Keeping regular: gut bacteria modulate transit time via bile acids

From the Dey Lab, Clinical Research Division

Efforts to raise gut health awareness, including the ‘blue poop challenge’, have recently made quite a, *ahem*, splash across social media. Participants eat dyed muffins to measure their individual gastrointestinal transit times - the time it takes for food to travel through the digestive system. Though many factors impact digestive wellbeing, transit time is emerging as a correlate of overall gut health. Diet, host factors, and the microbiome all intersect to regulate gut motility, but these interactions remain incompletely understood. Members of the Dey Laboratory, led jointly by research technicians Naisi Li and Sean Koester and graduate student Dan Lachance, in the Fred Hutch Clinical Research Division, studied the role of microbial bile acid metabolism in the control of gut motility. Recently published in iScience, “this paper adds to a body of literature demonstrating that metabolites generated by the gut microbiome regulate gut transit,” said Dr. Dey.

A product of liver cholesterol metabolism, host-derived (or primary) bile acids consist of steroid acids that are attached or conjugated to amino acids to form bile salts. These bile salts are secreted into the small intestine, the first stretch of intestinal tract downstream of the stomach. Within the gut, bile salts undergo a metabolic process known as ‘deconjugation’, in which microbial enzymes called bile salt hydrolases (BSHs) cleave the amino acids from the bile acids. Deconjugation is a critical first step in the bio-transformation of primary bile acids to a large variety of secondary bile acids, which confer myriad effects upon both host and microbiota. 

Colonic transit time is regulated through bio-transformation of bile acids by the gut microbiome, in a regional and sex-biased manner.
Colonic transit time is regulated through bio-transformation of bile acids by the gut microbiome, in a regional and sex-biased manner. Image taken from the original article.

Germ-free mice, which lack microbiota altogether, have slower gut transit than conventional mice, implicating a role for resident microbes in regulating motility. Interestingly, the Dey Lab previously showed that dietary turmeric, a so-called ‘cholekinetic’ spice that induces increased bile secretion, impacts transit time in a BSH-dependent manner, highlighting a complex interplay between diet, secreted host factors, and bacterial metabolism. They found that microbial BSH activity correlates with faster gut transit, suggesting that unconjugated bile acids may play a role in motility. In their current study, the Dey Lab sought to elucidate the underpinnings of bile acid-mediated control of gut motility.

The researchers developed two sets of BSH-high and BSH-low synthetic bacterial communities for the colonization of germ-free mice. Turmeric was added to the diets of the mice and the animals were fed dyes to track gut motility. As predicted, mice colonized with BSH-high microbiota exhibited higher fecal concentrations of unconjugated bile acids and faster transit times than those colonized with BSH-low consortia. Dissection of the gastrointestinal tract into segments revealed that the dye accumulated near the terminus of the small intestine (just before entering the colon) in both BSH-high and -low settings, suggesting that higher BSH activity specifically accelerates transit through the colon. Interestingly, sex was found to be a significant variable determining transit time, with larger pro-motility effects occurring in males, in concordance with clinical studies showing higher motility and different bile acid profiles in men compared to women.

Between BSH-high groups, mice colonized with the synthetic community associated with faster gut transit exhibited greater fecal concentrations of the secondary bile acid lithocholic acid (LCA), suggesting that, in addition to total BSH activity, variations in bile acid metabolism between bacterial communities might impact gut transit. Indeed, when the researchers infused individual bile acids directly into the colons of mice, different bile acids conferred varying impacts on gut motility, with LCA inducing the fastest transit times. Next, the researchers probed the interactions between BSH activity and the enteric nervous system (ENS; the meshwork of neurons that regulate gut function). The researchers hypothesized that LCA might signal through the bile acid receptor TGR5, expressed by enteric neurons. Indeed, pharmaceutical inhibition of TGR5 blocked the effects of LCA, indicating that gut microbiome-generated bile acids regulate colonic transit via TGR5.

Probing further, the group developed an approach for measuring expression changes in ENS genes, which they applied to intestinal sections collected from mice in each of several different colonization settings. Surprisingly, principal component analysis revealed neither BSH activity nor gut transit phenotypes as major drivers of gene expression changes. Instead, biogeography, or the location of the gut segment, was the largest factor contributing to ENS signature variance between samples. “We expected to see shared host transcriptional responses in mice harboring communities with similar metabolic profiles. HOWEVER, we did not see this for the most part!” explained Dr. Dey. “If anything, shared responses were regional, and these signatures did not cluster by BSH/motility phenotypes.” The group identified consortium-specific transcriptional changes in genes involved in ENS signaling, development, maintenance, and bile acid metabolism, and these differed across regions of the GI tract. Together these findings indicate that ENS transcriptional responses are regional and microbiome-specific.

“This remains a confusing part of the story for us — how is it that we can see predictable host motility responses when colonizing the guts of gnotobiotic mice with phenotypically defined communities, but the middle man (the host enteric nervous system) appears to have such varied responses?” said Dr. Dey. “It suggests that gut motility phenotypes that appear similar may in fact represent (when we look under the hood) diverse host physiologic phenotypes that we are just beginning to understand.”

These findings have potential implications for the treatment of gastrointestinal conditions. “Knowing that the site of bacterial BSH's greatest effects is the colon impacts design of potential future therapies,” said the authors. Moving forward, the group is leveraging support from the Fred Hutch/UW Cancer Consortium to understand the role of bile acids in tumorigenesis. “Funding from the Cancer Consortium supported bile acid profiling of various combinations of gut bacteria in vitro, an effort which informed the design of synthetic communities and which also supported [lead author] Dan [Lachance]'s thesis work investigating regulators of a carcinogenic bile acid — work we hope to report in a paper in 2022!” said Dr. Dey.

This work was funded by the National Institutes of Health, the National Cancer Institute, and the Fred Hutchinson Cancer Research Center.

UW/Fred Hutch Cancer Consortium members Julia Cui and Neelendu Dey contributed to this work.

Li N, Koester ST, Lachance DM, Dutta M, Cui JY, Dey N. Microbiome-encoded bile acid metabolism modulates colonic transit times. iScience. 2021 May 5;24(6):102508. doi: 10.1016/j.isci.2021.102508. PMID: 34142026; PMCID: PMC8188381.