Don’t freak out, but right now there are trillions of tiny bugs crawling all over and inside your body. But these aren’t the creepy crawlies that keep you up at night or give you a fright when spotted in a dusty corner. These “bugs” are part of your microbiome, a menagerie of mostly beneficial bacteria that scientists are now discovering can influence the functioning of everything from the immune system and gastrointestinal tract to the endocrine system and skin.

We have long known that bacteria exist within our bodies in abundance. In fact, there are 10 times more bacterial cells in your body than there are human cells: We are fully functioning, symbiotic organisms, groomed from birth to coexist and thrive with help from the countless microbes that inhabit both the areas on our bodies directly exposed to the environment (like the skin) and the body parts that interact with the outside world, such as the gastrointestinal tract (GI) and nasal membranes.

It’s the bacteria in the GI tract that have garnered the most interest among researchers. There are a thousand distinct bacterial species living in the GI at any given time. As you grow, the great mishmash of bacteria in your gut settles into something of a checks-and-balances system. Troublemaker microbes are typically canceled out by beneficial ones like Bifidobacterium and Lactobacillus. Scientists aren’t sure exactly what any of those bugs really do, but they know we have a complex, dynamic relationship with them.

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Sometimes, though, when your gut’s balance is tipped in the wrong direction (called “dysbiosis”), more insidious microbes begin to take over, prompting inflammation that can pave the way to diseases like type-1 or type-2 diabetes, obesity, or even neurological problems. Other disorders linked to GI tract microbial imbalances include inflammatory bowel disease, lupus, multiple sclerosis, psoriasis, rheumatoid arthritis, cancer, and cardiovascular disease. Dysbiosis triggers include poor diet, overprescription of antibiotics, or simply leading an overly sedentary lifestyle, according to a 2013 analysis in the journal Clinical Reviews in Allergy and Immunology.

Why Probiotics Matter

To keep your microbiome in a harmonious equilibrium, it’s important to eat a diet that contains probiotics. “Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host,” says Mary Ellen Sanders, Ph.D., executive science officer at the International Scientific Association for Probiotics and Prebiotics.

“Probiotics are thought to play a role in preventing and treating certain diseases and infections such as irritable bowel syndrome [IBS], UTIs, vaginal infections, and more,” adds Alissa Rumsey, R.D., C.S.C.S., founder of Alissa Rumsey Nutrition and Wellness. “They may also reduce the risk of infections and illness.” You can find probiotics in foods like yogurt and kefir (look for the “live and active cultures” seal) and aged cheeses and other fermented foods like tempeh, miso, unpasteurized sauerkraut, and kombucha.

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But for some people it can be hard to get the recommended 1 billion live microbes a day for general gut health from foods alone. For some specific ailments, up to 100 billion bugs may be needed to cause a healing effect. One easy way to make sure you are getting enough beneficial bugs is by taking a probiotic supplement. “Supplements are a good source of high numbers of different probiotic strains,” Sanders says. When selecting a probiotic, look for one that has a list of specific strains; amounts are usually identified by the term CFUs, or colony-forming units, an estimate of the number of viable bacteria in the product when packaged. Also, be sure the package itself protects the bacteria from UV light with opaque bottles or blister packs and has an expiration date.

For general health, the type of probiotic strain isn’t as important as having a variety of bacteria types, since research indicates that multiple strains may work synergistically to improve health. But if you have a specific ailment, narrowing down the strain can be helpful. (See “Probiotic Primer,” below.) “Some probiotics may help with nagging digestive problems or help you avoid diarrhea from a prescription antibiotic,” says Sanders. Other probiotics may reduce the incidence and duration of common respiratory and GI infections, especially if you’re in a heavy training period, she adds.

It’s also important to note that probiotics don’t take up residence long term—they stick around only a week or so before passing through your system. “When administered to healthy people, probiotics don’t seem to change the overall structure of the gut microbiota—they have their effects as they transit through the gut,” says Sanders. But during that time they can occupy sites that may otherwise be colonized by harmful bacteria.

The Role of Prebiotics

Think of prebiotics as fuel for probiotics, enriching GI tract microbes in a beneficial way. “A prebiotic is food preferentially used by your native, beneficial bacteria,” Sanders says. One easy way to feed your good microbes is by increasing your intake of high-fiber foods. Though all fiber-rich foods aren’t prebiotic, many fruits, veggies, beans, and grains with high amounts of a dietary fiber called inulin will provide fuel for bacteria. As this undigested fiber passes through the GI tract, bacteria employ enzymes to break it down into simple sugars, which are then fermented to create short-chain fatty acids. These fatty acids contribute up to 10% of the calories our cells need.

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Other super brous foods—asparagus, chicory, dandelion greens, Jerusalem artichokes, garlic, leeks, onions, broccoli, cabbage, kale—contain lots of other types of inulin that bacteria thrive on, like fructo-oligosaccharides (FOS) and galacto-oligosaccharides (GOS). Oligofructose-enriched-inulin, or OEI, is a potent mixture of prebiotics that’s considered a “full spectrum” prebiotic, as it has been found to work throughout the colon.

It can be tough to get the recommended minimum of five grams a day of prebiotics from food, so when choosing a supplement, look for FOS, GOS, or OEI or chicory and inulin. These ingredients fuel beneficial bacteria to help them pump out short-chain fatty acids to provide cells with energy and improve metabolism and immune function.

Probiotic Primer

All beneficial bacteria are not created equal. Here’s a look at some common probiotic species and the health benefits they may provide.

  • L. acidophilus: Supports nutrient absorption, helps digest dairy, and may alleviate some diarrhea and lower cholesterol.
  • B. longum: Helps maintain the integrity of the gut wall; scavenges toxins; and may promote immune system functioning, reduce infections, and lower inflammation.
  • B. bifidum: Breaks down complex carbohydrates, fat, and protein; shows antioxidant properties; supports GI tract health; and decreases symptoms of inflammatory bowel disease and syndrome.
  • L. rhamnosus: Prevents traveler’s diarrhea, benefits liver health, fights cavities, and boosts immunity.
  • L. fermentum: Helps increase nutrient absorption, lowers cholesterol, fights viruses and bad bacteria, and provides antioxidant activity against aging.

For a comprehensive guide to probiotic products, what strains they contain, and their benefits, go to or

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