You're Never Really Alone

There are roughly as many microbial cells in your body as there are human cells — about 38 trillion microorganisms, according to a widely cited 2016 estimate in Cell by Ron Sender and colleagues at the Weizmann Institute of Science. These bacteria, viruses, fungi, and archaea collectively contain about 150 times more genes than your human genome.

That's your microbiome — and it has opinions about basically everything your body does.

What the Microbiome Does

Your gut microbiome alone (the most studied part) performs functions your body literally cannot do on its own:

  • Digestion. Gut bacteria break down complex fibers and starches that human enzymes can't touch, producing short-chain fatty acids (SCFAs) like butyrate that fuel your colon cells.
  • Immune training. About 70% of your immune system resides in your gut. Your microbiome trains immune cells to distinguish friend from foe — a process critical for preventing both infections and autoimmune reactions.
  • Vitamin production. Gut bacteria synthesize vitamin K, several B vitamins, and biotin.
  • Mood regulation. About 90-95% of your body's serotonin is produced in the gut. The gut-brain axis — the bidirectional communication highway between your microbiome and brain — is one of the hottest areas in neuroscience research. A 2019 study in Nature Microbiology analyzing data from over 1,000 people identified specific gut bacterial species associated with depression and quality of life.
  • Metabolic regulation. The microbiome influences how you extract calories from food and how your body stores fat. Transferring gut bacteria from obese mice to lean mice caused the lean mice to gain weight, as demonstrated in landmark research by Jeffrey Gordon at Washington University.

What Shapes Your Microbiome

Your microbial community is influenced by:

  • Birth method. Vaginal birth exposes infants to the mother's vaginal microbiome; cesarean-born infants are initially colonized by skin bacteria.
  • Breastfeeding. Breast milk contains oligosaccharides specifically designed to feed beneficial bacteria.
  • Diet. The single biggest modifiable factor. Fiber feeds beneficial bacteria. Processed foods and excessive sugar promote less beneficial species.
  • Antibiotics. Broad-spectrum antibiotics kill beneficial bacteria alongside pathogens. A single course can alter the microbiome for months to a year.
  • Environment, pets, stress, sleep, and exercise all contribute to microbial diversity.

Diversity Is the Goal

Microbial diversity — having a wide range of different species — is consistently associated with better health outcomes. Low diversity has been linked to inflammatory bowel disease, obesity, Type 2 diabetes, and allergies.

The Human Microbiome Project, funded by the NIH, catalogued microbial communities across 300 healthy volunteers and found enormous variation between individuals — there is no single "healthy" microbiome, but high diversity appears to be a universal marker of good microbial health.

How to Feed Your Microbiome Well

  • Eat diverse plants. The American Gut Project found that people who ate 30+ different plant types per week had significantly more diverse microbiomes than those eating fewer than 10.
  • Prioritize fiber. 25-30 grams daily from varied sources — legumes, whole grains, vegetables, fruits, nuts.
  • Include fermented foods. A 2021 Stanford study published in Cell found that a diet high in fermented foods (yogurt, kimchi, kefir, sauerkraut) increased microbial diversity and reduced markers of inflammation.
  • Limit unnecessary antibiotics. Take them when prescribed, but don't demand them for viral infections.

When to See a Professional

Persistent digestive issues (bloating, irregular bowel habits, food intolerances), recurrent infections, or mood disorders that don't respond to conventional treatment may have a microbiome component worth exploring with a gastroenterologist or integrative medicine provider.

The Bottom Line

Your microbiome is a vast, dynamic ecosystem that profoundly influences your digestion, immunity, mood, and metabolism. Feed it diverse plants and fermented foods, protect it from unnecessary antibiotics, and respect the fact that you're really a collaborative organism — not a solo act.

FAQ

Should I take a probiotic supplement? Maybe, but don't expect miracles. Probiotic supplements contain specific strains that may help specific conditions (certain strains for antibiotic-associated diarrhea, for example), but they're not a substitute for a diverse, fiber-rich diet. Food-based probiotics (fermented foods) appear more effective at increasing microbial diversity.

Can you test your microbiome? Commercial gut microbiome tests are available, but the American Gastroenterological Association currently does not recommend them for clinical decision-making. The science of interpreting individual microbiome profiles is still too early to provide actionable personal recommendations.

Do antibiotics permanently damage the microbiome? Not permanently for most people, but recovery can take months. A 2018 study in Nature Microbiology found that while most bacterial species returned within 6 months of antibiotic treatment, some species had not recovered even after a year.

A note from Living & Health: We're a lifestyle and wellness magazine, not a doctor's office. The information here is for general education and entertainment — not medical advice. Always talk to a qualified healthcare professional before making changes to your health routine, especially if you have existing conditions or take medications.