One in five Americans​ — about 50 million people in the United States — have an autoimmune disease.

These include conditions such as lupus, rheumatoid arthritis, and multiple sclerosis​ which occur when the immune system begins attacking the body’s own organs, tissues, and cells. Research​ suggests that these diseases are on the upswing, with reports showing that Type 1 diabetes, lupus, and celiac disease, for example, are being diagnosed more frequently.


Medical experts are still mystified about what exactly causes autoimmune diseases and why some people are more susceptible to them. But now, fascinating new research shows that your gut bacteria — yup, you read that right — may play an important role.

A 2017 study published in the Journal of Experimental Medicine found that mice carrying a mutated gene that made them more susceptible to autoimmune disorders also showed changes in gut bacteria at around the same time they began to develop autoimmune symptoms. But when researchers gave the mice a probiotic to “reset” their gut, the mice’s digestive systems returned to normal, and they had decreased inflammation and a longer lifespan.

“Eighty percent of your body’s immune system is located in your gut, so if you don’t have a healthy gut, you can’t have a healthy immune system,” Amy Myers, MD, an Austin, Texas, specialist in autoimmune diseases and author of The Autoimmune Solution, points out to Yahoo Lifestyle.

How your gut affects your health

Your gut does more than just digest your food. It’s home to trillions of bacteria, fungi, and viruses that make up your stomach’s microbiome. While some of these bugs are bad, some are also good, helping your gastrointestinal (GI) tract run smoothly by breaking down food, synthesizing vitamins and other nutrients, and helping fight against germs that can cause infections, Shajan Sugandha, MD, a GI specialist at the University of Alabama in Birmingham, tells Yahoo Lifestyle.

When your microbiome is in tiptop shape, your digestion works well. But if it’s thrown off — which can happen due to anything ranging from a poor diet to medications like antibiotics to stress or a bout of the stomach flu — then some undigested toxins and unfriendly bacteria can stray from your GI tract, causing inflammation throughout your body, explains Myers.

This may help explain why research is now increasingly linking the microbiome to conditions such as obesity, Parkinson’s disease, and depression. Another theory is that some people’s bodies respond by sending their immune system into overdrive, so that anytime you come into contact with these bad bugs, your immune system fires off a cascade of inflammatory chemicals that cause you to develop chronic inflammation, and in time, an autoimmune disease, notes Myers.

This may be particularly true when it comes to multiple sclerosis, a type of autoimmune condition in which the body begins to attack the central nervous system — the brain, spinal cord, and optic nerves. This disorder, which affects over two million people worldwide, can be devastating, causing symptoms like trouble walking, muscle weakness, and vision, bowel, and bladder problems. But a University of California, San Francisco study published in 2017 in the journal Proceedings of the National Academy of Sciences sheds new light on the disease. When researchers analyzed the microbiomes of 71 people with MS versus 71 healthy controls, they found that patients with MS had four times the amount of two types of bacteria: Acinetobacter calcoaceticus and Akkermansia muciniphila. In addition, they had one-quarter of another type of bacteria, Parabacteroides distasonis, compared to people without the disease.

Researchers then took the study one step further, injecting gut bacteria from the MS patients into mice and then inducing brain inflammation in mice that received gut bacteria from healthy individuals. Within three weeks, the MS-infused mice had developed much more severe brain inflammation than those given the normal gut bacteria.

In a second German study published in October 2017, also in PNAS, researchers examined 34 pairs of twins in which only one of each had MS. They then took samples of their gut microbes and injected them into mice already predisposed to develop a disease like MS. More of the rodents who got the MS microbiome ended up developing MS-like symptoms, such as brain inflammation, than those who got the healthy microbiome.

Most of this research has been done only in mice, and experts caution that it needs to be replicated in humans before coming to firm conclusions. But, “I think all of these studies lend credence to the belief now that keeping your microbiome healthy, with a diversity of bacteria, is important for overall health, especially if you have a genetic predilection or other risk factors for developing an autoimmune disease,” Daniel Freedberg, MD, a gastroenterologist and assistant professor of medicine at Columbia University Medical Center, tells Yahoo Lifestyle.

How to keep your gut in tiptop shape

The best way to keep your microbiome healthy is through a good diet, says Freedberg. The good bacteria in your gut thrive on high-fiber foods (think: lentils, green peas, and raspberries), as well as fermented foods, such as plain yogurt with active cultures, sauerkraut, miso, and pickled vegetables.

A 2016 study in the journal Science found that plentiful consumption of those foods — as well as, surprisingly, coffee, tea, and wine — helped keep gut bacteria healthy.

Foods high in sugar, on the other hand, such as whole milk and sodas, had the opposite effect. A 2013 Harvard study also found that an animal protein-rich diet filled with meat and cheese dramatically alters your microbiome, and not in a good way: It promotes the rise of certain types of bacteria linked to inflammation.

Certain drugs, such as antibiotics, can also harm your microbiome. These meds kill the good bacteria in your gut along with harmful ones, and your microbiome may not recover for months after a course of antibiotics. That’s one reason why you shouldn’t take those drugs unless you really need them, notes Sugandha. Other drugs that can impact your gut microbiome are medicines that kill off stomach acid, like antacids and protein pump inhibitors, and the diabetes drug metformin.

The research on probiotics is murky, according to Sugandha, and it’s not quite clear yet which strains are best for your microbiome and who might need them. That’s why most doctors recommend trying to get most of your probiotics through food. That said, if you’re on antibiotics or another drug that can kill off stomach bacteria, two types that have the most research behind them are Lactobacillus rhamnosus GG (aka LGG) and Saccharomyces boulardii. And although probiotics are considered safe for healthy people to take, it’s always best to check with your doctor first.

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