Murine models have become essential tools for understanding the complex interactions between gut microbes, their hosts, and disease. While many intra-facility factors are known to influence the structure of mouse microbiomes, the contribution of inter-facility variation to mouse microbiome composition, especially in the context of disease, remains under-investigated. We replicated microbiome experiments using identical mouse lines housed in two separate animal facilities and report drastic differences in composition of microbiomes based upon animal facility of origin. We observed facility-specific microbiome signatures in the context of a disease model [the Ednrb (endothelin receptor type B) Hirschsprung disease mouse] and in normal C57BL/6J mice. Importantly, these facility differences were independent of cage, sex, or sequencing-related influence. In addition, we investigated the reproducibility of microbiome dysbiosis previously associated with Ednrb-/- (knock-out; KO) mice. While we observed genotype-based differences in composition between wild-type (WT) and KO mice, these differences were inconsistent with the previously reported conclusions. Furthermore, the genotype-based differences were not identical across animal facilities. Despite this, through differential abundance testing, we identified several conserved candidate taxa and candidate operational taxonomic units that may play a role in disease promotion or protection. Overall, our findings raise the possibility that previously reported microbiome-disease associations from murine studies conducted in a single facility may be heavily influenced by facility-specific effects. More generally, these results provide a strong rationale for replication of mouse microbiome studies at multiple facilities, and for the meticulous collection of metadata that will allow the confounding effects of facility to be more specifically identified.

This study investigated gut microbiota composition along with food, host, and microbial derived metabolites in the colon and systemic circulation of healthy mice following dietary rice bran and fermented rice bran intake. Adult male BALB/c mice were fed a control diet or one of two experimental diets containing 10% w/w rice bran fermented by Bifidobacterium longum or 10% w/w non-fermented rice bran for 15 weeks. Metabolomics was performed on the study diets (food), the murine colon and whole blood. These were analysed in concert with 16S rRNA amplicon sequencing of faeces, caecum, and colon microbiomes. Principal components analysis of murine microbiota composition displayed marked separation between control and experimental diets, and between faecal and tissue (caecum and colon) microbiomes. Colon and caecal microbiomes in both experimental diet groups showed enrichment of Roseburia, Lachnospiraceae, and Clostridiales related amplicon sequence variants compared to control. Bacterial composition was largely similar between experimental diets. Metabolite profiling revealed 530 small molecules comprising of 39% amino acids and 21% lipids that had differential abundances across food, colon, and blood matrices, and statistically significant between the control, rice bran, and fermented rice bran groups. The amino acid metabolite, N-delta-acetylornithine, was notably increased by B. longum rice bran fermentation when compared to non-fermented rice bran in food, colon, and blood. These findings support that dietary intake of rice bran fermented with B. longum modulates multiple metabolic pathways important to the gut and overall health.

Rice bran, removed from whole grain rice for white rice milling, has demonstrated efficacy for the control and suppression of colitis and colon cancer in multiple animal models. Dietary rice bran intake was shown to modify human stool metabolites as a result of modifications to metabolism by gut microbiota. In this study, human stool microbiota from colorectal cancer (CRC) survivors that consumed rice bran daily was examined by fecal microbiota transplantation (FMT) for protection from azoxymethane and dextran sodium sulfate (AOM/DSS) induced colon carcinogenesis in germ-free mice. Mice transfaunated with rice bran-modified microbiota communities (RMC) harbored fewer neoplastic lesions in the colon and displayed distinct enrichment of Flavonifractor and Oscillibacter associated with colon health, and the depletion of Parabacteroides distasonis correlated with increased tumor burden. Two anti-cancer metabolites, myristoylcarnitine and palmitoylcarnitine were increased in the colon of RMC transplanted mice. Trimethylamine-N-oxide (TMAO) and tartarate that are implicated in CRC development were reduced in murine colon tissue after FMT with rice bran-modified human microbiota. Findings from this study show that rice bran modified gut microbiota from humans confers protection from colon carcinogenesis in mice and suggests integrated dietary-FMT intervention strategies should be tested for colorectal cancer control, treatment, and prevention.

Dietary rice bran (RB) has shown capacity to influence metabolism by modulation of gut microbiota in individuals at risk for colorectal cancer (CRC), which warranted attention for delineating mechanisms for bidirectional influences and cross‐feeding between the host and RB‐modified gut microbiota to reduce CRC. Accordingly, in the present study, fermented rice bran (FRB, fermented with a RB responsive microbe Bifidobacterium longum), and non‐fermented RB were fed as 10% w/w (diet) to gut microbiota‐intactspf or germ‐free micegf to investigate comparative efficacy against inflammation‐associated azoxymethane/dextran sodium sulfate (AOM/DSS)‐induced CRC. Results indicated both microbiota‐dependent and independent mechanisms for RB meditated protective efficacy against CRC that was associated with reduced neoplastic lesion size and local‐mucosal/systemic inflammation, and restoration of colonic epithelial integrity. Enrichment of beneficial commensals (such as, Clostridiales, Blautia, Roseburia), phenolic metabolites (benzoate and catechol metabolism), and dietary components (ferulic acid‐4 sulfate, trigonelline, and salicylate) were correlated with anti‐CRC efficacy. Germ‐free studies revealed gender‐specific physiological variables could differentially impact CRC growth and progression. In the germ‐free females, the RB dietary treatment showed a ∼72% reduction in the incidence of colonic epithelial erosion when compared to the ∼40% reduction in FRB‐fed micegf. Ex vivo fermentation of RB did not parallel the localized‐protective benefits of gut microbial metabolism by RB in damaged colonic tissues. Findings from this study suggest potential needs for safety considerations of fermented fiber rich foods as dietary strategies against severe inflammation‐associated colon tumorigenesis (particularly with severe damage to the colonic epithelium).

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