I’ve written quite a lot about the gut microbiome – the trillions of bacteria that live mostly in the colon – in protecting and sustaining good health. They help the gut immune system react to, and avoid over-reacting to, potentially harmful bacteria and other toxins that we take in with our food. They’re a key piece of the gut assembly line that produces important vitamins and neurohormones like serotonin and dopamine.

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If I’m doing my job, this should all be old news. What you might not know and what researchers are increasingly coming to appreciate is that the human body is not just made up of human cells and a bunch of bacteria in the gut. We are a collection of microbiomes. Humans and the bacteria that live inside us co-evolved over the millennia, one giant quid pro quo – our bodies provided the bugs with a moist, warm home, complete with a steady food source, and they sustain us in a variety of ways, most numerously and elaborately in the gut. Attempting to capture his expansive sense of self, the poet Walt Whitman famously wrote, “I contain multitudes.” Well, guess what, we all do!

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Here’s the low-down on the multiple microbial universes that exist alongside our gut microbiomes – on the skin, in the mouth, the nose, the lungs, and the genitals –how we can best take care of them so they can take best care of us.

The skinny on the skin.

The bacteria (and fungi and viruses) that live on the skin make up the skin microbiome. It’s a close cousin of the gut microbiome. With the help of their resident bacteria, they both protect the body from unwelcome visitors, in the skin’s case, from toxins in the air and the soil, in the gut’s case, from harmful microbes that travel down the GI tract with our food.

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When, because of poor diet or stress, the “bad” gut bacteria in the gut get the upper hand over the “good,” toxins can escape through tiny holes in the gut wall (aka, “leaky gut”) into the bloodstream, triggering systematic inflammation. And one of the most common places — certainly the most visible place — for that inflammation to wreak havoc is the skin. And the skin’s own bacteria can be thrown out of whack by the same things that disrupt a healthy gut, namely a poor diet (think low-fiber-carbs, loads of sugar, processed foods) and too much stress. One comprehensive research review found a clear link between a skin microbiome that was out of balance – too many “bad guys,” not enough good – and a range of skin conditions, everything from everything from the routine (acne) to the more serious (dermatitis). And new research makes a connection between excessive numbers of some bad bacterial actors and a decline in collagen fibers, the scaffolding that keeps skin looking firm and youthful. What I know first-hand: when I work with a patient to improve their gut health, I, and they, often see clearer, more glowing skin.

The skin-gut prescription.

Whether the source of skin problems is the bacteria in the gut or on the skin, or some combination of the two, my prescription is the same. Ditch the crappy “comfort” food and go all in on non-starchy veggies with their plentiful, and good-bacteria-friendly, plant fiber. Probiotics, either in the form of fermented foods or supplements, can provide a bacterial health boost. Manage stress with your good sleep habits, your favorite meditative techniques, and plenty of everyday movement. That’s good advice for any “biome” I can think of but it’s particularly on-point for the gut and the skin.

Tending to the microbiome in your mouth matters.

Granted, it may make you feel slightly queasy to consider, but your mouth is home to over 700 species of bacteria, not to mention its fair share of fungi, viruses and protozoa. They colonize the surface of your teeth as well as the soft tissues of the mouth, for instance the tongue and the cheeks. When your mouth bacteria are in working order, your teeth should be cavity-free and your gums, pink and healthy. When they’re not, opportunistic bacteria can eat away at the tooth enamel, setting the stage for cavities and infections inside the tooth, as well as inflammation of the soft tissue, causing gum bleeding and recession and sending you down the road of periodontal disease, bad news for teeth and gums alike.

Your oral microbiome needs a good defense.

Good oral hygiene is non-negotiable which means regular brushing and flossing. You may want to explore tongue-scraping with an integrative practitioner or one who’s familiar with the ayurvedic medical tradition which places great value on the practice. As far as diet goes, what’s good for the gut and the skin is good for the mouth, but here we can get even more specific. Crunchy veggies like leafy greens, celery and kale are rich in minerals that help with teeth “re-mineralization,” building back up the enamel that gets eaten away by cavity-promoting bacteria. And those same veggies are high in nitrates which, inside the mouth, reduce acidity, limiting the growth of those bacteria. Foods and beverages high in the polyphenol antioxidant family (think cacao nibs, coffee and tea) serve the same purpose and omega 3-rich foods (best bet: small, oily fish) have a welcome all-purpose anti-inflammatory effect on your mouth, making them must-have allies to help protect against periodontal disease.

The oral microbiome no-fly list.

Smoking is out (for every reason, of course) and if you do drink, limit your alcohol consumption as much as possible. Sugary carbs are always bad news, especially sugary (and high-acid) sodas, no surprise. But you may not realize that crackers are worse for the health of your mouth than say, candy. The cracker remnants lodge between your teeth and provide a handy food source for the acid-producing bacteria that damage your dentition. Ditto for dried fruit.

The nosy microbiome.

Working down the body we come to the nasal microbiome, a space dominated by only a handful of bacterial species. As with the mouth and the gut, the nose provides the body with a filter to help protect it from any potentially harmful threats from the outside world, in this case, in the air that we breathe. We do know the bacterial balance in the nose can be disrupted by excessive exposure to air-borne toxins, including garden-variety air pollution, as well as allergens. And bacterial imbalances have been linked with chronic sinusitis and nasal allergies. Alcohol may weaken the nose’s defenses. One small study found that nasal microbiomes of winetasters had fewer bacteria and fewer bacterial species. (Not great news for your wine-obsessed friends who may like to congratulate themselves on their refined noses and palates!)

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When bad bugs do evade the nose’s defenses, we know they can use the nasal space as a base of operations for respiratory infections. Even more disturbingly, we have evidence that microbial byproducts produced by some unfriendly nasal bacteria may cross the blood-brain bacteria and be implicated in the development of neurological diseases like Parkinson’s and Alzheimer’s.

Your lungs come with a microbiome too.

Until fairly recently, the lungs were thought to be sterile. But not so. They have their own (modest) microbiome, likely the result of inhaling mucus secretions from the mouth and the nose. And a robust lung microbiome may well be a defense against respiratory infections and diseases like COPD and pneumonia, but that story is just beginning to be written.

The genital microbiome: last but not least.

There is, in case you were wondering, a microbiome inside the penis and there’s evidence that a weakened or imbalanced one may contribute to male UTIs. But the vaginal microbiome is the bigger story here, with its much more extensive collection of bacteria that plays a major role in women’s sexual health. Recall that we wanted to lower the acid level in the mouth. In the vagina, it’s just the opposite. An acidic environment, rich in the lactobacillus strain, helps keep the bad bugs at bay, reducing the risk of common problems like vaginitis, yeast infections and STDs. The research record also show links between vaginal dysbiosis and pelvic inflammatory disease, miscarriage and premature births. There’s even some evidence that a healthy vaginal microbiome can help protect against cancer.

Mind your vaginal microbiome.  

The vaginal microbiome is similar to the oral microbiome in that lifestyle and good hygiene habits count. Frequent sex and a more numerous sexual partners may stress the system so pay extra attention to your internal defenses. Smoking is out (you needed another reason to quit?). And, interestingly, we think that diet plays a role in the health of this microbiome. A high sugar, low-fiber diet has been linked with bacterial vaginosis, and susceptibility to frequent UTIs is linked with high sugar intake, so steering clear can make a big difference in vaginal health – and your health over all.