Bile Acids and Gut Health: Everything You Need to Know

What are bile acids?

Bile acids are molecules the liver creates from cholesterol. The liver produces two main primary bile acids: cholic acid and chenodeoxycholic acid.

Before these primary bile acids leave the liver, they get conjugated, or tagged, with the amino acids glycine or taurine. This conjugation process creates bile salts, which are stored in the gallbladder until a meal containing fats is eaten. When fats reach the small intestine, the gallbladder releases bile salts to break them into smaller droplets. This makes it easier for pancreatic lipase to turn them into fatty acids and glycerol for absorption. Without this process, the small intestine struggles to absorb dietary fats and fat-soluble vitamins, such as A, D, E, and K [1].

How is the microbiome involved? 

Once bile salts have finished emulsifying fat in the small intestine, most travel to the terminal ileum (the last part of the small intestine), where they're reabsorbed and sent back to the liver through the portal vein. This recycling process, called enterohepatic circulation, is remarkably efficient—about 95% of bile acids get reused [2]. But what happens to the remaining 5% that isn’t reabsorbed and passes into the colon? That’s where the gut microbiome takes control.

Certain gut bacteria produce enzymes called bile salt hydrolases (BSHs). These enzymes can "deconjugate" bile salts, essentially removing those amino acid tags we mentioned earlier. This process creates unconjugated bile acids (uBAs).

This might seem like a small change, but it has big effects. uBAs behave differently than their conjugated counterparts and can even act as antimicrobials because they can slip through bacterial cell walls more easily because they repel water [3]. Since uBAs can be harmful to certain microbes, some bacterial species have evolved mechanisms to further modify them, converting uBAs into secondary bile acids (sBAs).

How do gut microbes convert uBAs into sBAs?

There are two primary ways this conversion process happens:

1. Dehydroxylation requires specific genes (bai genes) in the microbiome: 

• Cholic acid (uBA) → deoxycholic acid (sBA)
• Chenodeoxycholic acid (uBA) → lithocholic acid (sBA)

2. Oxidation and epimerization use enzymes called hydroxysteroid dehydrogenases (HSDHs). Sometimes, existing sBAs get changed into new forms: 

• Chenodeoxycholic acid (uBA) → ursodeoxycholic acid (sBA)
• Deoxycholic acid (sBA) → isodeoxycholic acid (sBA)
• Lithocholic acid (sBA) → isolithocholic acid (sBA)

These transformations require specific bacterial species and enzymes [4]. Not all gut microbiomes can do these transformations equally well. This means the types and amounts of sBAs vary a lot from person to person. The science on sBAs is mixed: both high and low levels can be problematic.

Are there specific microbes that metabolize bile acids?

Four major bacterial phyla (which encompass many species) can create unconjugated bile acids because they have BSHs: Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria [5], [6].

But only a few taxa can turn those unconjugated bile acids into secondary bile acids [7], [8]:

• Dehydroxylation is possible in just a few bacterial taxa: Lachnospiraceae, Peptostreptococcaceae, and Clostridium.
• Oxidation and epimerization are also limited to a few bacterial genera such as Clostridium, Mycobacterium, Eggerthella, Ruminococcus, and Collinsella. 

A diverse gut microbiome supports not only digestive health but also plays a key role in shaping the bile acid profile. Remarkably, a recent study reported that only 37 bacterial species can produce both unconjugated and secondary bile acids [8]. Having a more diverse gut microbiome increases the likelihood of having the right enzymes for these complex transformations.

How do different bile acids interact with the body?

Bile acids are more than digestive detergents—they're signaling molecules that regulate inflammation, protect the gut barrier, and influence the microbiome [9], [10]. How they interact with your body depends on their chemical form: conjugated, unconjugated, or secondary.

Conjugated bile acids

Conjugated primary bile acids (attached to glycine or taurine) emulsify dietary fats for absorption and signal through FXR receptors to regulate their own synthesis [11]. At normal levels, they support intestinal barrier function [12].

Unconjugated bile acids

At moderate levels:

• Support barrier function and provide antimicrobial protection against pathogenic microbes [13].

At elevated levels:

• Stimulate water secretion, causing diarrhea [14].
• Disrupt epithelial cells, increasing permeability and triggering inflammation [15].
• Released taurine feeds problematic bacteria like Bilophila wadsworthia [16].

Secondary bile acids

At moderate levels:

• Activate TGR5 receptors, reducing inflammatory cytokines [17].
• Promote tight junction integrity and mucus production [18], [19]. 
• Resist pathogen colonization, including C. difficile [18], [20].

At elevated levels:

• May contribute to DNA damage and oxidative stress [21].
• Associated with increased colonic inflammation and colorectal cancer risk [22].

What health issues commonly affect bile acid balance?

Certain conditions can alter total fecal bile acid levels or impair the microbiome’s ability to convert them into unconjugated and secondary forms. 

• Inflammatory bowel disease, which includes Crohn’s disease and ulcerative colitis, was associated with higher levels of bile salts (or conjugated bile acids) and unconjugated bile acids and lower levels of secondary bile acids [6], [8], [23]-[29]. However, the microbiome’s capacity to metabolize bile acids appears to shift in both directions in these conditions, indicating that maintaining a balance of bile acids is important [6], [8], [23]. Altered metabolism results in a more toxic bile acid pool, which can disrupt the integrity of the intestinal barrier. 
• In people with colorectal cancer, the enzyme responsible for creating unconjugated bile acids, BSH, was at lower levels [8]. However, there was also an increase in oxidation and epimerization via the HSDH enzyme, suggesting an increase in some types of secondary bile acids [8]. These specific secondary bile acids are known to antagonize intestinal receptors, which typically suppress tumor growth. 
• Non-alcoholic fatty liver disease patients had altered potential for secondary bile acid production, which may disrupt lipid metabolism and contribute to hepatic fat accumulation [8], [30], [31].
• Patients with type 2 diabetes had reduced metabolism of bile acids altogether, likely resulting in more conjugated bile salts, leading to reduced insulin sensitivity [6].
• Antibiotic use was associated with decreased deconjugation potential of the microbiome via BSH, driven by changes in its composition [32], [33]. 

Scientists haven't yet figured out what an "ideal" bile acid profile looks like. The key to supporting healthy bile acid metabolism is maintaining a diverse microbiome capable of performing all necessary transformations in a balanced manner.

What is bile acid malabsorption? 

As we discussed, under normal circumstances, approximately 95% of bile acids are efficiently reabsorbed in the terminal ileum and returned to the liver via enterohepatic circulation. However, several conditions can disrupt this process, leading to bile acid malabsorption (BAM), where more than 5% of bile acids pass into the colon. BAM can be caused by:

• Crohn’s disease [34]
• Surgical resection of the terminal ileum [35]
• Radiation injury [35]
• Celiac disease [35]
• Chronic pancreatitis and exocrine pancreatic insufficiency [35]
• Microscopic colitis [36]
• Small intestine bacterial overgrowth [35]
• Post-cholecystectomy [34]

When excess bile acids reach the colon, they act as potent secretagogues, stimulating water and electrolyte secretion into the colonic lumen [37]. This results in bile acid diarrhea (BAD), characterized by chronic watery diarrhea that can significantly impact quality of life. 

When elevated levels of bile acids pass into the colon due to malabsorption, you might assume this would simply increase secondary bile acid production. However, the reality is more complex, as microbiome dysbiosis may leave an individual without the capacity to produce secondary bile acids, and accelerated intestinal transit time may not even allow for bacterial bile acid metabolism.

As a result, unconjugated bile acids can accumulate in the colon, with significant implications, including disruption of the epithelial barrier, promotion of inflammation, and microbial dysbiosis.

What is the difference between fecal and urinary bile acid levels? 

Bile acids show up in stool because the recycling system (enterohepatic circulation) isn't 100% efficient. Remember how about 5% of bile acids make it to the colon? After microbiome-powered deconjugation and transformations occur, about half of this portion is absorbed in the colon and then returned to the liver. The rest is lost through stool. This is completely normal.

Bile acids in urine happen for a different reason. After the liver produces bile acids, they should be sent to the gallbladder to wait until fat is consumed. If this transport system fails, bile acids build up in the blood. Eventually, they overwhelm the kidneys and are excreted in the urine. This is not normal and may signal liver or bile duct problems.

Are there ways to improve the bile acid profile?

Yes, several approaches can help balance your bile acids.

Diet

• Drink teas with epigallocatechin. This antioxidant powerhouse is found in many green teas, and preliminary rodent studies suggest it may alter bile acid levels, both increasing and decreasing them [38].
• Prioritize high-fiber foods. Fiber feeds the beneficial gut bacteria that metabolize bile acids to support bile acid balance [39], [40]. 
• Limit excess fat intake to avoid strain on the liver, where bile acids are produced [41].
• Try Konjac glucomannan-enriched noodles. They are a great alternative to gluten noodles, and have been shown to reduce levels of secondary bile acids [42].

Probiotic supplements

• A probiotic containing three strains of Lactiplantibacillus plantarum reduced levels of both conjugated and secondary bile acids in serum in overweight adults [43]. 
• A Lactobacillus reuteri probiotic increased levels of unconjugated bile acids [44]. 

Therapeutics for bile acid malabsorption and diarrhea 

• Bile acid sequestrants are a first-line treatment for bile acid diarrhea that typically require a prescription [45]. They act by binding bile acids in the intestine, preventing their secretagogue effect in the colon.
• An herbal blend known as rikkunshito is also recommended for bile acid malabsorption due to its ability to adsorb bile acids [46]. 

Where can I find the uBA and sBA metrics in Tiny Health’s Gut Health Test results?

You’ll find them in the Microbial Enzymes & Metabolites section under Modified Bile Acid Production Capacity. Our metric measures the microbiome's ability to produce unconjugated and secondary bile acids via the presence of genes.

• Deconjugation via BSH (BS -> uBA) is indicated by the presence of the cbh gene.
• Dehydroxylation (uBA -> sBA) is measured by the presence of the genes baiB, baiH, baiCD, and baiF. 
• Oxidation and Epimerization (uBA -> sBA) are measured by the presence of the genes hdhA, E1.1.1.201, E1.1.1.393, and E1.1.1.52. 

What does it mean if the uBA or sBA capacities are imbalanced on a Tiny Health test? 

• Low uBA: Reduced barrier integrity and antimicrobial defense against pathogens like C. difficile [13].
• High uBA: Increased diarrhea risk, barrier damage, and dysbiosis promotion [14]-[16].
• Low sBA: Loss of anti-inflammatory signaling, weakened barrier, reduced antimicrobial activity [17], [18].
• High sBA: Context-dependent—may be beneficial if moderate, but very high levels increase inflammation and cancer risk [22].

Are these metrics available in the PRO Gut Health Test?

Yes. To find unconjugated and secondary bile acid results, navigate to the All Insights page and look for the Microbial Enzymes & Metabolites section under Modified Bile Acid Production Capacity.

Disclaimer: For educational purposes only. Tiny Health does not diagnose, treat, or cure any conditions. Each practitioner is responsible for their own clinical decisions. We provide microbiome interpretation support, not personalized medical advice.