Dataset for 'Gut microbe-derived short-chain fatty acids regulate alphavirus arthritis and activation of infiltrating and resident macrophages'

Using mouse models of alphavirus-induced arthritis, we investigated how antibiotic-induced gut dysbiosis shapes inflammatory responses in the joint. We found that depletion of microbiota-derived short chain fatty acids (SCFAs) activated pathogenic immune cells in the gut that drove more severe arthritis, while restoring SCFAs or SCFA-producing bacteria attenuated disease. Data were generated using flow cytometry, fluorescent activated cell sorting, RNA sequencing, qRT-PCR, in situ hybridization, H&E staining, Toulidine blue staining, TRAP staining, focus forming assay, ELISA, liquid chromatography-mass spectrometry, virus and bacterial cultures, bacterial engineering, and in vivo characterization. There are 10 main Figures and 7 Supplementary Figures. Data were obtained using gnotobiotic and specific pathogen free C57BL6/J wild type mice, as well as specific pathogen free Rag1 KO (Rag1tm1Mom, 034159); Tcrbd KO (Tcrbtm1Mom Tcrdtm1Mom, 002122); µMT (Ighmtm1Cgn, 002288); Myd88 KO (MyD88tm1.1Defr, 009088); Il1r KO (Il1r1tm1Imx, 003245); Tlr7 KO (Tlr7tm1Flv, 008380); Tlr9 KO (Tlr9M7Btlr, 34329-Jax); Tlr2 KO (Tlr2tm1Kir, 004650); Tlr4 KO (Tlr4tm1.2Karp, 029015); Pou2f3 KO (Pou2f3em1Cbwi, 037040); CD45.1 OT-II Rag1 KO; Myd88f/f (008888) x Villin-Cre (004586); and Myd88f/f (008888) x Ccr2-Cre-ERT2 (035229) mice. Vero CCL-81 cells were also used in this project.