GEO series

Microbiome-produced nicotinic acid controls colon regional identity and injury susceptibility (Colon and Cecum scRNAseq)

GSE311538 Mus musculus Expression profiling by high throughput sequencing 8 samples Submitted 2026/03/26 Platform GPL34290

Summary

The gut epithelium exhibits regional specialization critical for its function and susceptibility to disease, as gut diseases localize to specific regions of the organ. However, how regionalization is established and its influence on disease susceptibility remain poorly understood. Here, we investigate the role of the gut microbiome—which comprises all microorganisms residing in the gut lumen and is itself regionalized—in regulating regionalization of the colon. We demonstrate that the regional identity of colonocytes is disrupted in mice lacking a microbiome. Mechanistically, we show that the proximal colonic microbiome produces high levels of nicotinic acid, which induces Pparα expression to establish proximal colonocyte identity. Furthermore, we find that microbiome-driven proximal identity confers protection against tissue injury in the mouse. Finally, we show that colon regionalization and the loss of proximal identity during disease are also present in human.

Published in

Microbiome-produced nicotinic acid controls colon regional identity and injury susceptibility

Rispal J, Garcia JR, Palikuqi B et al. · Cell 2026 · PMID 41812662 · doi:10.1016/j.cell.2026.02.007

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Direct links to NCBI, no account and no request form: the whole study as GSE311538_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 8 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA1369826 and SRA study SRP649193. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41812662) ↗

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