Project Reference: ICS27-SCI-ST1

Project title: Gut to Blood: Resident versus Circulating Bacteria-Reactive T Cells

Project outline

This project addresses a fundamental question in immunology: how does the host tolerate commensal bacteria at barrier surfaces? Distinct tissue microenvironments, or ""niches"", shape immune cell behaviour, and resident microbes act as key antigens that educate T cell development and function. We lack a detailed, spatially-resolved understanding of how these microbial antigens direct immune cell fate, and whether this can be captured non-invasively through blood.

This project addresses this gap using spatial transcriptomics, custom probe design, and industry collaboration.

Using the gut as a model mucosal system, the student will firstly design a bespoke panel of spatial probes targeting bacteria that act as key antigens driving local immune responses, enabling precise detection of bacterial taxa within tissue, alongside whole-transcriptome gene expression.

Second, using this probe panel with spatial transcriptomics, the student will map microbe and immune cells organisation within distinct niches of the gut, and reveal how these signals coincide spatially.

Third, our industry partner IMU Biosciences provides expertise in high resolution immune profiling  across innate and adaptive responses (~2500 immune cell subsets from a single blood sample). Using this platform, the student will test whether niche-derived immune signatures in tissue are detectable in blood, and whether these signatures reflect their gut niche of origin.

Together, these aims build a mechanistic and translational framework for how microbial antigens shape immune behaviour at mucosal surfaces, and how this can be monitored through blood to predict health. This work has broad relevance to human health, offering insight into how tolerance is maintained at barrier tissues, and its relevance to local and systemic immunity. The project combines probe design, spatial genomics, computational biology, and industry-partnered research, with training across academic and commercial settings. 

Principal Supervisor

Professor Sarah Teichmann

Email address: sat1003@cam.ac.uk

Department / Partner Institute: Cambridge Stem Cell Institute

Website: https://www.teichlab.org

Industrial Partner

IMU Biosciences 

BBSRC strategic theme

Understanding the rules of life