Systematic screening of tryptophan metabolism identifies site- and microbial-specific signatures of tryptophan utilization in experimental colitis

Welz, L.; Alsaadi, A. I.; Harris, D. M. M.; Yu, M.; Mekdoud, T.; Bornhaeuser, J.; Springer, E.; Gilloteau, C.; Pothakamury, A. A.; Smith, J. D.; Jenkins, B. C.; Sommer, F.; Waschina, S.; Rosenstiel, P.; Schreiber, S.; McReynolds, M. R.; Aden, K.

doi:10.64898/2025.12.16.693850

bioRxiv · 10.64898/2025.12.16.693850

Systematic screening of tryptophan metabolism identifies site- and microbial-specific signatures of tryptophan utilization in experimental colitis

Welz, L.·Alsaadi, A. I.·Harris, D. M. M.·Yu, M.·Mekdoud, T.·Bornhaeuser, J.·Springer, E.·Gilloteau, C.·Pothakamury, A. A.·Smith, J. D.·Jenkins, B. C.·Sommer, F.·Waschina, S.·Rosenstiel, P.·Schreiber, S.·McReynolds, M. R.·Aden, K.

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Abstract

BackgroundAltered tryptophan (Trp) metabolism and disrupted nicotinamide adenine dinucleotide (NAD) synthesis are hallmarks of IBD, yet how intestinal microbiota contribute to these metabolic shifts during intestinal inflammation remains poorly understood. MethodsWe used targeted metabolomics to systematically profile Trp- and NAD-related metabolites across multiple biological compartments - including tissues, luminal contents, stool, and serum - in mice treated with dextran sulfate sodium (DSS) alone or in combination with a broad-spectrum antibiotic (ABX) cocktail. ResultsMicrobial depletion significantly attenuated colitis and increased host Trp bioavailability, implicating the gut microbiota as a competitive Trp consumer. In DSS colitis, Trp degradation along the kynurenine pathway (KP) was exaggerated but blocked at the key KP enzyme quinolinate phosphoribosyltransferase (QPRT), resulting in mucosal NAD(H) depletion. ABX co-treatment normalized metabolite conversion along the KP and restored mucosal NAD(H) levels, revealing a dual role of the gut microbiota during colitis: while they compete with the host for Trp utilization, they simultaneously shape host KP regulation and NAD de novo synthesis, supporting host energy homeostasis. ConclusionOur findings demonstrate that mucosal NAD de novo synthesis is a microbially regulated metabolic process that alleviates intestinal inflammation and may represent a novel therapeutic target in IBD through modulation of the gut microbiota or their metabolites.

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Welz, L., Alsaadi, A. I., Harris, D. M. M., Yu, M., Mekdoud, T., Bornhaeuser, J., Springer, E., Gilloteau, C., Pothakamury, A. A., Smith, J. D., Jenkins, B. C., Sommer, F., Waschina, S., Rosenstiel, P., Schreiber, S., McReynolds, M. R., Aden, K.. 2025-12-18. Systematic screening of tryptophan metabolism identifies site- and microbial-specific signatures of tryptophan utilization in experimental colitis. https://doi.org/10.64898/2025.12.16.693850

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