The microbiome is the collection of all microbes, such as bacteria, fungi, viruses, and their genes, that naturally live on our bodies and inside us. Although microbes are so small that they require a microscope to see them, they contribute in big ways to human health and wellness. They protect us against pathogens, help our immune system develop, and enable us to digest food to produce energy.

Because the microbiome is a key interface between the body and the environment, these microbes can affect health in many ways and can even affect how we respond to certain environmental substances. Some microbes alter environmental substances in ways that make them more toxic, while others act as a buffer and make environmental substances less harmful.

The human microbiome plays a vital role in health, with the number of microbial cells in the body roughly matching the number of human cells. This complex ecosystem varies across body sites—such as the gut, skin, mouth, and nasal passages—each hosting distinct microbial communities.

While a person’s core microbiome is established early in life, it continues to evolve, influenced by factors like diet, medication, and environmental exposures. These changes can affect how our bodies respond to the environment and may influence susceptibility to various diseases.

Disruptions in the microbiome have been linked to a range of health issues, including diabetes, obesity, cardiovascular and neurological disorders, allergies, and inflammatory bowel disease.

The relationship between the human body (the host) and its resident microbes is not just peaceful coexistence—it’s a dynamic interaction that plays a critical role in training and regulating the immune system.

From birth, exposure to microbes helps the immune system learn to distinguish between harmful pathogens and harmless or beneficial organisms. This process is essential to developing a balanced immune response that can fight infections without triggering chronic inflammation or autoimmune diseases.

Beneficial gut microbes, for instance, stimulate immune cells in the intestinal lining and produce molecules like short-chain fatty acids (SCFAs), which help regulate inflammation. These interactions help maintain a strong barrier between the gut and the bloodstream while preventing overreactions to harmless substances like food or pollen.

A healthy microbiome supports immune tolerance—the ability of the immune system to recognize and ignore the body’s own cells and benign external elements. Dysbiosis (an imbalance in the microbial community) has been linked to an increased risk of allergies, asthma, inflammatory bowel disease, and even autoimmune conditions like type 1 diabetes or rheumatoid arthritis.

Recent research has shown that the microbiome can influence how patients respond to immunotherapy, especially in cancer treatment. Certain gut bacteria seem to enhance the effectiveness of immune checkpoint inhibitors—an exciting insight that could guide future therapies.