Understanding the Gut Microbiome
Our intestines contain an enormous community of microorganisms. Most are bacteria, but the community also includes viruses, fungi, and other microscopic organisms.
Together, these microorganisms and their genetic material are known as the gut microbiome.
Scientists have discovered that the microbiome plays important roles in digestion, metabolism, and immune function. It also communicates with other parts of the body, including the brain.
We are learning that our health depends partly on the microorganisms living within us.
How Many Microorganisms Do We Have?
Researchers estimate that the human body contains roughly as many bacterial cells as human cells, although the exact numbers vary.
Most of these bacteria live in the large intestine.
There are hundreds of bacterial species in the human gut, but the particular combination differs considerably from one person to another.
Even healthy people can have very different microbial communities.
This makes it difficult to define a single ideal microbiome.
What Do Gut Bacteria Actually Do?
One of their most important jobs is helping us digest food.
Our digestive enzymes cannot break down certain dietary fibers and other carbohydrates. Some intestinal bacteria can ferment these substances and produce compounds called short-chain fatty acids.
Three important examples are acetate, propionate, and butyrate.
Butyrate is particularly interesting because it provides energy for cells lining the colon and helps maintain the intestinal barrier.
Short-chain fatty acids also participate in metabolic and immune signaling.
Gut microorganisms perform other functions as well. They help metabolize certain substances in food, produce some vitamins, and compete with potentially harmful microorganisms.
However, the effects of individual bacteria depend on the overall microbial community and the environment within the intestine.
The Gut Barrier and Immune System
The intestinal lining performs two seemingly opposite tasks.
It allows nutrients and water to enter the body while helping prevent harmful microorganisms and unwanted substances from passing through.
The gut microbiome helps maintain this protective barrier.
It also interacts extensively with the immune system.
Much of the body's immune activity is associated with the gastrointestinal tract, where immune cells must distinguish between harmless substances, beneficial microorganisms, and potential threats.
Researchers are investigating how disruptions in these interactions may contribute to inflammation and disease.
What Is Dysbiosis?
You may encounter the term dysbiosis, which generally refers to an imbalance or disruption in a microbial community.
Researchers have identified altered microbial patterns in people with inflammatory bowel disease, obesity, type 2 diabetes, and several other conditions.
But dysbiosis is not a single, clearly defined medical diagnosis.
Different studies use different definitions, and there is no universally accepted test that determines whether an individual's microbiome is healthy or unhealthy.
Importantly, changes in the microbiome may sometimes be consequences of disease rather than causes.
What Changes Our Microbiome?
The composition of our gut microbiome is influenced by many factors.
Diet is particularly important. Changes in the foods we eat can alter microbial activity, sometimes within days.
Antibiotics can substantially disrupt intestinal microbial communities because they affect beneficial bacteria as well as the bacteria responsible for an infection.
Other medications, including metformin and acid-suppressing drugs, can also influence the microbiome.
Illness, aging, travel, and changes in living environment may contribute additional effects.
Our microbiome is therefore not fixed throughout life.
How Do Scientists Study the Microbiome?
Researchers can analyze stool samples to identify microbial DNA and estimate which microorganisms are present.
More advanced techniques can investigate microbial genes, proteins, and metabolic products.
These methods have transformed microbiome research.
However, stool samples provide an incomplete picture. They primarily reflect microorganisms present in the intestinal contents and may not fully represent communities attached to the intestinal lining or living elsewhere in the digestive tract.
Scientists also cannot always determine what microorganisms are doing simply by identifying them.
Knowing which bacteria are present is not the same as knowing whether they are helping or harming our health.
Can Commercial Microbiome Tests Tell Us What to Eat?
Several companies now offer microbiome testing directly to consumers.
Typically, customers submit a stool sample and receive a report describing their intestinal microorganisms. Some companies also recommend foods or supplements based on the results.
See the section on Supplements for more about commonly used supplements and what research tells us about their benefits and limitations.
These tests can provide interesting information, but their clinical usefulness remains limited.
Different testing methods may produce different results, and researchers have not established reliable standards for interpreting most individual microbial profiles.
There is currently insufficient evidence that commercial microbiome testing can consistently identify the best diet or supplements for an otherwise healthy person.
Why Is the Microbiome Receiving So Much Attention?
The microbiome represents an important development in our understanding of human biology.
Researchers are discovering that microorganisms participate in processes previously attributed almost entirely to human cells.
There are already established medical applications of microbiome research. For example, certain microbiota-based treatments are approved for preventing recurrent Clostridioides difficile infections in selected patients.
But for many other conditions, including obesity, diabetes, and Alzheimer's disease, microbiome-based treatments remain experimental.
See the section on Brain Health for more about Alzheimer's disease, cognitive health, and approaches being investigated to protect the aging brain.
The challenge now is to determine which discoveries can be translated into treatments that genuinely improve human health.
Learn More
A clear introduction to how microorganisms help with digestion, immune function, and maintaining health.
Background on the research initiative that helped establish modern microbiome science.
An accessible introduction to the microorganisms living in and on our bodies.
Dr. Mark Hyman interviews Dr. Emeran Mayer about the microbiome, gut-brain communication, diet, and what the research has—and hasn't—established.