Better Living

Our Marvelous Microbes

We cohabitate with trillions of bacteria and other microorganisms—and that’s a good thing
BY Jennifer Margulis TIMEApril 25, 2022 PRINT

Each human is an ecosystem, and we play host to countless microscopic life forms. As strange as it may sound if you’re not a microbiologist, our bacteria are an integral part of who we are, participating in nearly every aspect of our health.

My mother was a preeminent scientist who held the microbial world in high esteem, and I had the unusual experience of learning since I was a child that we should appreciate microbes. My mom used to talk to my three older brothers and me about how disappointing it is that we humans malign bacteria and misunderstand their importance. She explained that, rather than being invisible and evil purveyors of disease, bacteria are actually essential for us humans to live and be healthy.

Bacteria Balance

Most of us associate bacteria with infections, and see them as our enemies. We have to wash these “dirty germs” off our bodies, scrub them from every surface, and sterilize our food to keep it safe. We obsessively use antibacterial soaps and hand sanitizers, and take antibiotics to combat infections. When I wiped the curdled milk from under the many folds of fat in my baby daughter’s pudgy neck, I always worried about the places where there was some redness, indicating that she had the beginnings of a rash caused by “bad bacteria.”

We have trillions of bacteria and other microscopic organisms living on our skin, in our guts, and elsewhere in our body. Collectively, scientists refer to this community of microbes as the human microbiome. Some scientists prefer to call it the human “biome,” since some of our non-human symbionts—organisms living in symbiosis with one another—aren’t microscopic.

There’s so much we still don’t know or understand about our symbionts. But we do know that many of the bacteria cohabitating with us are beneficial. Health problems are usually not caused by the bacteria themselves, but when our bacteria get out of balance. Take my baby’s rashy neck fat, which could have been caused by staphylococcal or streptococcal bacteria or by a number of other microbes; every human has staphylococcal and streptococcal bacteria on their skin, but these may have gotten out of balance in my daughter’s case because the fat on her neck wasn’t allowing air to circulate and was creating the perfect moist environment to encourage bacterial overgrowth.

The bacteria on our skin live in a complex balance with us and with other bacteria, fungi, and even viruses. When the conditions on the skin change, that balance can be thrown off, favoring the overgrowth of some bacteria while discouraging others that keep them in check. Everything about our biome, like any biome, is about balance and harmony.

In addition, I wasn’t as educated about healthy eating as I should have been. Research published in the February 2021 edition of The Journal of Nutrition concluded that “maternal diet shapes the composition and diversity of breast milk microbiota” and “has a key impact on infant microbiota development,” contributing to infant health outcomes in both the short and long term. I was exclusively breastfeeding, but I was eating too many sweets and sugary foods, which may in turn have been encouraging the overgrowth of certain bacteria.

What Our Bacteria Do

The bacteria in our bodies help us survive and thrive. Without them, we wouldn’t be able to maintain life. Our very humanity depends on species that are so unlike ourselves that we barely recognize them as being alive.

At least 700 different species of bacteria live in our mouths alone. They live on our teeth and our tongues, inside our cheeks, and in the pockets between our teeth and our gums. While we don’t want to encourage plaque buildup and tooth decay caused by an overgrowth of harmful bacteria, much, if not most, of the bacteria in our mouths are beneficial. They keep bad bacteria in check, protect us against invasive bacteria that we may inadvertently imbibe via contaminated food, and even help us taste our food.

In fact, the composition of the oral microbiome, as scientists from Australia discovered in a 2021 study published in the Journal of Agricultural and Food Chemistry, may determine whether we like broccoli, cauliflower, and other brassicas.

Other recent research has connected our mouth bacteria with how we smell and taste wine and other fermented beverages. The bacteria in our mouth also help in generating mucus membranes and beginning the process of digestion, as well as performing a host of other functions.

“Your body is essentially a condominium for your microbiome or, as I like to call them, your bugs,” writes Dr. Steven R. Gundry, a cardiac surgeon and author of the bestselling book “The Longevity Paradox: How to Die Young at a Ripe Old Age.” “You are their home. Our relationship with our bugs has always been, and continues to be, symbiotic; in other words, their health is dependent on you and vice versa.”

Our Gut Guests

While the oral microbiome (the microorganisms in your mouth) hasn’t been extensively studied, in the past two decades there has been an explosion of interest in the gut microbiome—the bacteria and other microbes that live inside our intestines.

These microbes help us digest our food, protect our stomachs and intestines from leaking unwanted substances into the bloodstream, and play a key role in keeping us safe from infectious diseases. Some experts argue that it’s healthier to have a wide diversity of bacteria in the human gut.

Gundry is convinced that one of the most important factors in living a long and healthy life is feeding our gut microbiomes the foods that help them survive and thrive. He tells his patients that they can get younger from the inside out. By eating the foods that help beneficial bacteria thrive, we will have more energy and less risk of getting cancer, and can help stave off Alzheimer’s disease. Proinflammatory gut microbes have been linked to depression and other brain disorders, so much so that researchers from the California Institute of Behavioral Neurosciences and Psychology argue that microbes even affect the way we think.

“The common misperception is that ‘germs’ are bad things, and that we should avoid them and need to keep things clean,” Dr. Andy Kumitz, a retired family physician based in Ashland, Ore., told me. “That’s just not the case. Most bacteria are beneficial in the big picture. When it comes to health, if you don’t have the right bacteria in your gut, it will have an effect on your metabolism and your risk of disease.”

Dr. Bethany M. Henrick agrees. In 2019, a team of scientists led by Henrick, an adjunct professor at the University of Nebraska, found that infants who had Bifidobacterium longum infantis in their intestines had fewer markers of intestinal inflammation than infants who did not.

“Our guts are the biggest window into the environment,” Henrick said. “The newest research, including mine, is showing that the bacteria produce metabolites that impact how the immune system is developed. In other words, the bacteria provide a critical function in how the immune system is programmed. My guess is that these benefits from the interaction between human breastmilk and the microbiome go far beyond the immune system, probably affecting cognition and metabolism, as well.”

What about the rash under my baby’s chin? Instead of sterilizing it or using antibiotics, I gently wiped out the curdled milk with a wet washcloth, dried her skin well, and held her in the sunshine with her head comfortably back a few times a day. For too long, that fold of chin had stayed dark and damp, which isn’t the environment that human skin needs. With the help of sunlight and fresh air, her rash quickly went away.

By the time my youngest child was born, I had radically changed my diet. That baby, our fourth, never had a single rash.

We need not wage war on our microbiomes. We just need to learn to help them live in balance with each other and with us.

Probiotics Versus Prebiotics: What’s the Difference?

Probiotics are various strains of beneficial bacteria thought to be good for us, especially for our digestion. Functional medical doctors and other holistic health practitioners often recommend taking probiotics in pill form to help seed our guts with beneficial bacteria. Foods that contain probiotics include plain yogurt and fermented vegetables like kimchee and sauerkraut. It’s thought that eating probiotic foods and taking supplements may help our bodies bring our microbiome into a better balance.

Prebiotics are nutrients that help support beneficial bacteria. These compounds within our food encourage the healthiest bacteria to thrive inside our bodies. Fruits and vegetables, including apples, artichokes, dandelion greens, garlic, leeks, onions, sunchokes, chicory root, and some whole grains, are all high in prebiotics.

The Zoo in You

Here are just some of the marvelous creatures cohabitating with us.

Face Mites: These microscopic creatures live in our hair follicles, eyelashes, and eyebrows. We may pluck unwanted hairs, but for face mites—Demodex folliculorum—our peach fuzz is a perfect habitat, each hair like a tree in a forest for them. As entomologist Michelle Trautwein, at the California Academy of Sciences, explains: “You aren’t even the only animal using your face. Right now, in the general vicinity of your nose, there are at least two species of microscopic mites living in your pores.” In a 2014 experiment, published in the peer-reviewed journal PLOS One, every adult sampled had mites on his or her face.

These creatures have eight legs and are related to arachnids, which means they’re in the same class as spiders, ticks, and scorpions. As depicted in a YouTube video produced by KQED public radio, during the day they live inside our hair follicles, feasting on sebum, the oily substance that coats and protects our skin. At night, they crawl out to mate with other mites.

Scientists don’t really understand why it’s beneficial to humans to have mites on our faces. One theory, according to, is that they are part of a natural cleaning system, helping us to remove dead cells from our skin. Another theory, proposed by an Indian scientist in a 2007 paper, is that the mites actually defend our skin against pathogenic bacteria, particularly Staphylococcus aureus and Streptococcus pyogenes. Other research, however, suggests that when face mites get out of balance, they can cause skin inflammation and rosacea, a common condition that manifests as bumpy redness on the skin.

A Menagerie of Mushrooms: Referred to collectively as the “mycobiome,” the fungi that inhabit our bodies have received more attention from scientists in the past few years. Fungi include yeasts, molds, and mushrooms.

Anyone who has had thrush (an overgrowth of candida fungus) or who’s been plagued by jock itch, caused by fungi that live between our toes and in other warm crevices, may already be aware that there is a world of microscopic mushrooms inside human beings. While many of these species are believed to be harmful (Cladosporium can trigger asthma; Aureobasidium can cause infection in patients who receive organ transplants), it’s likely that the different fungal strains that we harbor—and that live in balance with our bacteria and other microbiota—also offer us health benefits. For example, one gut fungus in particular, S. cerevisiae, has been found to help the body fight against E-coli, an invasive bacteria; overcome the stomach flu; and even mitigate symptoms of irritable bowel syndrome, according to recent research done by a team of Chinese scientists.

Bacterial Guests in Our Guts: In the intestines alone, there are at least 8,000 strains of bacteria, and possibly many more. Every human’s gut has a different composition of bacterial hitchhikers (determined by your mother’s microbes and your mode of birth, diet, and lifestyle). Scientists have found that healthy people have gut bacteria quite different than the gut bacteria of people who suffer from diseases like Type 2 diabetes and ulcerative colitis.


Jennifer Margulis, Ph.D., is an award-winning journalist and author of “Your Baby, Your Way: Taking Charge of Your Pregnancy, Childbirth, and Parenting Decisions for a Happier, Healthier Family.” A Fulbright awardee and mother of four, she has worked on a child survival campaign in West Africa, advocated for an end to child slavery in Pakistan on prime-time TV in France, and taught post-colonial literature to non-traditional students in inner-city Atlanta. Learn more about her at
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