The Microbiome Makeover: Conditioning Your Gut for a Healthier You

microbiome makeover

The human microbiome refers to the vast and diverse community of microorganisms that inhabit various regions of the human body. Microbiomes live in a symbiotic relationship with humans and thrive within our gut, on our skin, and in our mouth, respiratory tract, and even our sex organs.

Comprised of trillions of microbial cells, the microbiome plays a crucial role in maintaining your overall health and influencing various physiological processes. It contributes to digestion, nutrient absorption, mood balance, and immune system development while also aiding in warding off the harmful activity of opportunistic microbes.

The composition of the human microbiome is highly individualized and influenced by factors such as diet, environment, genetics, and lifestyle. Research on the human microbiome has revealed its intricate connections to health functions associated with digestion, cellular health, brain & cognitive function, heart health, immunity, mood, and resilience to stress. Ongoing studies continue to unravel the complexity of the microbiome and its implications for personalized medicine and therapeutic interventions.

This community of bacteria, viruses, fungi, archaea, and other microscopic organisms that live within our intestines is called the gut microbiome.1 Scientists have learned that some of these little creatures naturally support immunity, crowding out potentially harmful microbes before they can invade our bodies.2

But, sometimes, we have trouble maintaining a healthy microbiome balance. Here are a few tips to help keep you on track and feeling your best.

Eat Foods Rich in Prebiotics 

It makes sense that one of the best-known ways to care for our gut microbiome is with the food we put into our gut. Prebiotics are foods that are high in special types of fiber humans can’t digest, but that the gut microbes in our intestines use as food.3,4

Prebiotics are generally plant foods. Providing nutrition for your gut microbiome is a great reason to choose a plant-based diet. These foods include:3,4

  • Vegetables like asparagus, broccoli, cabbage, Jerusalem artichokes, jicama, kale, and onions.

  • Fruit like apples, bananas, kiwifruit, and pomegranates.

  • Whole grains like barley, oats, rice, and whole wheat.

  • Nuts and seeds like almonds, flaxseed, pistachios, and walnuts. 

Eat Fermented Foods 

Some foods have helpful active and live microbial cultures already in them. Fermentation is the process of adding living microbes to certain foods, changing the foods into something new. For example, yogurt is made by adding lactic acid bacteria to milk.5

Almost every ancient culture has made and consumed their own version of fermented food for thousands of years. Some of the living microbes within these delicacies make their way to our intestines after we eat them, improving the microbiome population.5 

Some examples of fermented foods include:5 

  • Kefir, or fermented milk.

  • Yogurt, which is also fermented milk.

  • Miso, or fermented soy paste.

  • Sauerkraut, or fermented cabbage.

  • Kimchi, generally a combination of fermented chili peppers, garlic, and other vegetables.

  • Tempeh, or fermented soybeans. 


Physical Activity also seems to have a positive impact on microbiome health, especially for people who choose low to moderate intensity aerobic exercise.6,7,8 This includes activities like:

  • Easy bike riding

  • Yoga

  • Fast walking or light jogging

  • Swimming and water aerobics

Scientists aren’t sure why exercise helps, but one reason may be because the movement speeds digestion time, allowing less time for harmful bacteria to take up residence in the intestines. This allows the friendly bacteria to maintain a robust population.6,7,8

Spend Time in Nature

Microorganisms in our intestines aren’t the only part of our microbiome that may contribute to good health. Researchers are also looking at the balance of microbes on our skin, in our mouths and within our respiratory tract and their positive impact on seasonal sensitivities and oral health.9 

Some research shows that rural living and getting outdoors in nature may increase the diversity of our overall microbe population. Consider activities like walking out in nature, hiking in the woods, and vegetable or flower gardening and getting your hands in the soil.9,10 

Find Out What You’re Missing

Probiotics supplements may be helpful for some people having trouble maintaining a microbiome balance. Unfortunately, there’s no way to know which supplements are best for any person without careful testing. Simple blood and fecal tests could determine which supplements may be best for an individual.

By eating the right foods, exercising regularly, enjoying outdoor activities, and supplementing when recommended, you can work toward maintaining a healthy balance in your gut microbiome.  




1. Mohajeri, M. Hasan, Robert J. M. Brummer, Robert A. Rastall, Rinse K. Weersma, Hermie J. M. Harmsen, Marijke Faas, and Manfred Eggersdorfer. 2018. European Journal of Nutrition 57 (Suppl 1): 1–14.

2. Gilbert, Jack A., Martin J. Blaser, J. Gregory Caporaso, Janet K. Jansson, Susan V. Lynch, and Rob Knight. 2018. Nature Medicine 24 (4): 392–400.

3. Davani-Davari, Dorna, Manica Negahdaripour, Iman Karimzadeh, Mostafa Seifan, Milad Mohkam, Seyed Jalil Masoumi, Aydin Berenjian, and Younes Ghasemi. 2019. Foods (Basel, Switzerland) 8 (3).

4. “Gut Insight.” n.d. Accessed June 8, 2022.

5. Dimidi, Eirini, Selina Rose Cox, Megan Rossi, and Kevin Whelan. 2019. Nutrients 11 (8).

6. Monda, Vincenzo, Ines Villano, Antonietta Messina, Anna Valenzano, Teresa Esposito, Fiorenzo Moscatelli, Andrea Viggiano, et al. 2017. Oxidative Medicine and Cellular Longevity 2017 (March): 3831972.

7. Peters, H. P., W. R. De Vries, G. P. Vanberge-Henegouwen, and L. M. Akkermans. 2001 Gut 48 (3): 435–39.

8. Allen JM, Mailing LJ, Niemiro GM, Moore R, Cook MD, White BA, et al. Med Sci Sports Exerc. (2018) 50:747–57. doi: 10.1249/MSS.000000000000

9. Selway, Caitlin A., Jacob G. Mills, Philip Weinstein, Chris Skelly, Sudesh Yadav, Andrew Lowe, Martin F. Breed, and Laura S. Weyrich. 2020. Environment International 145 (December): 106084.

10.  Sobko, Tanja, Suisha Liang, Will H. G. Cheng, and Hein M. Tun. 2020. Scientific Reports 10 (1): 21993.