You are not alone. In fact, you are outnumbered. For every human cell in your body, there is at least one microbial cell living in or on you. Trillions of bacteria, viruses, fungi, and other microscopic organisms call your body home, collectively forming what is known as the human microbiome. These tiny tenants are not passive passengers. They are active participants in your health, influencing everything from your digestion and immunity to your mood and even your risk of chronic disease. The discovery of the microbiome’s profound importance has revolutionized our understanding of human biology and opened up exciting new avenues for treating and preventing illness.
The Microbiome: How Tiny Organisms Rule Our Health
Who Lives There and Where
The human microbiome is incredibly diverse. Different parts of your body host distinct microbial communities. The skin, with its varying conditions of moisture and oil, is home to a different set of microbes than the mouth or the gut. But by far the largest and most important microbial community resides in the gut, specifically the large intestine. This is a dense, complex ecosystem containing trillions of bacteria from hundreds of different species.
The composition of your gut microbiome is as unique as your fingerprint. It is shaped by a multitude of factors: how you were born (vaginal delivery versus C-section), whether you were breastfed, your diet, your environment, your medication use (especially antibiotics), your age, and even your stress levels. This microbial community is dynamic, constantly changing in response to these factors. A healthy microbiome is generally characterized by high diversity—a wide variety of different microbial species. Low diversity, on the other hand, is associated with various diseases.
What They Do For You
Far from being freeloaders, your gut microbes perform essential functions that your own body cannot. They are masters of digestion. Many of the carbohydrates you eat, particularly dietary fiber from plants, are indigestible by your own enzymes. They pass through the small intestine intact and arrive in the colon, where your gut microbes go to work. They ferment these fibers, breaking them down and producing beneficial compounds called short-chain fatty acids (SCFAs). SCFAs, such as butyrate, are the primary energy source for the cells lining your colon. They also have powerful anti-inflammatory effects and help strengthen the gut barrier, preventing harmful substances from leaking into your bloodstream.
Your gut microbes also produce essential vitamins. They synthesize vitamin K, which is crucial for blood clotting, as well as several B vitamins, including biotin, folate, and B12. They help metabolize bile acids and cholesterol. They produce neurotransmitters that influence your brain and mood. And they play a critical role in educating and regulating your immune system. From birth, your microbiome helps train your immune cells to distinguish between friend and foe, teaching them to tolerate harmless substances while attacking pathogens.
The Gut-Brain Axis
One of the most exciting areas of microbiome research is the gut-brain axis, the bidirectional communication system between your gut and your brain. This connection is physical, via the vagus nerve, and chemical, via the signaling molecules produced by gut microbes. As mentioned in earlier articles, your gut microbes produce an astonishing array of neurochemicals. They produce about 95% of your body’s serotonin, the “feel-good” neurotransmitter that regulates mood, appetite, and sleep. They produce GABA, a neurotransmitter that has a calming, anti-anxiety effect. They produce dopamine, involved in reward and motivation.
Through these chemical signals, and through their influence on the immune system and inflammation, your gut microbes can directly affect your brain function and mental health. Studies have found that people with depression, anxiety, and other mental health conditions often have different gut microbiomes than healthy controls. This has led to the intriguing possibility of using probiotics or dietary interventions to improve mental health by modulating the microbiome. The idea of “psychobiotics”—bacteria that benefit mental health—is no longer science fiction.
When Things Go Wrong: Dysbiosis
When the delicate balance of the gut microbiome is disrupted, a condition known as dysbiosis, it can contribute to a wide range of health problems. Dysbiosis can involve a loss of beneficial microbes, an overgrowth of potentially harmful ones, or a decrease in overall diversity. It has been linked to inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis. It is associated with irritable bowel syndrome (IBS), obesity, type 2 diabetes, allergies, asthma, and even certain autoimmune diseases like rheumatoid arthritis.
Antibiotics are a major cause of dysbiosis. While they are essential for fighting bacterial infections, they are non-selective and can wipe out large swaths of beneficial gut bacteria along with the harmful ones. This is why antibiotic use is associated with an increased risk of various health problems, and why it’s important to use them only when necessary. Diet is another major factor. A diet high in processed foods, sugar, and unhealthy fats, and low in fiber, can starve beneficial microbes and promote the growth of harmful ones.
Nurturing Your Microbial Self
The good news is that you have significant control over your microbiome, primarily through what you eat. The single most important thing you can do is eat a diverse range of fiber-rich plant foods. Different microbes prefer different types of fiber, so eating a wide variety of fruits, vegetables, legumes, whole grains, nuts, and seeds promotes a diverse and resilient microbiome. Think of fiber as fertilizer for your good bacteria.
Fermented foods are also powerful tools. Foods like yogurt, kefir, sauerkraut, kimchi, kombucha, and miso contain live beneficial bacteria (probiotics) that can add to your gut’s diversity. Prebiotic foods, such as garlic, onions, leeks, asparagus, and bananas, contain specific types of fiber that feed beneficial bacteria. Limiting processed foods, sugar, and unnecessary antibiotics also helps protect your microbial ecosystem. The microbiome is a newly recognized organ, essential to our health. By caring for it, we care for ourselves.