechanisms in intestinal inflammation. Annika is fascinated by how our intestinal mucosa manages to maintain a stable relation with commensal microbes, while protecting us against enteropathogen infections at the same time.


Nicola Realini
PhD student
After completing his studies at the University of Lausanne and ETH Zürich, Nicola joined the Hausmann group for his PhD. His research focuses on the complex interactions between the intestinal epithelium, microbiota, and immune system with a focus on the molecular mechanisms determining antigen sampling in the gut, using in vivo and in vitro models.

Nimisha Khurana
PhD student
Nimisha completed her Bachelor’s degree in Biochemistry at the University of Delhi and a Master’s in Molecular Biosciences with a specialization in Cancer Biology at the University of Heidelberg and DKFZ, Germany. During her academic journey, she developed a deep fascination with how the microbiome influences host glycobiology and immune responses. For her PhD, Nimisha joined the Hausmann group, driven by her enthusiasm for unraveling the complex interplay between the gut microbiome, host epithelial cells, and the immune system. She is particularly passionate about using and modeling advanced, physiologically relevant in vitro systems, including co-culture models, and combining these with in vivo approaches to gain novel insights into these intricate relationships. Her work aims to shed light on how these interactions contribute to conditions such as inflammatory bowel disease (IBD) and other disorders.

Alisia Borri
Scientific Assistant
Having completed her MSc in Biotechnology at Wageningen University, Alisia joined the Hausmann group to investigate the molecular wiring of subpopulation-specific responses to cytokine exposure in intestinal epithelial cells using organoid models.

Donovan O’Brien
PhD student
Donovan is a PhD candidate in Cell Biology & Immunology at Wageningen University (NL), specialising in antigen presenting cells of the intestine. With a focus on inflammation biology and tissue engineering, his interests lie in developing advanced in vitro methods for modelling immune cell interactions within the lamina propria for disease modelling and toxicological screening. Donovan is visiting the Hausmann group for six months for training in organoid work and their integration in his in vitro models.

Valeria Stylianou
MSc student
Valeria is a second-year master’s student in Biology, majoring in Microbiology and Immunology at ETH. She will joins the Hausmann Group  for her second semester project, where she will focus on visualizing M cell spatial patterning in a three-dimensional intestinal organoid model. For this, she will work with Nicola Realini.

Simran Khatri
BSc student
Simran is a final-year undergraduate student pursuing a BSc (Hons) in Pharmacology at University College Dublin (UCD), Ireland. During her degree, she spent a full academic year at the National University of Singapore (NUS). In summer 2025, she expanded her research experience as a Naughton Fellow at the University of Notre Dame in the US.
Building on these experiences and eager to deepen her skills in 3D cell culture and disease modelling, Simran has joined the Hausmann group to conduct her bachelor’s thesis project under supervision of Nimisha Khurana.

Funding

We thank our funders for supporting our research!

Get in touch

We are hosted by the Mucosal Immunology Lab (Prof. Emma Slack) at ETH Zürich.

Dr. Annika Hausmann
SNSF Ambizione Group Leader

ETH Zürich
Vladimir-Prelog Weg 1-5/10
8093 Zürich
Switzerland

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