Neutral-genetic barcodes
Project 01
Within-host dynamics of gut commensals
Most pictures of the gut microbiota come from sequencing or selective culture — useful for semi-quantitative snapshots, but blind to the parameters that actually govern a community: the availability of niches for incoming commensals, capacity for growth, and rate of clearance from the gut lumen.
Project 02
Next-generation oral vaccines
Recombinant vaccines against protein antigens are safe and easy to produce — but the surface of many bacterial pathogens is densely covered by complex carbohydrates, and targeting those glycans is the most effective way to prevent bacterial disease. Glycans are poorly immunogenic alone, so glycoconjugate vaccines link them to a carrier; today that production is a tedious, expensive multi-step process.
Glycoconjugate render
Host physiology gradient
Project 03
Cross-talk between host physiology, diet & microbiota
Bulk descriptions of faecal communities make causal links hard to establish — they are one-off measurements of an intricate interplay between thousands of species and their host, and the microbiota varies in space along the intestine as well as in time.
We use a gnotobiotic mouse model with a simplified microbiota that recapitulates major functions of the full system, accounting for the variable physiology of the intestine — pH, bile salts, bicarbonate, osmolarity, flow — and the metabolites the microbiota secretes back. Controlled in vitro assays, in vivo data and mathematical modelling combine into a dynamic framework for hypothesis generation, with a clear path toward treating microbiota-related disease.
Funding · Swiss National Science Foundation
Collaborators
Project 04 · Botnar Centre for Child Health
Precision microbiota engineering for child health
From shortly after birth, the large intestine is colonized by billions of bacteria. We are only beginning to understand how they influence child health — yet current studies support causal roles in diseases as diverse as allergy and autism, and we still have no accurate way to "fix" the microbiota.
We are developing two tool-sets: one to replace a "bad" bacterial species with a desirable one using intestinal antibodies, and one to target individual genes in the microbiota using CRISPR-Cas directly in the gut. We begin with the most serious diseases of newborns — inborn errors of metabolism, neonatal sepsis and necrotizing enterocolitis — where mortality is high and treatment options are limited.
Colony plate, OMM¹²
Epithelium, confocal
Project 05 · Hausmann subgroup
Epithelium–microbiota crosstalk
The intestinal mucosa is the barrier between our bodies and the outside world — permeable to essential nutrients, yet protective against microbial translocation. A tight balance between epithelium, immune cells and the luminal microbiota maintains homeostasis; when it breaks, the result can be infection, metabolic disorder or chronic inflammation such as inflammatory bowel disease.
The Hausmann group focuses on the epithelium itself — in direct contact with the microbiota, yet poorly understood at the molecular level. Using gnotobiotic mice, organoids combined with anaerobic culture, single-cell omics and bioengineering, we characterize the impact of commensal microbes on epithelial barrier function across mouse and human.