What is the Gut Health Microbiome?

The importance of having a healthy “gut microbiome” is being touted in popular media, and we often see ads for an array of products offering to improve our gut health. We know that healthy eating is important to our overall wellbeing, but what is a microbiome and why is an intestinal microbiome so integral to overall health?

Biome is a term used by ecologists to describe a large area inhabited by specific plants and animals, such as a desert or tropical rainforest. The word microbiome is not simply a small biome: the word is actually a combination of the words microbe (not micro) and biome. A microbiome, therefore, is a group of microbes, including bacteria, fungi, viruses, and genetic material that naturally lives in and on our bodies, explains the National Institute of Environmental Health Sciences (NIEHS).

According to the American Society for Microbiology, the term was first used in 2001, but the underlying science of microbial ecology dates back to the 19th century. An article in the Human Microbiome Journal stresses the importance of understanding the microbiome as a “community” occupying a habitat, noting that the surrounding environment is as important as the microbes themselves in understanding interactions and health implications.

Despite their microscopic size, microbes affect our health and wellbeing, working as an intermediary between our bodies and our environment. This can mean protecting us from invading pathogens, supporting our immune system, and helping us digest food and convert it to energy. Some microbes, however, can interact with substances in our external environment, making them more toxic to our bodies, explains the NIEHS.

The Cleveland Clinic tells us that our intestinal tract, or “gut,” consists of the stomach and large and small intestines. This area is its own biome, home to trillions of microorganisms, including bacteria, fungi, viruses, and parasites. Describing the relationship between our bodies and our gut microbiome as symbiotic, the Cleveland Clinic uses the analogy of a diverse native plant garden providing us with nutritious food and medicine: when our garden is thriving, we thrive.

Interestingly, every individual’s gut microbiome is unique, with identical twins barely more similar than non-identical twins. Because of this, researchers make the inference that environmental rather than genetic factors play a larger role in shaping the microbiome later in life. The “colonization” of the microbiome begins during and shortly after birth, and is affected by both the mother and the environment, stabilizing by about the first year of life. These research findings suggest that where and how we live are critical to our health, particularly as we age.

More recent research findings from the National Institute on Aging (NIA) note the emergence of three distinct gut microbiome stages throughout the lifespan:

• Infancy to age three
• Stability to middle age
• Accelerated change beginning in late adulthood

Because of the age-related acceleration of microbiome changes and the significance of the microbiome to healthy aging, it is critical that seniors make lifestyle choices that support care and wellbeing.

An article entitled the Role of Normal Gut Microbiota in the World Journal of Gastroenterology notes that a growing body of research supports the critical role the gut microbiome plays in human health, including diseases of the bowel (irritable bowel syndrome), metabolic diseases (obesity, diabetes), and allergies. Genetic sequencing technology is facilitating new research, allowing scientists to more accurately pinpoint the number, type, and function of gut microbiome cells.

We most often think of digestion when we think of the gut—and processing food is a primary role of the GI tract. Northwestern Medicine summarizes the importance of gut bacteria to the digestive process by noting that our bodies have absorbed 90% of nutrients as food passes from the small to large intestine because of these bacteria.

The gut microbiome serves functions in addition to digestion. The Cleveland Clinic identifies these other benefits to the body, starting with specifics about the digestive system:

Digestive System

• Convert complex carbohydrates and dietary fiber to nutrient fatty acids
• Provide enzymes needed to absorb certain vitamins
• Break down bile for reabsorption by the liver

Immune System

• Beneficial microbes support the largest immune system in the body—the gut—containing 80% of the body’s immune cells
• Train the immune system to identify and remove pathogens
• Prevent harmful microbes from occupying too much space
• Produce short-chain fatty acids that keep toxins from entering the bloodstream by maintaining a “gut barrier”

Nervous System

• Bacterial production of neurotransmitters, such as serotonin, that connect to the brain
• Production of short-chain fatty acids that seem to help the nervous system
• Connection with the brain via the “gut-brain axis,” a two-way communication pathway between the neurons of the gastrointestinal (GI) tract and the brain

Endocrine System

• Microbes in the GI tract interact with endocrine cells, which secrete hormones and regulate metabolism, sensations of hunger and satiety, and blood sugar

Results of a study of more than 9,000 subjects published in the journal Nature Metabolism explore the significance of a healthy gut microbiome to aging well. Researchers note that from mid-to-late adulthood, gut microbiomes of study participants became increasingly more unique to an individual. The NIA adds that the differences in patterns among intestinal microbes between older adults who are lean and physically active as opposed to their contemporaries who are not is significant. While this field of study is emerging, initial research connects the early onset of frailty to less gut microbial diversity.

The NIA further shares longitudinal research findings regarding older adults with greater microbial diversity:

• Lower levels of LDL cholesterol
• Higher levels of Vitamin D
• Anti-inflammatory markers in the blood
• Greater mobility and ability to walk quickly

Shuo Han, PhD, assistant professor in the Department of Biochemistry at Duke University School of Medicine, works to understand the interaction between gut microbial health and healthy aging. Dr. Han’s research transplanting microbiota from young to older host mice acted “as a reset button for aging mice, increasing lifespan, and changing metabolism.” Dr. Han sees such studies as a “promising indication that the gut microbiota communities do not merely coexist with the host but play a functional role in shaping a response to the aging process.”

ScienceDirect explains that dysbiosis is the term researchers and physicians use to describe a state of the GI tract in which dysfunctional organisms have replaced the normal gut flora. These changes to the gut microbiota can result in inflammation, which can become chronic, particularly in older adults. Physical conditions suspected to result from this inflammation include physical frailty, type 2 diabetes, fatty liver disease, obesity, coronary heart disease, cancer, polycystic ovary syndrome, and autoimmune diseases.

Patterns emerging from a variety of scholarly sources show how we can have a healthier microbiome. Of particular ongoing interest to researchers is the favorable combination of diet and exercise:

Diet Avoiding processed foods; follow a diet (such as the Mediterranean Diet) that emphasizes fruits, vegetables, and whole grain, high-fiber foods. NIA-sponsored research suggests that the “aging gut” is particularly vulnerable to diets heavy in salt, sugar, and fatty, processed foods. Avoid artificial, non-nutritive sweeteners, such as aspartame, sucralose, and saccharine. Stevia does not adversely affect the gut microbiome.

Exercise New research from UCLA Health is finding connections between exercise and microbiome health. Vijaya Surampudi, MD, Clinical Chief of the UCLA Center of Human Nutrition, explains that both moderate and intense exercise create favorable conditions for beneficial bacteria by oxygenating the bloodstream.

Probiotics & Prebiotics The Agricultural Research Service, part of the US Department of Agriculture, explains that probiotics are edible forms of bacteria, such as yogurt, miso, kefir, and pickles. Prebiotics are nondigestible fiber-rich foods that promote the growth of healthy gut bacteria already present in the gut microbiome. They are found in foods such as almonds, bananas, flax, soy, and whole grains.

Avoiding Alcohol A July, 2025 article in the journal Alcohol entitled Alcohol, Aging, and the Gut Microbiome reports that alcohol consumption “disrupts gut microbial communities.” Aging and genetic factors add to the risk of disruption by heightening the effects of alcohol and contributing to chronic low-grade inflammation and impaired immune responses.

The NIA and Cleveland Clinic add that overuse of antibiotics can affect the health of the gut microbiome.

These research-based findings indicate the importance of home environment and lifestyle choices to the health of our gut microbiome and our aging process.

The scientific understanding of the gut microbiome and its implications for health and aging are emerging with new research. Following are areas of particular interest to physicians and scientists:

From the Cleveland Clinic:

• the role of the gut microbiome in affecting mood disorders, nerve pain, and other behavioral and neurological conditions
• the relationship between gut microbiota and excess fat stored in the liver and metabolic conditions, such as obesity and type 2 diabetes

From the journal Nature Microbiology:

• the use and monitoring of “engineered” microbes as therapeutic intervention; tracking progress with LED monitors and smartphones

From the journal Drugs, The Future of Microbiome Therapeutics:

• live biotherapeutics, synthetic biology (engineered changes to existing bacteria or creation of new ones), phage therapy (the use of bacteria, or phages, to treat bacterial infections—an alternative to antibiotics)

From the journal Genome Medicine: Microbiome-based Therapeutics Towards Healthier Aging and Longevity:

• promoting healthy aging through the prevention and treatment of age-related diseases via targeted microbiome therapies

Research continues to find definitive connections among a healthy gut microbiome, lifestyle choices, and aging well. Smart choices about where and how we live—including the community we choose—are integral to our long-term health and quality of life.

Come explore Plymouth Harbor and learn more about this extraordinary community where the wellbeing of our residents is priority one. Call 941-365-2600 to schedule your private tour and discover why life truly is better on Sarasota Bay!