Bile is produced in the liver and stored in the gallbladder. Its composition is mostly water, but it also involves bile salts (acids), bilirubin (a breakdown product of red blood cells), and fats (cholesterol, fatty acids, and phosphatidylcholine.)

The primary purpose of bile is to help us absorb fat from our food—without this, fat would pass right through us, along with all the fat-soluble vitamins. But bile also plays a role in keeping our microbiome healthy, as well.

Bile and Your Microbiome

The majority of your good gut bacteria should be in your large intestine: up to 1012 bacteria per mL, compared to around 104 bacteria per mL in the small intestine.

The small intestine is also quite high in conjugated bile acids, or it should be—and these bile acids do in fact decrease bacterial growth. (This does not apply to our “good” bacteria, though, as they are resistant to the antimicrobial effects of bile.)

This study also shows that when bile acid levels are lower (in cases of liver disease, for instance, or in animal models that have undergone surgical ligation, or closure, of the bile duct), SIBO (Small Intestine Bacterial Overgrowth) tends to occur. 

Aside from their antimicrobial role, bile acids also help to decrease small intestinal motility (where the actual nutrient absorption happens), while increasing large intestinal motility. The underlying cause of SIBO is very often low colonic gut motility, and bile plays a role here too.

Bile also helps regulate and may even initiate the Migrating Motor Complex (MMC), the process that sweeps the intestines clean in between meals. Impairment in the MMC also predisposes to SIBO.

Phospholipids and Your Microbiome

So this means bile acids are important — but you also need your bile to flow properly in order to deliver them to the small intestine via the bile duct. This is where phospholipids come in.

Phospholipids, primarily phosphatidylcholine (since about 96% of the phospholipids in bile are this), help to emulsify bile, joining the water with the cholesterol so that the latter doesn’t precipitate out of solution. (Too much cholesterol and too little phosphatidylcholine can lead to gallstones, or cholestasis: decreased bile flow.)

In other words, if your phospholipids are low, you get less bile delivered to your small intestines—which is why low phosphatidylcholine levels can also lead to SIBO. Low phosphatidylcholine can occur due to low intake of its precursors (choline, high in eggs, liver, milk, and peanuts), or due to a backed up methylation pathway (MTHFR: according to Dr Ben Lynch, some 70% of methylation gets used up in the production of phosphatidylcholine), .

The Upshot

You can’t isolate any one digestive process from the rest. Bile isn’t just about fat absorption: it also plays an integral role in maintaining the health of the microbiome, which is critically important to all aspects of your digestive health.

If your bile needs some extra ‘flow’ support, I usually recommend a powdered version of phosphatidylcholine, just because that way you can take a lot of it without taking a huge handful of pills. This will also relieve excess stress on your methylation pathway. Dosing is up to 9 grams daily in water.