Male body,man surrounded by microbiome spherical cloud of bacteria, viruses, microbes.

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.

How can the microbiome affect health?

The critical role of the microbiome is not surprising when considering that there are as many microbes as there are human cells in the body. The human microbiome is diverse, and each body site – for example, the gut, skin, and oral and nasal cavities – has a different community of microbes.

A person’s core microbiome is formed in the first years of life but can change over time in response to different factors including diet, medications, and environmental exposures.

Differences in the microbiome may lead to different health effects from environmental exposures and may also help determine individual susceptibility to certain illnesses. Environmental exposures can also disrupt a person’s microbiome in ways that could increase the likelihood of developing conditions such as diabetes, obesity, cardiovascular and neurological diseases, allergies, and inflammatory bowel disease. For example, specific changes in the gut microbiome have been linked to liver health. NIEHS-funded researchers and collaborators developed a rapid, low-cost tool that uses stool samples to detect microbial changes that can accurately diagnose liver fibrosis and cirrhosis.

What is NIEHS Doing?

NIEHS studies the microbiome to gain a better understanding of its complex relationships with the environment, and how these interactions may contribute to human wellbeing or disease. This knowledge could help us revolutionize the way new chemicals are tested for toxicity, and design prevention and treatment strategies for diseases that have environmental causes.

As part of efforts to implement the NIEHS Strategic Plan, a cross-divisional faculty was created with the goal of fostering collaborative research on the microbiome across the NIEHS Division of Intramural Research, Division of Translational Toxicology, and Division of Extramural Research and Training.

NIEHS-supported research related to the microbiome includes a variety of environmental factors, including:

Air pollution  NIEHS–funded research found breathing ultrafine particles, a component of air pollution, altered the gut microbiome and changed lipid metabolism in mice with atherosclerosis. Another study showed that exposure to traffic-related air pollution (TRAP) altered the respiratory microbiome in children.

Antimicrobials – A study found a profound effect from triclosan, a common ingredient in antimicrobial products, on the gut microbiome in mice. Mice that consumed triclosan through drinking water displayed an uptick in bacterial genes related to the stress response, antibiotic resistance, and heavy metal resistance.

Artificial sweeteners – Sucralose, an artificial sweetener, changes the gut microbiome in mice and may increase the risk of developing chronic inflammation. Another study found acesulfame potassium, also an artificial sweetener, induced weight gain in male, but not female, mice.

Cancer - Dietary restriction of methionine, a protein amino acid, has been effective in decreasing tumor growth and promoting antitumor immunity in people with certain cancers. NIEHS supported a 2023 study of intestinal cancer in a mouse model that showed an opposite effect in mice with healthy immune systems. This difference results from varying effects of methionine on gut microbiota involved in systemic immunity. If similar results are seen in humans, this finding could have implications for the treatment of colon cancer patients with dietary interventions to influence their microbiomes.

Chronic stress – Chronic stress disturbs the gut microbiome in mice, triggering an immune response and promoting the development of colitis, a chronic digestive disease characterized by inflammation of the inner lining of the colon.

Diet  NIEHS researchers showed a high–fat diet affected the gut microbiome of mice in a way that predisposed them to gain weight and develop obesity.

Flame retardants Early life exposure to types of flame retardants called polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) can have a life-long impact on disease risk, which may be shaped by the gut microbiome.

Heavy metals – Arsenic exposure in mice changed the gut microbiome and altered molecular pathways in bacteria that are important to biological functions like DNA repair. A separate study suggested that the microbiome could protect mice from arsenic or methylmercury toxicity. In addition, research in a mouse model of Alzheimer’s disease demonstrated that exposure to cadmium altered an important communication pathway between the gut microbiome and the central nervous system called the gut-brain axis.

Infant Health – Birth mode, by C-section or natural birth, and what is eaten, formula or breast milk, during the first six weeks of life may affect the type of microbes in the gut microbiome of infants. The composition of the vaginal microbiome at birth can have lasting effects on offspring metabolism, immunity, and the brain.

Pathogens – Certain microbes, or pathogens, in the human oral microbiome may play a role in either increased or decreased risk of pancreatic cancer.

Pesticides – Exposure to the widely used agricultural insecticide diazinon changed the gut microbiome of mice. These changes were more pronounced in male than female mice, providing insight into previously reported sex–specific effects of this toxicant on the nervous system.

What questions remain about the microbiome?

Research has yielded tremendous insight into the links between the microbiome, environmental exposures, and human health. Yet big questions remain and are the focus of continuing research supported by NIEHS. These questions include:

  • What are the associations between biological responses to exposures and the microbiome?
  • What information about the microbiome should be collected to understand how the microbiome responds to environmental exposures?
  • In what ways does the microbiome affect exposure to toxic chemicals?
  • Are current tools for manipulating the microbiome sufficient to develop interventions to prevent disease?

Further Reading

Stories from the Environmental Factor (NIEHS Newsletter)


Parkinson’s Disease, Pesticides, and the Gut Microbiome (2021) - This podcast explores how the environment, gut microbiome, and brain interact to influence the development and progression of Parkinson’s disease. We’ll also hear how better understanding these complex interactions can help scientists develop interventions to slow, or even stop, progression of the disease.

Additional Resources

Related Health Topics