(A) Experimental design to determine which human sample type best recapitulates the SI microbiome in GF mice (n = 3 donor samples, n = 3–4 mice/donor/sample site). (B) Principal coordinate analysis ordination of Bray-Curtis β-diversity (n as in A; Supplemental Table 1). (C) Shannon diversity and observed ASVs (n as in A). (D) Experimental design to delineate in vitro and in vivo effects of mouse SI aspirates or SI species. (E) VMRs to CRD in AP mice (n = 4–12 mice/donor, 3 donors) and HC mice (n = 6–7 mice/donor, 3 donors). (F and G) Ca²⁺ response elicited by mouse SI aspirates in QGP-1 cells (Cal 520) and SI organoids (GCaMP) (1–3 SI aspirates/group tested, details in Supplemental Table 3). (H and I) Amplitude of the Ca²⁺ response and number of neurons activated by mouse SI aspirates in T8–T11 DRG neurons (DRGs from 3–5 mice/aspirate, Supplemental Table 3). (J) Relative abundance of Enterobacteriaceae in the SI aspirate of patients with symptoms of abdominal pain and bloating. (K) Ca²⁺ response evoked by A. aphrophilus, S. oralis, and E. hormaechei supernatants in QGP-1 cells (n = 4–5 plates/supernatant, Supplemental Table 5). (L and M) Ca²⁺ response and number of activated T8–T11 DRG neurons by bacterial supernatants (n = 3–5 mice/species, Supplemental Table 5). (N) VMRs to CRD in GF mice and GF mice colonized with listed species (n = 7–24 mice/group). The following statistical tests were used: ANOVA with Tukey’s HSD (C); mixed-effect model corrected for donor (E–I); Wilcoxon’s rank-sum test with continuity correction (J); 1-way ANOVA (K–M); and repeated measures 2-way ANOVA (N). Data are represented as median with 1.5 × IQR (box plots) or mean ± SEM. ****P < 0.0001, ***P < 0.001, **P < 0.01, *P < 0.05.