Microbiome-derived Short Chain Fatty Acids modulate microglial inflammatory responses in a sex- and metabolite-specific manner

Towriss, M.; Dang, V.; Goeres, J.; Choudhary, J.; Aube, A.; Montoya Sanchez, J.; Anindya, C.; Morgan-Banke, K.; Hamden, J.; Whidbey, C.; Ciernia, A. V.

doi:10.64898/2026.06.30.735602

bioRxiv · 10.64898/2026.06.30.735602

Microbiome-derived Short Chain Fatty Acids modulate microglial inflammatory responses in a sex- and metabolite-specific manner

Towriss, M.·Dang, V.·Goeres, J.·Choudhary, J.·Aube, A.·Montoya Sanchez, J.·Anindya, C.·Morgan-Banke, K.·Hamden, J.·Whidbey, C.·Ciernia, A. V.

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Abstract

Microbes residing in the gastrointestinal tract exert immunomodulatory impacts on the brain through the gut-brain axis. Short-chain fatty acids (SCFAs) produced by bacterial fermentation of dietary fiber can enter the brain parenchyma and are implicated in microglia-mediated inflammation. While the gut microbiome is required to maintain microglial homeostasis, the mechanisms by which microbiota-derived metabolites affect microglia remains unknown. We examined the roles of SCFAs, specifically butyrate, propionate and acetate, on microglial function in response to SCFAs both in vitro using BV2 cells and in vivo in mice. We observed in vivo that SCFAs impact microglial transcriptional responses to LPS in a sex- and metabolite-specific manner with butyrate having the strongest effect. Enriched gene sets included signatures associated with LPS-responsive microglia, Arg1-positive microglia, microglial cell cycle related genes and genes affiliated with changes in microglial morphology. We observed a similar effect in vitro, where metabolite administration enhanced phagocytosis, blunted proliferation and nitric oxide production. We then evaluated global histone modification levels following metabolite treatment and detected an enhancement of H3K9ac, H3K27ac, and H3K4me3 both in vivo and in BV2 cells treated with butyrate. Finally, we showed that butyrate is a potent HDAC inhibitor possibly contributing to enhanced acetylation. Hence, our findings suggest that SCFAs impact microglial function in a metabolite- and sex-specific manner, and that butyrate blunts inflammation by regulating microglial histone acetylation. Our results provide a more in-depth understanding of gut microbiome-microglia crosstalk, opening the door for new microbiome- and microglia-targeted therapies. HighlightsXxxx

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Towriss, M., Dang, V., Goeres, J., Choudhary, J., Aube, A., Montoya Sanchez, J., Anindya, C., Morgan-Banke, K., Hamden, J., Whidbey, C., Ciernia, A. V.. 2026-07-04. Microbiome-derived Short Chain Fatty Acids modulate microglial inflammatory responses in a sex- and metabolite-specific manner. https://doi.org/10.64898/2026.06.30.735602

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