Are you eating your bugs or are they eating you?

The microbiome is the collection of bacteria, fungi, protozoa and viruses that live in and on us. Research on this topic is in its infancy but it is clear that these organisms help or hurt us in fundamental ways, depending on the balance of good and bad bacteria.

Why does our immune system tolerate having all these creatures inside and on us? Because they give us things we need. Gut bacteria make vitamin K and short chain fatty acids, essential for blood clotting and calming inflammation, respectively. They also help us extract nutrients from the food we eat that would otherwise go unharvested. Everyone has a balance of good and bad bacteria. Good bacteria make more short chain fatty acids, which calm the immune system. So when things are going well, good bacteria make stuff for us and calm the immune system in the gut.

When the system gets out of balance, and there aren’t enough calming, good bacteria, the immune system becomes more active, doing what it really was designed to do – attack the bugs. This is called “dysbiosis” (dis-by- osis). This leads to inflammation, and what some people refer to as “leaky gut.”

Inflammation causes the fabric of the intestinal lining to become more loose-knit. The goal of this change is to allow more immune cells to travel out of the bloodstream and between the cells, to get to the area where the threat is coming from. But it works both ways – immune cells can migrate through tissue to get to the gut, but bacteria can migrate out, too. In this way, an imbalance in the microbiome has been linked to autoimmune diseases. When the immune system encounters bacteria or bacterial products, or even things that look like bacteria or bacterial products, it attacks them. Dysbiosis has been linked to Multiple Sclerosis and other autoimmune diseases are under investigation. Dysbiosis may also be part of the reason that some people with fat in the liver get elevated liver enzymes and even scarring, while others do not. And it may be linked to diseases like Primary Biliary Cholangitis and even colon polyps and colon cancer.

So how do we get a healthy microbiome? The short answer is by feeding your bugs and eating your bugs.

Good bacteria love fiber and inulin. Inulin is a kind of starch found in root vegetables like onions, garlic, and chicory root (a common source of inulin in nutrition bars). It is also found in bananas. Fiber and inulin are pre-biotics. Once you’ve got plenty of good food in your gut, you can seed it with probiotics. Probiotics are good bacteria. Look for a brand that has lots of different kinds of bacteria. They have names like b. infantalis or L. acidophilus. One will do but 10 is better. Start with a brand that has 4-5 billion bacteria and work your way up – you don’t want to shock your system.

And for the long haul – because remember, building a healthy microbiome is a marathon, not a sprint – follow a Mediterranean Diet. Eat lots of different colored fruits and vegetables to get the micronutrients that good bacteria love. Avoid being too clean – antibacterial soaps and gels do more harm than good. And ask your doctor if you really need that antibiotic, or if there is a topical choice instead.

- Shannon Scholl, MD