Profiling Bile Acids in the Stools of Humans and Animal Models of Cystic Fibrosis

Cystic fibrosis (CF) is associated with dysbiosis of the gut microbiome, alterations in intestinal mucus production, aberrant bile acid (BA) metabolism, fat malabsorption, and chronic inflammation. As little is known about BAs in CF, we performed both comprehensive and targeted BA profiling in stool of children with or without CF. Our results reveal that select BA species and metabolites are significantly different between children with CF (cwCF) and healthy controls. There is also a trend towards higher primary cBA and total BA levels for cwCF. Matched bacterial metagenomic analyses showed no change in alpha-diversity between groups in our small cohort, at odds with previous studies, whereas changes in relative abundance of Bacteroides (lower) and E. coli (increased) species is consistent with prior reports. A robust trend was noted toward reduced abundance of bsh gene families (Wilcox test, p = 0.052), a key rate-limiting enzyme required for bacterial synthesis of secondary BAs, in cwCF. Modest changes in both BAs and microbial BA metabolism-related gene abundances may be attributable to small sample sizes, but also suggest likely combination defects in both host and microbial BA metabolic pathways in cwCF. Importantly, although fecal BA profiles from both ferret and mouse CF models showed significant differences from human BA profiles, only the ferret model reproduced significant differences between CF and nonCF animals, highlighting ferrets as a potentially more appropriate model for studying BA in stool in the context of CF. Together, these results provide new insights into CF-related BA dysmetabolism in cwCF, and highlight limitations of CF animal models for BA functional studies. IMPORTANCEChanges in the abundance and/or composition of intestinal bile acids (BAs) may contribute to dysbiosis and altered gastrointestinal physiology in CF. Here, we report shifts in select fecal BA classes and species for children with CF (cwCF). Matched metagenomic analysis suggest possible defects in both host intestinal BA absorption and gut microbial BA metabolism. Additional analyses of mouse and ferret CF stool for BA composition suggest great care must be taken when interpreting BA functional studies using these animal models. Together, this work lays technical and conceptual foundations for interrogating BA-microbe interactions in cwCF.