Gut Dysbiosis and Bile Acids

//Gut Dysbiosis and Bile Acids

Gut Dysbiosis and Bile Acids

Everything in the body is interconnected. We know that by now, right? Just like there’s a “gut-brain axis”, there’s also now the bile acid-gut microbiome axis as well. This is because the two are mutually reinforcing. I wrote here on how bile keeps SIBO in check, and therefore gallbladder dysfunction (or removal) can encourage SIBO.

But it goes the other way too: the microbiome is responsible for the formation of secondary bile salts in the gut as well. If your microbiome is unhealthy, this will also affect the bile acid pool, leading to yet more digestive discomfort.

Physiology 101: What Bile Is and How It Works

Bile is necessary for the absorption of fat and fat-soluble nutrients, as well as binding and eliminating fat-soluble toxins. As mentioned above, bile is also antimicrobial, and helps to keep the small intestine relatively sterile, compared to the colon.

Primary bile acids are produced in the liver from cholesterol. Bile acids become bile salts with the addition of one of two amino acids: glycine (also a calming neurotransmitter) and taurine (which also has several effects on neurochemistry). Incidentally, which amino acid gets used for conjugation depends on diet: those on high animal protein diets will have primarily taurine, while vegetarians will have more glycine.

These primary bile acids get kicked into the small intestine, where they do their job of absorbing and eliminating.

But the microflora that are present (which again, shouldn’t be very high compared to the colon) deconjugate the salts, turning them into secondary bile salts by removing the glycine and taurine. These salts can’t do the job that primary bile salts can do. They (along with some 95% of all bile) basically just get recycled when they get to the ileum, the last part of the small intestine (when the work of digestion should be done anyway), and kicked back up to the liver to start the process all over again. Only 5% should get eliminated via the colon (hopefully whisking away with them whatever fat-soluble toxins we want to get rid of).

SIBO and Fat Absorption

So here’s the other side of the SIBO coin: while yes, bile keeps SIBO from overgrowing, once you have SIBO, it fights back by deconjugating bile acids. This deconjugation should occur only in the colon primarily, because that’s where the vast majority of the bacteria is supposed to be. But SIBO is Small Intestine Bacterial Overgrowth—so the bacteria get dibs on the bile salts early, meaning there’s fewer of them around to do their job.

If the overgrowth is significant enough, this means two things: 1) possible fat or fat-soluble nutrient malabsorption (in addition to the intestinal discomfort from the SIBO itself), and 2) possible increased difficulty in fat-soluble toxin elimination. This will especially affect those trying to eliminate solvents or pesticides, as these tend to be fat-soluble.

The Upshot

If you have SIBO, and the numbers on the lactulose breath test show up high, you can assume low primary bile acids to some degree as well. Of course treat the SIBO, but consider also supporting bile production in the meantime (either by taking OxBile outright, or with precursors to bile salts, such as glycine and taurine).

Another way to infer it is if on certain kinds of testing, taurine or glycine levels show up abnormally high (comprehensive urinary neurotransmitter testing, for example). This can indicate that the bacteria are winning the battle, because bacteria are deconjugating a high percentage of primary bile salts. At that point, it’s a good idea to test for SIBO.

Likewise, if you’ve done micronutrient testing and you’re especially low on fat-soluble nutrients (A, D, E, and K), look for SIBO.

If you know you’re dealing with solvent toxicity, it also becomes that much more important to address SIBO if it’s present, to make sure you adequately eliminate toxins. (Though in the short-term you can also add in activated charcoal during a detox protocol to bypass the bile issue as much as possible!)

By |2019-10-25T11:39:17-07:00October 25th, 2019|Categories: Articles|0 Comments

About the Author:

Dr. Lauren Deville is board-certified to practice medicine in the State of Arizona. She received her NMD from Southwest College of Naturopathic Medicine in Tempe, AZ, and she holds a BS in Biochemistry and Molecular Biophysics from the University of Arizona, with minors in Spanish and Creative Writing. She also writes fiction under a pen name in her spare time. Visit her author website at

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