Microbiology Session:

Thursday, September, 29th, 2022: 09:00 am

Chairs: Christin Koch and Hyun-Dong Chang

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Deutsches Rheuma-Forschungszentrum Berlin, a Leibniz-Institute
Berlin, Germany


Text Abstract

Jakob Zimmermann

Noninvasive assessment of gut function using transcriptional recording sentinel cells

Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland


Background: The mammalian immune system is heavily influenced by environmental factors such as diet and the intestinal microbiota. The latter provides key stimuli for proper immune system functioning and is a potent biomarker for diseases and treatment decisions. While commonly sampled from the stool, such measurements are poorly reflective of the luminal conditions at the site of host engagement. Noninvasive tools are required to report the environmental cues encountered through the gut that shape the immune system.
Methods: Here we used transcriptional recording sentinel cells that through a reverse transcriptase-Cas1–Cas2 complex record their own short-lived mRNA expression into long-lived DNA-based CRISPR arrays to report on gut function. We mono-colonized germ-free mice with E. coli sentinel cells and performed Record-seq on fecal samples to reconstruct their cellular histories as they passed along the gastrointestinal tract. 
Results: Upon mono-colonization of mice, sentinel cells reported on diet, inflammation, and microbial interactions. Through transcriptome-scale information, Record-seq elucidated E. coli’s adaptations to intraluminal conditions including pH, oxygen levels, and ion availability. Unlike RNA-seq, Record-seq performed on stool samples retained information from proximal gut sections to non-invasively report on the luminal conditions in vivo. Using barcoded CRISPR arrays enabled multiplexed Record-seq in two isogenic E. coli strains coinhabiting the intestine to reveal compensatory responses of a single-gene mutant to competition with the WT.
Conclusions: Transcriptional recording sentinel cells noninvasively report on gut function and reveal environmental cues such as diet, inflammation, and microbial interactions.


Dr. Zimmermann obtained his PhD in immunology at the German Rheumatism Research Center Berlin in the lab of Andreas Radbruch and Hyun-Dong Chang investigating the contribution of various T helper cell subsets to the pathophysiology of inflammatory bowel disease. He then moved to the University of Bern where he currently develops new tools to study the mucosal immune system and its relationship to the intestinal microbiota in the lab of Andrew Macpherson. He is also interested in how gnotobiology – performing mouse experiments with defined microbiotas – can synergize with bacterial flow cytometry and cell sorting to improve the understanding of host–microbial mutualism.