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Your Microbiome, Nutrition and Health:The Latest by Christina Badaracco, MPH, RD

Did you know that our gut bacteria are involved in regulating sleep and muscle function? While most of us now know that they play a role in gastrointestinal function and perhaps even that they contribute to immune function, there's much we're still learning about how our microbiome impacts our health. Let's look at some of the latest research into the microscopic organisms living all over our bodies—and how they affect our health. There are some exciting new findings.

Overview of the microbiome

The human body contains trillions of microorganisms, with unique composition in each body part. All of the genetic material in these microorganisms is referred to as the "microbiome," while "microbiota" refers to the organisms themselves. Most of the microorganisms are bacteria; there are also viruses, protists, fungi and archaea. These organisms play a role in digestion, vitamin synthesis, immune function (both in the intestine and elsewhere in the body), formation of new blood vessels—and more. The bacteria in our gut metabolize certain molecules from our diet, and the types of food we eat (as well as our other behaviors and environmental exposures) can encourage the growth of bacteria that tend to promote either good health or inflammation and disease. While we are born with distinct populations of bacteria, we can change our diet and other behaviors to encourage the growth of the health-promoting species.

The simplified pathway between dietary intake and microbial-mediated health and disease. Note that short chain fatty acids (SCFAs) are beneficial molecules produced by gut bacteria.


Dietary recommendations to foster healthy microbiota have traditionally focused on eating fiber-rich foods (especially those containing prebiotics, or molecules that fuel beneficial bacteria) and fermented foods containing probiotics (or live beneficial bacteria). Recent research suggests that gut bacteria metabolize phytonutrients, which are the chemicals produced by plants that we have long known to be beneficial to our general health—indicating these chemicals are also an important fuel for our microbiota. A 2021 study showed that various types of carotenoids (one group of phytonutrients) were associated with a greater diversity of gut bacteria, which is typically a marker of good health. Microbiota may modify these phytonutrients and/or their metabolites to increase their bioavailability or functions in the body and lead to health benefits.

Many of the foods rich in phytonutrients are also rich in fiber—e.g., brightly colored berries, leafy green vegetables, nuts, seeds, etc. However, this new evidence adds an additional avenue through which they benefit our health; it could also suggest that using cooking methods that maintain phytonutrient content (or even facilitate synergistic effects), taking supplements containing phytonutrients and eating heirloom plant varieties or foods grown with organic or regenerative practices can be additionally beneficial for our microbiota.

Brain health

The gut-brain axis is comprised of biochemical signaling between the gastrointestinal tract and the central nervous system (CNS) and has been well-described. Gut microbiota produce molecules that maintain the blood-brain barrier (the tightly packed cells in the blood vessels leading to the brain that block harmful substances from accessing the brain) and neurochemicals (such as serotonin, a hormone that stabilizes mood) that enable them to communicate with and affect the CNS. Dysbiosis (or microbial imbalance) leads to inflammatory conditions that can also drive various pathologies of the CNS (e.g., Alzheimer's disease, autism spectrum disorder).

New information about specific areas of disease and promising interventions continues to be revealed. For example, a 2021 study demonstrated that Parkinson's disease—a disorder of the CNS that impairs movement—is associated with changes in gut microbiota composition. The onset of the disease hinders the bacteria's ability to break down fat and produce and process bile acids, which are needed to facilitate digestion and absorption of fats and fat-soluble vitamins in the small intestine. These findings suggest that bile acid production disturbances could be a potential indicator of the condition and that treatments targeting the microbiome and bile acids could help delay the disease progression. Of course, consuming an anti-inflammatory diet continues to be important to help prevent such diseases in the first place.

Gut microbiota are also associated with sleep quality. Bacterial metabolites and their effects on the nervous and immune systems can regulate sleep; further, changes in gut microbiota composition have been shown to align with sleep disorders/disturbances in humans. These relationships suggest that dietary modifications—like increasing your intake of prebiotics and probiotics—may be appropriate treatments to improve your sleep quality.

Pulmonary health

The connection between the gut microbiota, lung function and disease is known as the "gut-lung axis." While they should typically exist in homeostasis (or equilibrium), the inflammation and other impairments to immune function caused by dysbiosis contribute to acute and chronic lung disease. SARS-CoV-2 infection, for example, has been shown to disrupt this relationship, and COVID-19 patients with gastrointestinal symptoms (which is indicative of dysbiosis) were more likely to also have acute respiratory distress syndrome—further suggesting a link between these two seemingly disparate areas of the body.

New targets for treatment are arising from our growing understanding of these connections. More specifically, dietary interventions have been shown to reduce the risk of and improve the outcomes for several respiratory diseases. For example, a fiber-rich diet—which helps to modify the composition of the gut microbiota and increase the production of their beneficial metabolites—has been observed to reduce airway inflammation in asthma and chronic obstructive pulmonary disorder (COPD). Also, high fiber intake, specifically from grains and fruit, was associated with a reduced risk of COPD.

Skeletal muscle and physical activity

The gut microbiota are also connected to exercise and muscle mass and function. Results of a recent study by McCarthy et al. suggest that dysbiosis can impair the growth of skeletal muscles following exercise. While physical activity breaks down muscle, it is followed by a period of regrowth when sufficient nutrients are available. This subsequent regrowth is necessary to develop resilience and increase our capacity to withstand the activity in the future; healthy gut microbiota apparently support this process.

A 2020 systematic review showed that physical activity (regardless of type) significantly affects the composition of the gut microbiota and the metabolites they produce. Unfortunately, there is currently insufficient information to generate any specific recommendations for physical activity to promote the healthy composition of the gut microbiota.

Supporting a healthy microbiome

Precision nutrition—or the application of evidence-based, personalized nutrition recommendations—has accelerated thanks to the advent of digital health technologies that collect data and the science informing the analyses of those data (including information about the microbiome). Notably, this is a nascent area, and it is not used frequently in clinical practice. Further, many of the technology companies that generate information about patients' microbiota (or other data) do not provide sufficient explanation, dietary advice or follow-on support to facilitate healthy behavior change based on the findings. Absent any such information, most people can follow the recommendations listed below to foster a thriving and diverse microbiome that maintains good health.

  • Focus on consuming a nutrient-dense, diverse and plant-forward diet. Minimize processed foods, eat a mix of raw and cooked foods and try to consume fermented foods with probiotics (such as sauerkraut and miso) regularly. (Note that while a recent study from researchers at Stanford found that eating fermented foods may be even more effective in increasing microbial diversity and reducing inflammation than fiber-rich foods, both are important aspects of a healthy diet and can lead to myriad health benefits.)

  • Complement this healthy diet with regular physical activity, quality sleep and minimal stress—and avoid unnecessary antibiotics.

  • Consult a dietitian for more tailored guidance about making these changes to your own lifestyle and needs.

  • Discuss any implications for (or interactions with) medications and comorbid conditions with your physician. Also talk with your doctor or dietitian if you're considering testing your microbiome.

The first Soulful Insight about the microbiome was published in January 2018; it included a description of the carbohydrates that are metabolized by our gut bacteria and dietary and lifestyle recommendations to keep them healthy. The microbiome's connection to mental and behavioral health was reviewed in this Insight from January 2021.


Click here for the full list of resources.

Christina Badaracco, MPH, RD

Christina is a registered dietitian and author who aims to improve access to healthy and sustainable food and educate Americans about the connections between food and health. She loves to experiment with healthy recipes in the kitchen and share her creations to inspire others to cook.

Christina completed her dietetic internship at Massachusetts General Hospital and earned her Master of Public Health degree from the University of California, Berkeley. Previously, she graduated with a degree in Ecology and Evolutionary Biology from Princeton University, after conducting her thesis on sustainable agriculture and energy in Kenya. She has done clinical nutrition research at the National Institutes of Health, menu planning and nutrition education at the Oakland Unified School District and communications at the Environmental Protection Agency's Office of Water. She has also enjoyed contributing to children’s gardens, farmers markets and a number of organic farms.

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