Bile acids (BA) through G protein-coupled bile acid receptor 1 (GPBAR1 or TGR5) and nuclear receptors like Farnesoid X receptor (FXR) regulate mammalian inflammation, and lipid, glucose, energy, and xenobiotic metabolism. The gut microbiota modulates the enterohepatic circulation of BA and microbially produced secondary BA appear to be more potent receptor agonists than primary BA, providing a mechanistic link between microbiome structure/function and regulation of host physiology. Evidence mainly from animal studies shows that dietary fibers and polyphenols and exercise can impact on BA metabolism. Similarly, certain bile salt hydrolysing (BSH) bacteria modulate circulating bile acid (CBA) profiles and strongly influence cholesterol uptake. However, human data confirming dietary modulation of CBA profiles and subsequent regulation of physiological homeostasis remains elusive. Using samples from the RoCAV cohort and existing randomised control trials (RCT), we correlated CBA profiles with Mediterranean (MED) diet adherence and measures of metabolic health. In a bespoke short-term RCT we measured the effect of Limosilactobacillus reuteri NCIMB 30242 (BSH positive probiotic), oats (prebiotics) and  Renetta Canada apples (polyphenol rich) on CBA and demonstrated that L. reuteri could increase host postprandial unconjugated and hydrophobic CBA profiles, and that oats and apples may modulate cardiovascular disease (CVD) risk markers in both chronic and acute settings. In a long term (18 month), large-scale (n=300) existing dietary and lifestyle intervention, we demonstrated how a polyphenol rich green-MED diet and exercise promotes metabolic health in prediabetics through modulation of the gut microbiota and CBA signalling (DIRECT-PLUS study). Finally, we  modelled BA profiles or metabotype with microbiome signatures and BA biotransformation potential using high-resolution metagenomics and established the molecular basis of BA regulation of immune and metabolic homeostasis by measuring the relative receptor activation potential of individual CBA and BA-metabotype profiles using novel pre-clinical human cell-based reporter systems. CABALA_diet&health has provided direct evidence in humans that CBA profiles influence CVD risk supporting their consideration as biomarkers of health, related to the microbiome and modulated by diet and exercise. We have also demonstrated in humans, that autholgous faecal microbiome transfer, after green-MED dietary intervention retards weight regain and maintains metabolic health. Moreover, we propose that global BA species diversity may be an indicator of health and bile acid convergence a function of disease, and additionally, that lowering total CBA concentrations may be a viable target for improving metabolic health at the population level.

Diet-microbe-gut health dialogue centers on bile acid (BA) activation of signaling receptors in dictating both metabolic and health status.  Our work indicates global diversity as an indicator of health, bile acid convergence is a function of disease. In Cork Ireland, we have determined, through cellular systems, signaling and gene expression overlap along with independence of process between three bile acid receptors (FXR, VDR, TGR5), functionally and regionally.  Finally, bile acids are emulsifiers of lipid.  Our work has shown that lipids can act as a sequesterants of certain bile acids negating their signaling effects, at the level of gene expression and cell organelle fitness.

We have demonstrated, in a bespoke mixed chronic and acute postprandial challenge dietary intervention conducted in Reading UK, that functional foods specifically, oats (prebiotic), polyphenol rich apples (Renetta Canada apples) and a BSH positive probiotic, (Limosilactobacillus reuteri NCIMB 30242), can influence post prandial circulating BA (CBA) profiles on an individual basis but may mediate their respective health effects via different mechanisms, especially during the postprandial phase. Apples reduced fasting apoB, a marker of low-density lipoprotein cholesterol (an independent CVD risk factor), and both oats and apples influenced postprandial glycaemic control and triacylglycerol response.  L. reuteri had a significant effect on postprandial secondary CBA concentrations. 

From the RoCAV cohort study in Varese Italy, we confirmed that diet was associated with CBA profiles, which were in turn associated with metabolic health. Specifically, high levels of CBA were associated with unhealthy metabolic parameters, whereas high levels of the BA responsive hormone FGF-19 was confirmed to be associated with reduced HOMA index and waist-to-hip ratio. 

In the DIRECT-PLUS dietary intervention with a polyphenol enriched Mediterranean diet conducted at the Ben Gurion University of the Negev in Israel, 6 month weight loss could be directly attributed to dietary microbiota modulation. Moreover, total CBA concentrations positively correlated with metabolic disease risk factors and autochthonous faecal microbiome transplant (aFMT) after green-MED diet microbiome modulation retarded weight regain over an 8 month follow up and maintained metabolic health.  

Strong correlations between individual CBA species or ratios with individual bacterial taxa were rare within the datasets and not consistent between different studies. Correlations between CBA profiles and enterotype-like community structures were apparent but not conserved across different data-sets. Microbial BA metabolism may therefore be more correctly considered as a community activity, possibly with different taxa performing similar chemical conversions in different individuals. Shotgun and strain level analysis did not resolve CBA:taxa associations but revealed relatively low prevalence and abundance of BA metabolizing genes across samples, suggesting a gap in knowledge concerning annotation of microbial BA metabolising genes.