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Spring Clean Your Microbiota: Trillions of Tiny Lives That Influence Your Health

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Integrative practitioners know that good health requires a comprehensive and holistic approach. Genes, diet, lifestyle, and environment all influence your physical and mental wellbeing. But the root of wellness might lie in the microbiota — the trillions of microscopic organisms living in and on each person. A growing body of evidence suggests that these trillions of tiny lives significantly influence your health far beyond digestive and immune health.

What is the Microbiota?

The human body is home to more than 100 trillion microscopic organisms. Most are bacteria, but other microbes like yeasts, viruses, protozoa, and fungi are in the mix.1,2  These trillions of tiny lives live and work together as part of an ecosystem. The collection of microbes is known as your microbiota and the collection of their genes is known as your microbiome.

Microbes reside throughout your body — in your digestive tract, on your skin, in your mouth, nose, and respiratory tract, in your urogenital tract, and other places. The gut microbiota gets significant attention because it’s home to a vast majority of microbes.

The Microbiota’s Influences on Health

Most bacteria in the microbiota are beneficial. They perform essential functions throughout your body and influence health in various ways, including:

  • Producing essential vitamins like vitamin K and several B vitamins.3
  • Metabolizing fiber from plant foods and producing compounds that nourish and strengthen the digestive tract lining.2,3,4
  • Limiting the spread of harmful bacteria and other pathogens.1,2
  • Helping maintain a balanced pH level in the female urogenital tract by producing lactic acid and other acidifying compounds.2
  • Helping fight off harmful oral bacteria that cause cavities and gum disease.2
  • Helping prevent the overgrowth of bacteria and yeasts associated with skin infections and eczema.2
  • Positively influencing your mental health, cognitive function, and mood through the gut-brain axis connection.1,4
  • Influencing metabolic health including weight regulation, blood sugar levels, and cardiovascular health. 1,4

Although different types of bacteria live in various parts of the body, a healthy microbiota has a diverse and balanced blend of bacteria and microbes. Some research suggests that less microbial diversity or a lower amount of healthful microbes (known as dysbiosis) may be at the root of many health problems.1,2,3,4  For example, scientists note that people with inflammatory bowel disease, certain autoimmune diseases, irritable bowel syndrome, diabetes, and obesity often have a less diverse gut microbiota.1,4

How to Support the Microbiota

Everyone’s microbiota is as unique as their fingerprint, and what’s more, it changes over time. Your diet, lifestyle, medications, and even sleep quality all influence the mix of bacteria and microbes in your body.3 There are ample opportunities to nurture and improve the health and balance of your microbiota. The following tips can help support a more diverse microbiota.

Eat a variety of plant foods

Bacteria must eat, and their preferred food is fiber from plant foods like fruits, vegetables, legumes, nuts, seeds, and whole grains.3 Each of these foods provides different types of fiber and a unique blend of nutrients, so daily variety is crucial. An easy way to increase variety is by eating the rainbow — aim to eat a wide variety of colorful whole foods with your meals and snacks daily.

Moderate sugar and highly processed foods

Eating large amounts of sugar, unhealthy fats and food additives from highly processed packaged and fast foods promotes inflammation. Diets high in these foods and ingredients are associated with less microbial diversity.3,4 Avoid packaged food and cook at home using whole foods and healthy fats like olive oil as ingredients as much as possible. Substitute plain or fruit-flavored seltzer water or herbal tea for sugar-sweetened beverages. If you have a sweet tooth, reach for fruit first, and save baked goods or pastries for an occasional treat.

Prioritize sleep

Sleep disturbances, inadequate sleep, or disruptions to your sleep-wake cycle from travel can also affect the balance of bacteria in your microbiota.4 To optimize sleep, establish a regular, relaxing bedtime routine and be consistent with your sleep and wake time. Make sure the room is cool and dark and that there are no electronics with lights visible. And power down all devices 45 minutes before bedtime.

Manage stress

Chronic stress does a number on your entire body, boosting inflammation and impacting how your digestive tract works. These also lead to changes in your microbiota and may reduce beneficial bacteria.4 There is no single best way to manage stress, so it’s vital to try different things and see what works for you. Helpful stress-reduction techniques include:

  • Exercise, especially outdoors. Try walking, biking, or hiking in the sunshine.
  • Doing yoga or tai chi. Sign up for classes or try YouTube videos at home.
  • Meditation. Download an app and use it before bed and during the day, especially when you feel stressed.
  • Start a gratitude practice. Keep a journal and write down who and what you’re grateful for each day.
  • Treat yourself to a relaxing massage, take a warm bath, or pamper yourself in some way.

Incorporate probiotics and prebiotics

Probiotic supplements contain the same beneficial live bacteria and yeasts as those in your microbiota. Taking probiotics in their recommended amounts provides various health benefits. There are different types of probiotics. Some are helpful for general gut or immune support, while others are designed to support a specific microbiota, like in a woman’s urogenital tract.

Some probiotics also contain prebiotics. These are compounds that help feed and promote the growth of probiotics. Probiotic blends that contain probiotics are known as synbiotics. Taking the right probiotic or synbiotic can give the microbiota extra support as you work toward a healthy diet and lifestyle changes.

Eating right and living a healthy lifestyle are the best ways to support the trillions of tiny lives in your body. Making these positive changes can cause relatively quick improvements in your  microbiota and microbiome, which can lead to better health in the long run.



  1. Valdes AM, Walter J, Segal E, Spector TD. BMJ. 2018 Jun 13;361:k2179.
  2. Belizário JE, Napolitano M. Front Microbiol. 2015 Oct 6;6:1050
  3. Conlon MA, Bird AR. Nutrients. 2014 Dec 24;7(1):17-44.
  4. Redondo-Useros N, Nova E, González-Zancada N, Díaz LE, Gómez-Martínez S, Marcos A. Nutrients. 2020;12(6):1776.


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