How Gut Bacteria Influence your Gallbladder

A microbiome is an ecosystem of millions of different bacteria that exist in our outer environment as well as on and inside the body. The skin has its own microbiome system; the eyes have another. The one we hear of the most is the gut or intestinal microbiome. We all know that it is of huge health benefit to having a populace of good gut bacteria overwhelming the bad and that when the balance is off, disease results. We also all know about and take probiotics to assist in this process, but did you know that the probiotics we take are only a few of the millions of existing bacteria in the gut?

Well, the gallbladder, the liver, and the bile, also known as the biliary system, have their own microbiome or ecosystem of positive and negative bacteria as well. Actually, bacteria only becomes negative when it overpopulates and takes over the positive. It’s all a matter of balance.

Relationship Between Gut Bacteria and other Body Systems

Research is growing on the possibility of understanding the microbiota of the different systems of the body, including the bile. Some of the things they have found are:

  • Gallstones are formed in the presence of bacteria that are out of balance – pigment and cholesterol stones.
  • There is also a link between gallstones and an imbalance of gut microbiota, not just bile microbiota.
  • The presence of liver flukes (a parasite found in raw and smoked fish) changes the microbiome negatively and may cause gallstone formation as well as other gallbladder diseases.
  • The presence of gut microbiota in the bile of someone with what’s called lithogenic bile (or stone-forming bile) could indicate intestinal permeability or leaky gut. This could lead to increased inflammation and stone formation.
  • The gut microbiome plays a role in regulating the composition of bile as well as the amount of bile salts available (called the bile salt pool.)
  • Dietary fat can alter the composition of bile, encouraging the proliferation of inflammatory gut microbes.
  • Bile affects the type of gut bacteria present.
  • There seems to be a connection between the microbes present in bile and small intestinal bacterial overgrowth (SIBO).

So one of the questions asked is, does the gut bacteria influence the biliary microbiota, or is the bacteria in the bile that influences the gut microbiome? Well, just as in the ecosystems of nature, none are isolated unto themselves, but all exert an influence on the other. The more out of balance one system gets, the more it affects the other systems.

The bacteria in the large intestine is a very large population compared to the small intestine. There is a valve that prevents the backflow of digesting food and the bacteria into the small intestine, just as there is a valve that prevents the backflow from the small intestine going up into the stomach, and likewise, the esophageal sphincter that prevents flow from the stomach up into the esophagus – at least theoretically. Things go wrong as we know.

But even when these checkpoints are functioning optimally, there is still movement of bacterial colonies between them.

The bile salts flow into the small intestine, where 95% is rerouted back into the liver to re-circulate. This is called the bile salt pool. So it could potentially pick up particular bacteria from the small intestine and carry it to the liver. 5% of it continues out with the feces, giving it a chance to leave some of its species in both the small and large intestines.

And then there is the condition of one or more of those fail-safes being faulty and allowing backflow all over the place – GERD, bile reflux, ileocecal valve dysfunction, sphincter of Oddi impairment, and so forth. Bacterial types have all sorts of potential to move and colonize elsewhere. This is one theory of the cause of disease – including gallstones.

You might well ask about the survival of bacteria in different pHs. Bile has a pH of 7 and stomach acid has a pH of 5.2. Different species of bacteria thrive in each.In general, many of the bacteria accompanying the bile will be destroyed when the acid chyme from the stomach joins the bile in the small intestine. And species that thrive in acid will be destroyed by the alkalinity of the bile. But then there are those that will adapt to the middle-of-the-road pH made from the blending of the two. And bacteria, like viruses, can mutate and learn to adapt to different environments.

The Role of PPIs

The increased use of proton pump inhibitors which lower the protective acid pH, is contributing to an increase in different colonies of bacteria thriving in a more alkaline environment than was previously impossible.

It’s a budding new field of science that is taking many directions. For example, they have found that by inserting bacterial colonies from the bowel of a thin rat into the bowel of an obese rat, the thin rat becomes obese and vice versa. Will they be doing such things with gallbladder bacteria? Who knows what the future of science holds?

So this is all very interesting, but what do we do with all this information? More research needs to be done and techniques developed for altering disease-causing microbiomes. But in the meantime, doing what you can to provide an optimal environment for critters within your body is your best bet.


Avoiding foods that bad bacteria thrive on, such as:
            • refined foods and sugars
            • red meats
            • trans fats
            • hydrogenated and partially hydrogenated fats
Eating foods that promote a positive environment such as:
            • Lots of fresh fruits and vegetables – especially sulfur-containing vegetables like broccoli, kale, and Brussels sprouts
            • small amounts of lean meats
            • good fats like omega 3 fats eg. fish oils

Probiotic foods actually contain good bacteria whereas prebiotic foods prepare a friendly environment in which good bacteria can thrive.

Examples of probiotic foods:
            • Cultured and pickled foods such as kefir and yogurt (either from dairy or from coconut or soy), raw apple cider vinegar, kombucha fermented drinks, miso, and other fermented soy products such as natto and tempeh, kimchi, tempeh, sauerkraut, pickled ginger, Greek olives, etc
Examples of prebiotic foods are foods that are high in inulin fiber such as:
            • Jerusalem artichokes
            • Bananas
            • Leeks
            • Chickory root – which makes a great coffee-like drink
            • Dandelion root
            • Burdock root
            • Garlic
            • Jicama
            • Mushrooms
            • Leafy greens
            • Mushrooms

Suggested supplements:

1. RESTORE for repairing tight junctions of a leaky gut

2. Healthy Bowel Support containing 200 mg of chickory root inulin, asparagus stem, leafy greens, fruit extracts as prebiotics, and 800 million CFU of probiotics

3. HMF Multistrain Genestra Probiotic for your daily dose of prebiotics.

4. Digestive Enzymes support the breakdown of food and ultimately help gut healing.