Photo: Mikael Sjöberg

Florian Schmidt

Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland

Autobiography of a gut bacterium – Recordings of transient transcriptional events shed light on the gut microbiome

DOI: 10.1126/science.adf4442


The interactions of the gut microbiota with the host are complex and the capacity to investigate them is pivotal to our ability to understand human health and disease. As microorganisms traverse the intestine, they continuously adapt their gene expression to changes in their environment such as the availability of nutrients. The short-lived nature of these transcriptional events renders RNA-sequencing of fecal bacteria largely uninformative. We leverage transcriptional recording by CRISPR spacer acquisition from RNA to create bacterial sentinel cells as a tool to investigate intestinal and microbial physiology. We demonstrate that these microbial sentinels can traverse the gastrointestinal tract and record the transcriptional response to a plethora of interactions with the host, the diet, and other microbiota into DNA, which can be recovered non-invasively by deep sequencing from the feces.


Florian Schmidt is a Postdoctoral fellow in Prof. Randall Platt’s group at the Department of Biosystems Science and Engineering (D-BSSE) at ETH Zürich. He was born in Mainz, Germany, and obtained his BSc and MSc from the Ruprecht Karl University of Heidelberg, working on CRISPR/AAV gene therapy working with Prof. Dirk Grimm. After a short stint in Prof Feng Zhang’s laboratory at the Broad Institute of MIT and Harvard, USA, together with Prof Randall Platt, he transitioned to ETH Zurich, where they established the Record-seq technology used to create living microbial diagnostics.