An innovative organoid model to screen for bacteria and their metabolites that protect against inflammation-induced colonic barrier disruption.

Authors

Nicole Cady, Sophia R Meyer, Kwi Kim, Bernard C Lo, Ngai So, Grace Y Chen, Stephan P Rosshart, Yatrik M Shah, Gabriel Núñez, Jonathan Z Sexton, Thomas M Schmidt

Published in

mSphere. Pages e0092625. Jul 31, 2026. Epub Jul 31, 2026.

Abstract

Organoids provide a useful model system to study interactions between gut microbes and the activity of host tissues, including gastrointestinal (GI) barrier function. However, most organoid models have limited capacity to mimic the physiological hypoxia experienced by the colonic epithelium in vivo. While oxygen is required to support respiration in the host cells, many gut microbes are anaerobes that require anoxic conditions to grow. Using an innovative anaerobe co-culture system that maintains constant oxygen concentrations on the basolateral side of colonic epithelial monolayers and anoxic conditions on the luminal side, we demonstrate that colonic monolayers derived from a primary human cell line behaved more like in vivo epithelia when cultivated in the co-culture system than when cultured under ambient oxygen concentrations. We then identified interactions between the colonic epithelium and a strain of Bifidobacterium adolescentis-an oxygen-sensitive species that is prevalent and abundant in the adult gut microbiome. Co-culturing colonic monolayers with Bifidobacterium adolescentis U269-1 in the anoxic apical chamber mitigated loss of the barrier function in monolayers exposed to inflammatory cytokines. We identified indole lactic acid (ILA) as one metabolite from B. adolescentis that provides dose-dependent protection against inflammatory cytokines. Oral administration of ILA was well tolerated in mice and provided protection against immunotherapy-induced (anti-CTLA4) colitis in female, but not male mice. Together, we demonstrated the utility of the co-culture system for screening microbes and their metabolites for interactions with the colonic epithelium, as well as advancing our understanding of interactions between bifidobacteria and host barrier function.IMPORTANCEThe present study yielded strong evidence for the beneficial effects of B. adolescentis on the maintenance of colonic barrier function in an asymmetric oxygen system that mimics the colonic environment. The bifidobacterial metabolite indole lactic acid was implicated in this protection both in vitro and in a mouse model. We also refined and scaled the co-culture system to a 96-well plate format to provide the capacity for higher-throughput screening of microbes and microbial metabolites under physiologically relevant conditions.

PMID:
42536076
Bibliographic data and abstract were imported from PubMed on 31 Jul 2026.

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