Microbiome 101

You are home to a community of trillions of microorganisms, including 38,000,000,000,000 (that’s 38 trillion) bacteria, living in and on your body. The bacteria alone represent 50% of you by cell count.¹ Collectively, these microorganisms comprise your microbiota, and these trillions of microbial cells and all of their components and surroundings constitute your microbiome. The majority of these microbes reside in your gastrointestinal tract, but many others live in diverse places like your mouth, your skin, and your armpits, etc., each with their own unique microbiome.

Wait. 38,000,000,000,000 bacteria!?

But aren’t bacteria bad?

That’s the misconception of the century. Most bacteria are harmless (commensal). Many are beneficial (mutualistic). Many of the ones that live in and on you are absolutely essential.

You probably remember from sixth-grade biology that you inherit your genes from your parents. But did you know that your mother passes you a portion of your microbiome too? The process of receiving these foundational microbes is called seeding.

Seeding is generally regarded to start at birth, through the vaginal canal, skin-to-skin contact, and breastfeeding.² Eventually, the surrounding environment—other moms, dads, siblings, dogs, the ground outside and floors inside, nature—continues to contribute to this microbial biodiversity.^3,4,5

These first microbes colonize your gastrointestinal system and form the foundation of your immune system, serving as the instructors of what’s dangerous and what’s not.⁶ By the first few years of life, they stabilize into what is called the steady-state microbiome, resembling more or less what you have today.⁷

Well actually, what don’t they do? There’s almost no function in the human body that our bacterial symbionts and their metabolites aren’t connected to.

Let’s start with what you’ve probably already heard of—your gut. Trillions of beneficial bacteria reside along your epithelial wall and (partly by sheer strength in numbers) maintain your gut barrier integrity, making it difficult for inhospitable bacteria to penetrate.⁸ They help maintain an acidic environment to dissuade certain alkaline-loving pathogenic bacteria from taking root.⁹ And certain bacteria even produce neurotransmitters that stimulate intestinal muscle contractions—yes, we’re talking about poop.¹⁰

When we eat, certain microbial genes code for enzymes that break down food we otherwise couldn’t—think: fiber. Through this process, bacteria produce important byproducts like short-chain fatty acids, which fuel the cells lining your colon and strengthen your protective intestinal mucosa. Butyrate, specifically, has powerful anti-inflammatory effects beyond the gut, reducing oxidative stress (imbalance between free radicals and detoxifying antioxidants) and managing the production of regulatory T cells (the ones that help your body distinguish the self from an intruder).^11,12,13

Beyond this, bacteria also synthesize essential B vitamins and vitamin K, defend against pathogenic E. coli strains and other intruders in the urogenital tract, and balance pH and protect from unwanted, excessive yeast in the vaginal biome.^14,15,16 Their health is critical to the health of our entire body—from heart to skin to metabolism to gut immune function.^17,18,19

All this to say that our bacteria play an incredibly complex and critical role in helping us thrive. Scientists are constantly discovering new associations between our microbiota and our health. New findings around the gut-brain axis are emerging which indicate that our gut flora may even impact our mood, appetite, behavior, and circadian rhythm—functions we thought were relegated solely to the brain—where microbes do not appear able to take residence.^20,21,22

The human intestinal lining is formed by a single layer of epithelial cells and a thick layer of mucus. This is what we call your gut barrier. It has two jobs: absorbing beneficial nutrients and providing protection against harmful substances.²³ The space between each of your epithelial cells is sealed by tight junctions. Their job is to regulate the permeability of your gut barrier and act as the gatekeeper between the gut and the bloodstream.

With a much larger surface area than your skin (seriously,  the large intestine alone is the equivalent of half a badminton court—about 220 ft²—and thickness of one cell wall, or half a human hair), the gut is the largest exposed external surface on your body.^23,24 On a daily basis, it deals with the food you eat, the molecules you breathe, and at times, the potential toxins that seek entry. If your intestinal lining is damaged or compromised (you’ve probably heard this referred to as “leaky gut”), substances that don’t belong in your body can enter the bloodstream, triggering immune responses in the body—think inflammation, allergies, irritable bowels, migraines, pain, fatigue, and more.

Like your genome, your microbiome is unique to you. And it’s susceptible to change. External factors like diet, exercise, medicine, and even sleep can all impact and alter the composition of your microbiome on a daily basis.²⁵

Imagine Earth’s ecosystems as an analogy of your own inner world. Over days and weeks and seasons and years, there may be different kinds of trees or plants or animals in different forests and deserts and oceans. But the ecological functions that make up that forest and keep each ecosystem thriving are continuous and conserved. In other words, our microbiomes are all vastly different from one another, but the functions they maintain for our health are relatively similar. Whatever microbes exist within us, they’ve evolved to be there.

We don’t know what a healthy microbiome looks like. We may never. While it would be remarkable to say, “You’re missing Lactobacilli, here’s a supplement for it,” it’s simply not how the human body works. The ideal microbiome probably doesn’t exist. As diverse as we are, so are our microbiomes, and for good reason.

What you can ask is this—are my bacteria working optimally with my body to perform the functions critical to my health? How can I support my microbiome in the daily choices I make? Am I eating for myself or also for my 38,000,000,000,000 bacteria within? Should I be incorporating probiotics and prebiotics into my routine?

The study of the microbiome radically redefines our sense of self. Where we once thought ourselves fully human, we now know we are in fact, superorganisms—walking, talking ecosystems—half human, half bacterial.

This is the new biology. It demands a new approach to medicine, hygiene, diet, and health.

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2. Dunn, A. B., Jordan, S., Baker, B. F., & Carlson, N. S. (2017). The Maternal Infant Microbiome. MCN: The American Journal of Maternal/Child Nursing, 42(6), 318–325. https://doi.org/10.1097/nmc.0000000000000373
3. Lane, A., McGuire, M. K., McGuire, M. A., Williams, J. B. W., Lackey, K. A., Hagen, E. H., Kaul, A., Gindola, D., Gebeyehu, D., Flores, K. E., Foster, J. A., Sellen, D. W., Kamau-Mbuthia, E. W., Kamundia, E. W., Mbugua, S., Moore, S. E., Prentice, A. M., Kvist, L. J., Otoo, G. E., . . . Meehan, C. L. (2019). Household composition and the infant fecal microbiome: The INSPIRE study. American Journal of Physical Anthropology, 169(3), 526–539. https://doi.org/10.1002/ajpa.23843
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