Your microbiome — the teeming community of trillions of bacteria in your colon — plays a central role in both a healthy digestive system and a healthy brain. The two are connected through your body's complex immune system.

When the gut microbiome is out of balance, the immune impacts can affect not just digestion but also the brain.

The gut-brain immunity link starts with the digestive tract. From mouth to anus, your digestive tract is in constant contact with both friendly and unfriendly microbes. Not surprisingly, at least 70 percent of your immune cells are found in the digestive tract.

Wrapped around your small and large intestine is a layer of tissue crammed with immune cells called the gut-associated lymphatic tissue, or GALT. The tissue is in close contact with the gut lining and your enteric nervous system. It's poised to pounce on any dangerous microbes that make it into the intestines and multiply enough to be a threat.

A diverse gut microbiome is the best way to keep the bad bacteria from becoming a problem — the neutral and beneficial bacteria crowd the bad ones so much that they can't usually get enough room to multiply. They usually can't get a foothold large enough to provoke your immune system into responding.

When they do, your body generates an immune response to get rid of the invaders. Immune cells rush to the rescue and produce a wide range of chemical messengers called cytokines. The immune cell messengers are vital to coordinating and controlling the inflammation and the immune response. They tell more immune cells to join the battle, control fever, make you feel tired, so you'll slow down, make your blood clot faster, and make you lose your appetite.

When the attacking bacteria have been dealt with, different chemical messengers tell your body to stop the acute stage of inflammation and begin the return to normal.

Acute inflammation may make you feel lousy for a few days, but the inflammatory response is temporary. Your body usually handles acute inflammation efficiently, turning it on and off smoothly.

But sometimes, acute inflammation doesn't resolve correctly. It lingers, causing ongoing low-grade symptoms. When inflammation is goes on for a long term, your immune system is stuck on high alert. Your production of inflammatory cytokines — such as interleukin-1 and interleukin-6 — continues unabated and the cytokines and other proteins that should turn them off don't get produced in the right amounts.

If you keep making inflammatory cytokines, they can damage cause brain fog, low mood, and irritability. Long-term, inflammatory cytokines also lay the groundwork for neurodegenerative disease and cognitive impairment.

When the gut-brain connection is disrupted by inflammation, the treatment goal is to restore a healthy balance and bring the immune system back to normal.

The first step is to help restore the balance in the microbiome through dietary improvements. I ask my patients to move away from the standard American diet (SAD), which is high in processed foods, sugary and salty snack foods, dairy foods, gluten, and artificial sweeteners and additives.

This diet is the underlying cause of most inflammation. It skews the bacteria in the gut toward those that produce inflammatory metabolites — byproducts of bacterial digestion — and force the immune system to respond.

The metabolites also are sensed by the vagus nerve, the cranial nerve that innervates much of the digestive system. The vagus carries the message to the brain, which can trigger a further inflammatory cascade.

I ask patients to switch to a diet rich in fresh vegetables, whole grains, beans, and high-quality fats and proteins. The change in the diet gives the microbiome the dietary fiber and good fats it needs to restore a healthy balance and stop sending inflammatory signals to the immune system.

Dietary changes take a while to kick in, however. Also, many of my patients have inflammation from poor diet and lifestyle. They need more help, and they need it faster than dietary changes alone can provide. I recommend a neuroimmune protocol that's designed to support the brain and the gut simultaneously.