Overview:
Although microbes were once mainly associated with diseases, they are now known to play essential roles in maintaining human health by supporting important bodily functions and living in a mutually beneficial relationship with us. Modern science has shown that humans have evolved alongside vast communities of microorganisms, making them a vital part of our survival and well-being.
Let’s begin with microbes
A microbe is a very small, living organism that’s usually visible only under a microscope. Its name comes from the Greek (mikros – small, bios – life). While scientists have discovered hundreds of thousands of species of these microorganisms, the number of microbial species on Earth is believed to be in the millions, possibly much higher. A collection, or community of microorganisms, is called microbiota.
Historically, microbes were viewed as harmful because the first microorganisms that scientists identified – and learned to control – were those that caused diseases like tuberculosis, cholera, anthrax, and the plague. We now know that only a small fraction of these microbes, referred to as pathogenic, are harmful.
The vast majority of microbiota are either neutral or benefit us and receive benefits in return. In fact, humans evolved alongside microbes for millions of years; we do not merely tolerate them; many of our bodily functions depend on them. Researchers have identified five groups of microorganisms that are the most important in this context: bacteria, archaea, protists, fungi, and viruses, which live inside virtually all plants and animals. I’ll get to these in a bit.
What is a microbiome?
A microbiome is a community of microorganisms – microbiota – living in a particular environment. Think of it as a microscopic ecosystem, analogous to large ecosystems such as rainforests, marine ecosystems, or deserts.
Microbiomes are everywhere – in lakes, rivers, oceans, plants, leaves, soil, wood, animals, and humans. The soil in your garden contains one of the most complex and diverse microbiomes on Earth. A spoonful of healthy soil may contain billions of bacteria, thousands of species of microorganisms, fungi and yeasts, protozoa, and microscopic worms.
Scientists have learned a great deal about how microorganisms function together as communities within these microscopic ecosystems. This functioning depends not just on individual microbes but on their collective genes and the interactions among them.
Some researchers now extend this view further, framing Earth itself as a planet shaped by interconnected microbiomes.
Where’s my microbiome?
We can extend this ecological perspective to our own bodies, viewing them as complex ecosystems that host a number of distinct microbiomes — microscopic communities of trillions of microorganisms — living in and on many parts of us.
The largest and most important microbiome, known as the gut microbiome, is in the gastrointestinal tract – in the large intestine and the lower part of the small intestine.
The colon is an ideal environment because it provides warmth, moisture, nutrients from undigested food, and low oxygen levels, which are preferred by many gut bacteria. This region harbors tens of trillions of microorganisms – about 90–95% of the body’s microbes – and plays important roles in digestion, immunity, metabolism, and overall health.
Our skin microbiome hosts billions of microorganisms that help defend against pathogens, influence immune function, and contribute to skin health. Different areas of the skin have different microbial communities.
Our mouth contains the oral microbiome, with hundreds of bacterial species living on the teeth, tongue, gums, and inner cheeks. They influence dental cavities, gum disease, and overall oral health. Recent scientific breakthroughs reveal that the oral microbiome is a critical regulatory hub for total body health, rather than just a marker of dental cavities; an imbalanced oral microbiome (known as dysbiosis) acts as a primary trigger for chronic systemic inflammation, directly influencing metabolic decline, cardiovascular disease, and Alzheimer’s.
The respiratory microbiome is in the nose, sinuses, and upper airways. These communities may affect susceptibility to respiratory infections. In women, the urogenital microbiome, combining the urinary and reproductive tracts, plays an important role in health and protection against infections. Microbiomes can also be found in our eyes, ears, and belly buttons!
What exactly does my microbiome do?
Bacteria, archaea, protists, fungi, and viruses are the principal microorganisms of human microbiomes. Bacteria make up around 90% of the total microbial cellular population in your gut; they drive the vast majority of daily digestion, vitamin manufacturing, and short-chain fatty acid production.
Fungi make up less than 0.1% of the gut population, interacting closely with bacteria to maintain the structural integrity of your gut barrier.
The primary role of archaea is cleanup—they consume the hydrogen gas waste produced by bacteria and turn it into methane. Protists act as microscopic predators that graze on bacteria to keep populations in check.
Viruses act as the primary regulators, genetic engineers, and defense shields of the human microbiome, helping to maintain a balanced microbial ecosystem.
An average adult body contains roughly 38 to 40 trillion microbial cells and 30 trillion human cells. However, microbial genes vastly outnumber human genes. The human genome contains about 20,000 protein-coding genes, while the collective genes of your microbiome number in the millions.
Microbial genes outnumber human genes by a ratio that varies from 100 to 1 up to 1,000 to 1, depending on how many distinct bacterial strains you carry. Our human genome provides the basic blueprint; however, as described below, it does not have the genetic tools to digest complex foods or build essential vitamins.
The human body survives by outsourcing these vital tasks to the millions of genes in our microbiome. Our microbes supply the necessary chemical toolkits that our own human DNA cannot provide.
Your microbiome acts as a vital, invisible organ system that runs daily chemical operations your human DNA cannot manage alone. In your gut, they serve as your primary digestive assistants.
When you eat fiber-rich foods like vegetables, grains, or beans, human digestive enzymes cannot break them down. Your gut bacteria step in, using their specialized genes to ferment these fibers into crucial compounds that nourish your gut lining, regulate your metabolism, and manufacture essential vitamins like B and K.
In addition, your gut microbes constantly communicate with your immune cells, training them to distinguish between harmless food particles and dangerous invaders.
While your gut manages digestion and core immunity, other specialized microbiomes guard the frontiers of your body.
On your skin, billions of microbes form a living shield, secreting acidic compounds that prevent harmful pathogens from taking hold and causing infections.
Inside your mouth, your oral microbiome acts as a gatekeeper, initializing digestion and fighting off foreign bacteria before they can enter your body.
Even unexpected areas like your lungs, eyes, and urinary tract host tailored microbial communities that keep tissues healthy and resilient.
Ultimately, you don’t just live with your microbes—you rely on their collective toolkits to breathe, digest, and survive every single day.
How does all this affect your health?
The gut microbiome is a significant factor influencing our health span (years lived in good health). It helps digest fiber and produce beneficial compounds called short-chain fatty acids, regulates the immune system, influences inflammation throughout the body, affects metabolism and insulin sensitivity, and interacts with the brain via the “gut-brain axis.”
Research shows that it may influence lifespan through its effects on inflammation, metabolism, immunity, and chronic disease risk. The evidence is strongest for links to diabetes, obesity, cardiovascular disease, and healthy aging. As people age, their gut microbiome tends to change.
Studies of healthy older adults and centenarians find that they have microbiomes that differ from those of less healthy peers, with greater representation of bacteria associated with anti-inflammatory and metabolic benefits.
An active area of aging and neuroscience research today is the gut-brain axis – the two-way communication system linking the gut microbiome, immune system, hormones, vagus nerve, and brain.
Evidence is now fairly strong that the microbiome can influence brain health by reducing inflammation, using chemical messengers that influence brain function, and sending signals via the vagus nerve.
How do I maintain a healthy microbiome?
Recommendations based on strong research evidence are surprisingly conventional – eat a high-fiber diet (vegetables, fruits, beans, lentils, whole grains); eat a wide variety of plant foods; include fermented foods if tolerated (like yogurt, idli, dosai, sauerkraut); exercise regularly; avoid unnecessary antibiotic use; get adequate sleep; and limit highly processed foods. These are the same guidelines already known to reduce the risks of heart disease, diabetes, frailty, and cognitive decline.
Research also points to the importance of maintaining a diverse microbial ecosystem. Diversity appears to be one of the strongest markers of a healthy microbiome, particularly in older adults.
There is currently no clinical test that can tell people whether they have an “optimal” microbiome. There is enormous variation among healthy individuals; two healthy people may have very different microbiomes.
Growing evidence suggests that exposure to natural environments (gardening, hiking, interacting with natural environments) may increase microbial diversity.
The trillions of microorganisms that live within us are not merely passengers but active participants in the story of our health. By understanding and supporting this hidden ecosystem through healthy daily habits, we can help cultivate a microbiome that supports vitality, resilience, and healthy aging throughout life.
