How Our Genes and Environment Shape Our Gut Microbiome
Right now, there are more microbial cells in your gut than there are stars in the Milky Way. And they are not just simply existing. They are working, competing, and negotiating on your behalf. This community of bacteria, fungi, and other tiny organisms is called the gut microbiome. Together, they help digest food, train the immune system, and even whisper signals to the brain. Interestingly, everyone’s microbiome is different and is shaped by our genes, our environment, and the choices we make (1, 2). In fact, your microbiome is as unique to you as your fingerprint. To better understand, let’s follow Maya, a fictional character whose gut ecosystem evolves with her from birth to adulthood.
Beginnings
Maya’s story starts in the delivery room. She’s born vaginally, which means her very first microbes come from her mother’s birth canal and skin (3). Within minutes, her gut is seeded with bacteria that help train her immune system. If Maya had been born by C-section, things would look a little different. Her first microbial passengers might have come from the hospital environment or the skin of her caregivers (3). Neither path is “good” or “bad,” but it shows how our earliest microbes depend heavily on circumstance.
Over the next few months, Maya is breastfed. Her mother’s milk doesn’t feed only her, it feeds her microbes too. Human milk contains special sugars, called oligosaccharides, that babies can’t digest but certain bacteria can. These oligosaccharides act like fertilizer for beneficial bacteria such as Bifidobacteria, which help build a healthy, protective gut ecosystem (4).
Childhood
As Maya grows, she crawls through the backyard, puts toys (and dirt) in her mouth, and wrestles with the family dog. Each new encounter introduces new microbes. The more diverse her exposures, the richer her gut ecosystem becomes (5).
But childhood is also when antibiotics typically make their first appearance. At age six, Maya gets strep throat and takes a 10-day course of antibiotics. The infection clears but so do many of her beneficial gut bacteria (1. It’s like a wildfire sweeping through a forest. Her gut ecosystem recovers over time, but it’s never quite the same.
By age ten, Maya’s gut looks very different from her infancy: more diverse, relatively stable, and already influencing how her immune system responds to the world around her.
Adolescence
When Maya hits her teenage years, her habits shift. Sleep schedules change, stress levels rise, and late-night pizza and soda runs become a new routine. Her microbes feel this too. Diet is one of the strongest shapers of the microbiome (6). Fiber-rich fruits, vegetables, and whole grains feed beneficial bacteria, while processed, high-sugar foods tend to favor less helpful ones.
Adolescence is also when Maya starts to notice the invisible tug-of-war between her gut and her mind. Before big exams, her stomach twists into knots. Stress makes her digestion unpredictable. This is what is known as the gut-brain connection (7). The gut and brain are in constant conversation through nerves, hormones, and chemical messengers. The vagus nerve, an “information highway,” sends signals both ways. At the same time, many gut microbes produce neurotransmitters like serotonin (the “happiness chemical”), dopamine, and GABA (8). In fact, scientists estimate that about 90% of the body’s serotonin is made in the gut (8).
That means Maya’s microbiome isn’t just digesting food, it’s also nudging her mood, stress response, and even her sleep. And it works in reverse too – when Maya pulls an all-nighter and floods her body with stress hormones like cortisol, her gut lining becomes more sensitive, and her microbial community shifts. Stress reshapes the gut, which in turn can feed back into how she feels emotionally.
By the end of high school, Maya has learned that her gut reacts to her lifestyle as much as to what she eats. The gut-brain connection makes her microbiome not just a digestive organ, but an important factor in her mental well-being.
Adulthood
In her twenties, Maya studies abroad in Japan. Suddenly, she’s eating foods her microbes have never seen before: fermented vegetables, new fruits, and spiced curries. Her gut adapts, shifting to digest these new diets. The change in diet introduces an entirely new set of microbes, reshaping her internal ecosystem.
At the same time, Maya’s genetics continue to hum in the background. Genes don’t dictate which microbes she gets, but they do shape her immune system. Certain genetic variations can make someone more prone to conditions like inflammatory bowel disease, which in turn reshape the microbial neighborhood (9).
By the time Maya is 30, her microbiome reflects not just her DNA, but her history: the antibiotics she took, the foods she ate, the pets she cuddled, the places she traveled, and the stress she weathered along the way.
Later Life
As people age, microbial diversity often decreases (1). Maya, now in her 60s, notices her digestion feels more sensitive than before. Part of this is because the microbial forest in her gut isn’t as lush as it once was. Lifestyle (diet, exercise, stress, medication use, etc) plays an even greater role in keeping the ecosystem resilient.
This stage of life highlights an important idea: our microbiome is both resilient and responsive. It adapts to new experiences, remembers old ones, and continues to influence our health, digestion, and mood. Your gut is uniquely yours. It has been growing, shifting, and adapting with you since the day you were born. By looking at it this way, we see that the gut is not just a collection of microbes, but rather a living record of our journey.