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The Human Microbiome: The Garden Within the Body

Trillions of microorganisms - bacteria, fungi, viruses - live within our bodies. These make up the human microbiome.

Trillions of microorganisms – bacteria, fungi, viruses – live within our bodies. These make up the human microbiome. They inhabit our gut, skin, mouth and genitals, among other places. Like a communal garden within the body, a healthy gut contains diverse species living together in balance. Each person has a unique microbiome. Its makeup is influenced by lifestyle, personal history and – especially – diet.

The health of the microbiome influences nearly all body systems. Weight, sleep, digestion, skin health, mood, and immune response are all impacted by the condition of the microbiome. The microorganisms in the gut metabolize nutrients and are critical to healthy digestion. Nutrient absorption, immunity, energy metabolism and gene expression are all influenced by the microbes within us.

Diet and the Gut

Gut microorganisms help us digest the foods that we consume, and they produce substances that our bodies need. The end products and by-products of the microbiome are largely influenced by the foods that we eat.

Over the long term, our diet has a major influence over the composition of the gut microbiome. By eating foods and supplements that feed the beneficial bacteria (prebiotics) and discourage disruptive “bad” bacteria, we can improve our gut microbiome. We can also help the gut microbiome recover by consuming probiotics (fermented foods and supplements that contain beneficial species of bacteria).

Recovering gut health takes time. One day of healthy eating will not reverse the effects that years of unhealthy dietary habits may have on the gut microbiome. Gut health is foundational to the health of the entire body and mind, and requires a commitment to healthy eating.

Health Impacts of the Microbiome

A diverse and balanced microbiome benefits health through many pathways. All of these pathways assist in balancing the body’s inflammatory and immune responses. It increases bioavailability of nutrients from the foods that we eat, produces short chain fatty acids (SCFAs) that provide energy, assists in nutrient absorption, and helps protect us from pathogens.

Conversely, negative changes in the gut microbiome are closely connected with chronic inflammation, poor immunity, insulin sensitivity and blood sugar imbalances. Gut microbiome imbalance (dysbiosis) can impact many chronic health conditions, including:

Lifestyle, Aging and the Microbiome

While our food choices are especially important in maintaining a healthy gut microbiome, other factors play a role too. Sleep habits, physical activity and exercise, environmental exposures, antibiotic use, stress and chronic illness can all impact the microbiome. The composition of the microbiome also changes as we age. There is no “one size fits all” optimal microbiome. Like a garden, the human microbiome changes with the seasons of life and responds to our care. A healthy gut is the result of many individual factors – genetic makeup, environmental factors, dietary choices, and lifestyle.

Gut Microbiome Analysis

Advances in molecular biology have made it possible to evaluate the health of the gut microbiome, using Next Generation Genetic Sequencing and bioinformatic analysis. A stool sample is used to discover the composition of bacteria and fungi that live in your gut. The results are compared to a profile of a normal/healthy gut. As part of the testing, you receive a “gut report” that outlines the microbial species diversity and balance. Working together with your health care practitioner, the “gut report” guides you in developing a regimen of lifestyle changes, dietary modifications and supplement choices tailored to your specific health needs. As your health improves, you can monitor changes in the microbiome by re-testing and evaluating.


Gut microbiome analysis is now available to patients of Elizabeth Zenger, Ph.D., L.Ac. at Inner Works Acupuncture in northwest Portland. For more information, call 503-227-2127.

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