How Your Microbiome Is Made—and How It Informs Your Lifelong Health

It seems that, practically every week, a new study comes out linking the bacteria living in your gut to some surprising new aspect of health or disease—from Parkinson’s to alopecia.^1,2 But if your microbiome determines your health, what determines your microbiome? Unlike the set of genes you’re born with, the microbiome is dynamic, presenting a uniquely powerful opportunity to take health into your own hands.

To fully grasp this power, you’ll need to understand that your body is an ecosystem. Trillions of bacteria from hundreds of different species live on and within you, and an ever-growing body of research shows that the makeup of this community—your microbiome—can impact nearly every aspect of health, at every stage of life. In a radical departure from medicine’s traditional view of bacteria as pathogens, parasites, or invaders to be vanquished, we’re coming to understand that our microbial partners represent an essential component of our biology: a whole second genome that’s almost as important for health as your 23 pairs of chromosomes. 

So what’s behind this paradigm shift? Why has science suddenly woken up to the fact that most bacteria are friend, not foe? And if a healthy and harmonious microbiome is really an essential prerequisite for proper immune, hormonal, cognitive, and metabolic health, how could we have gone so long without realizing it?

The answer is that, until recently, we didn’t have the tools to understand where these bacteria come from, what they can do, and how the choices we make shape this invisible jungle inside us. In fact, understanding where your microbiome comes from is the first step in recognizing the fundamental agency you have over your body.

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Planting the Seeds: Your Microbes As Family ‘Heirlooms’

When we talk about our microbes as “partners,” that isn’t just a turn of phrase. In actuality, a lot of your most important bacteria are human-unique species. These microbes need us to survive and thrive (and vice versa). Before the development of gene-sequencing technology, there was no way for us to know that many of our microbes aren’t found anywhere on Earth besides the human body, which means we can only get them from other humans. Incredibly, some of these species are found in almost every healthy human, no matter where in the world they’re from—implying that these bacteria are “heirlooms” that have been passed down from generation to generation since the dawn of humankind, and maybe even before.³

The process of acquiring these bacteria is called “seeding,” and it starts early in life. While the womb itself is largely a sterile “bubble,” the minute a mother’s water breaks, the baby is exposed to bacteria.⁴ From that moment on, there’s no such thing as “clean”—only the right kind of dirty—so a lot of work goes into seeding a child’s body with symbiotic microbes that will help them thrive.

Birth: The Truth About ‘Vaginal Seeding’

Before a human is born, their body is largely free of microbes, but it can’t stay that way for long. Our insides are warm, wet, dark, and full of nutrients—in other words, the perfect environment for bacteria to thrive. As a result, all it takes is a few cells of the right bacteria finding their way to the right spot in order for a community to establish itself.

Naturally, the first and most important source of bacteria that a newborn is exposed to is its mother. For a long time, it was thought that the bacteria in a woman’s vagina were key to establishing the child’s gut microbiome, but new research has since called this assumption into question.⁵  

The notion originated with the observation that children born by cesarean section tend to have different gut bacteria from their vaginally born counterparts, and that they’re more prone to diseases like ulcerative colitis, celiac, and even asthma.⁶ It’s easy to see why this led people to conclude that C-section babies’ lack of exposure to the vaginal microbiome was responsible. But scientists now think that this is more likely due to factors such as the use of antibiotics during C-section procedures, which can impact the child’s microbiome via its impact on the mother’s microbiome, interrupting the transmission of key bacteria (those aforementioned “heirlooms”) that are supposed to be inherited during the first few months of life, as we’ll get into below.

One major implication of this research is that the recent trend of “vaginal seeding”—swabbing the mouths or skin of C-section babies with vaginal fluid from their mothers—has traditionally not been supported by the science. However, a new pilot study from June 2023 suggests that swabbing C-section babies with their mother’s vaginal fluids may in fact be beneficial, and might improve brain development. While further studies are still required, this remains an exciting area of research.⁷

Another is that, when there’s a choice, vaginal birth is preferable to C-section, in terms of providing the child with a microbiome that gives them the best shot at lifelong health. However, some scientists have reported success in normalizing the gut microbiome of C-section babies using a preparation of the mother’s gut bacteria, collected a few weeks prior to delivery.⁸ While more research is needed before anything like that can become standard practice, it’s a promising indication of the direction that medicine might take in a more microbiome-conscious future.

No matter how we’re born, for the first few days after birth, the microbiome is in a state of chaos. In a day-old infant’s gut, you’ll find bacteria from all over a mother’s body—her gut, her mouth, her skin, her vagina—as well as from the environment.⁹ Over the next weeks, this community will shift and change, as the stray skin bacteria that found their way into the newborn’s GI tract are supplanted by more gut-adapted species. 

Infant-Feeding: How Breast Milk + Formula Impact Microbiome Development

Any gardener can tell you that planting seeds is only the beginning of the work, and here it’s no different: Shepherding a developing microbiome into a healthy state that supports the body’s growth is an active process for the first few years of life. That’s why evolution has shaped breast milk to be the perfect prebiotic (a food that promotes a healthy microbiome by supporting the growth of certain kinds of bacteria). Human milk contains unique oligosaccharides (called HMOs), which are highly complex sugar molecules that can only be consumed by certain kinds of microbes, that selectively nourish beneficial bacteria like Bifidobacterium. While these sugars are present to some extent in the milk of other animals (like cows), human milk is truly turbo-charged, with HMO levels 100–1000x higher than cow’s milk.¹⁰ By feeding beneficial bacteria, not only do HMOs prevent pathogens and other antibiotic-resistant bacteria from taking root, they lay a foundation for the right bacteria (like certain species of Bacteroides) to take over once solid food is introduced.¹¹

But the benefits of HMOs go beyond their role as food for “good” bacteria. Some types of HMOs are structurally similar to surface glycans, molecules found on our own cells that pathogenic bacteria can stick to and use as a point of entry to cause infection. As a result of this resemblance, pathogens that find their way into a child’s gut can end up sticking to the HMOs instead of the human cells, and—having fallen for the decoy—pass harmlessly out of the body in stool.¹²

It’s estimated that more than half of a baby’s microbiome comes from their mother¹³, but many of these bacteria appear to be transmitted in a passive way—relying on the ubiquity of dirt, and the fact that it only takes a few cells to establish a population that can stay with a person for the rest of their life (more on this below). But in recent years, studies have shown that a mother’s milk isn’t just prebiotic, but a probiotic as well: It contains live bacteria, which help play a role in seeding the child’s microbiome.¹⁴

Some research suggests that these bacteria are transported from the mother’s GI tract to the breast by immune cells, but their precise role—and even the origin of many of them—is still something of an enigma.¹⁵ A little over half of them can be traced back to the skin, or the microbes that live in the mouth, nose, or throat, but the remainder’s origins are mysterious. 

Regardless of where they come from, the microbes in milk play a small but substantial role in populating the child’s microbiome​​. This unique combination of pre- and probiotic activity is likely a large part of why breastfeeding continues to be the recommended way to nourish a growing body: It leads to a more stable microbiome than formula, as well as better health outcomes in multiple domains. For instance, the microbiomes of infants fed formula, versus exclusively breastfed infants, have been found to host higher levels of Clostridioides—the microbial pathogen which causes the antibiotic-resistant diarrheal disease known as “C. diff.”¹⁶ 

Of course, breastfeeding isn’t possible for everyone—which is part of the reason why scientists are striving to understand the relationships among milk, microbes, and human development. As a result of that work, a number of infant formula manufacturers have begun incorporating HMOs and, in some cases, probiotic strains from genera like Bifidobacterium into their products. We’ve got a long way to go before we can match nature’s recipes, but these innovations are an important first step toward a more health-equitable future.

Environment: Pets, Dirt, + Other Microbial Diversifiers

At any stage in life, the levels of the various bacteria that comprise a person’s microbiome can fluctuate heavily depending on their diet. So it should come as no surprise that in infancy, when the only food is breast milk or formula, the microbiome is dominated by a few select kinds of bacteria, like Lactobacillus, Bacteroides, Collinsella, and especially Bifidobacterium. These are like the training wheels, and milk is a biological mechanism for making sure that a baby’s first bacteria are ones that will do them no harm.

But this superficial simplicity masks a deeper, more subtle evolution that’s occurring in these first few months and years. With every new person they meet, with every environment they visit, a child’s microbiome has the chance to grow more diverse. When an aunt or uncle visits and holds the baby, the child might get a few new skin species—or even a new gut species, if a visitor is feeling particularly gassy that day. Although it’s known that our first microbes come from our birth mother, the rest of the family, caregivers, and even friends and neighbors all have the opportunity to make a contribution as well—likely in direct proportion to the amount of time they spend with the little one. Having siblings impacts a developing microbiome, and so does having pets in the house. Everyone we interact with quite literally shares a piece of themselves with us.^17,18,19

Infancy is a special time, when we’re primed to accept these new influences and incorporate them into ourselves. At first, these contributions seem minor—barely detectable beneath the protective blanket of the Bifidobacterium-dominated ecosystem encouraged by milk sugars. 

But at weaning, as a child transitions fully from breast milk to solid food, it’s as if the mother releases her grip on her child’s microbiome. The blanket of Bifidobacteria melts away, and suddenly it’s like a spring thaw: The “seeds” of dozens of different species that accumulated under the winter snow bloom into abundance.

The Long Haul: Diet, Antibiotics, + Beyond

The transition to solid food marks the last great scheduled change in the developing microbiome. After this, it enters a sort of steady state—but “steady state” does not mean “set in stone.” Like any ecosystem, a person’s microbiome fluctuates over time. 

Changes in the diet can cause some species to thrive, and others to die back—though rarely to the extent that they can’t return. A growing body of research suggests that the impact of diet on the microbiome is responsible for a large part (and maybe even most) of diet’s impact on overall health.²⁰ In places where people still eat by the cycle of the seasons, their microbiomes shift in time with these rhythms.²¹ New species can be acquired at any point in life, especially from people we live with—but never so easily or impactfully as when we’re just starting out.²² By the time we reach adulthood, most ecological niches in the microbiome are already occupied—so new acquisitions are relegated to marginal status, in the absence of major upsets that would give them the chance to take hold.

In fact, there’s only one other time when the microbiome has a “scheduled” shift: when a person becomes pregnant. Changing hormone levels signal the immune system to go on high alert, and the microbiome begins to shift again.²³ Bifidobacterium and other beneficial microbes rise in abundance, helping to ensure that the first bacteria the child is exposed to are the right ones—so the cycle can begin again.

Then, there is the topic of antibiotics. Just like a macroscopic ecosystem, the microbiome is fragile in certain ways. One of the greatest factors that impacts the microbiome later in life is the use of antibiotics.²⁴ Like a wildfire in the forest, antibiotics decimate the bacterial world inside you, and can devastate the biodiversity that’s necessary for health.

Similar to a patch of woods recovering after a fire, the microbiome will grow back after antibiotics—often in a matter of days or weeks—but it won’t always grow back the same as it was before.²⁵ Species that have been a part of you for practically your whole life, that have been in your family for generations, can suddenly go “extinct”: killed off by the drug, or else weakened and then driven out by a faster-growing species, or an antibiotic-resistant one.²⁶ 

To extend the forest analogy, think about bamboo: It grows quickly, which means it thrives after environmental catastrophe, by occupying all the available space and preventing other kinds of plants from getting the sunlight they’d need to return. This kind of dynamic can have far-ranging impacts, because the kinds of life supported by a slow-growing species like an oak—the owl that nests in its hollows, the squirrels that eat its acorns, the foxes that eat the squirrels—might have nowhere to call home in a bamboo forest. The same complex web of interdependencies exists in your gut, and biochemical functions that are key to health, like controlling cholesterol levels, can depend entirely on one or two species. If they go extinct within you, there’s currently very little that can be done to restore them.

There are times when antibiotic use is necessary, as in the case of life-threatening infections, but far too often they’re prescribed for diseases that would resolve on their own given time—and even sometimes when it’s unclear whether an illness is bacterial or viral in origin. Fortunately, these practices are changing, as more healthcare providers come to recognize the importance of the delicate balance within.  

Health in Your Hands (and Your Gut!)

So what does this all mean for you now? As an adult, which bacteria have made their way into your gut over the course of your lifetime is largely beyond your control, but how much of each kind comes down to the choices you make. Through this lens, a lot of the mysteries around the connection between food and health start to resolve, and we can see a remarkable new level of agency with respect to our own bodies. A diet that works fabulously for one person might spell disaster for another if they have a pro-inflammatory species in their gut that grows well on the components of that diet.

All of this adds another layer to the saying “you are what you eat.” Practically, it underscores the importance of listening carefully to the signals your body is sending, and using them to inform your future choices. A good place to start? Experiment with a deliberately diverse diet, and take careful note of the foods that make you feel your best (or not) to find what works for you and your unique microbiome.

As the appointed stewards of a garden that’s been under cultivation for millenia, it’s on us to learn about and appreciate the bacterial components of ourselves, and work with them to nurture our bodies through the many seasons of life. And as science continues to advance our understanding of the importance of this world inside, we should use that knowledge to help build and advocate for a more microbially conscious future: one where mothers are given more support during birth and postpartum, and where mainstream medicine takes a proactive approach to health, rather than reacting to diseases by over-prescribing antibiotics. While you can’t control many of the factors that initially shaped your microbial world within, you can sow the seeds of health in yourself—and a better world for the next generation.