The trillions of microorganisms that live in and on our bodies have a profound impact on our mood, behavior and overall health. By taking better care of your microbiota, you can dramatically reduce your risk of chronic disease, boost your brain function, and prevent age-related physical and mental decline. Few, if any, people in contemporary industrialized societies harbor a truly healthy microbiome, so chances are high that you will benefit from the steps below.

1. Eat an ancestral diet high in fibrous fruits and vegetables.

The first step toward building a healthy microbiota is to adopt a nutrient-dense Paleo diet. Pay particular attention to your intake of fermentable fiber, which is the substrate upon which your beneficial gut bugs depend for their survival and growth.

The average dietary fiber intake in contemporary, industrialized societies is extremely low when compared to that of hunter-gatherers and traditional people minimally affected by modern lifestyle practices. Western-style diets, which are characterized by a high intake of fatty meats, refined grains, dairy products and sugar-filled convenience foods, and a low intake of fruits and vegetables, are primarily digested and absorbed in the small intestine, leaving little for the critters in the colon. Basically, if you eat a refined Western diet, you’re starving your microbial self.18

If your goal is to become a more gracious host to your microbial friends, a slice of whole-grain bread for breakfast, a Pink Lady apple for lunch and some lettuce for dinner is not going to cut it. You have to make a conscious decision to seek out and eat more fiber-rich plants such as leeks, slightly green bananas, Jerusalem artichokes and onions.

2. Consider adding fermented foods to your diet.

Fermented foods such as kefir, sauerkraut and kimchi are a rich source of beneficial bacteria. The microbiota of these foods are dominated by lactic acid bacteria, which can help repair a damaged human gut.

It’s important to note that the yogurt and probiotic-containing milk you’ll find at your regular grocery store aren’t going to help you out much. Rather, you should make your own fermented foods at home or seek out a shop, friend or family member that makes and sells traditionally, lacto-fermented products.

Of all of the various fermented foods out there, fermented vegetables may be the most important addition to your diet. Every batch of fermented vegetables has its own unique microbial makeup, so to get optimal benefits, you should make several crocks or glasses with many different types of vegetables. Don’t go heavy on the salt, as high salt concentrations can lead to decreased microbial diversity in the final product.

It’s important to note that not everyone finds that fermented foods work well for them. If you experience negative reactions from eating fermented foods, even long after you’ve gotten through the initial die-off period that a lot of people experience, there’s no reason to continue eating them.

Fermented foods can help restore balance to a damaged ecosystem. However, if your gut is already healthy, you don’t necessarily have to eat fermented foods on a daily basis.

3. Spend more time in natural environments.

Humans evolved to live in nature, not in closed buildings. Today, most people spend more than 90 percent of their time inside buildings and cars. This is in stark contrast to our primal ancestors, who spent all of their time outside.

We’ve replaced trees, singing birds and rivers with concrete pavements, office buildings and vehicles. This is problematic for a number of reasons, one of which being that we’ve lost contact with microorganisms that have co-evolved with humans for millions of years.15,16

By going for a jog in the park, doing some gardening or otherwise spending more time in natural environments, you’ll not only get a feeling of clear-mindedness and good mood, but you may also reconnect with some old microbial friends.

4. Add some plants to your home and open your windows.

Most of us are not going to move out of our city apartments and take up residence on a farm in order to reconnect with nature and increase our exposure to microbial biodiversity. So we have to make compromises and do the best we can with what we’ve got.

One way to bring biodiversity from the natural environment into your house is to place plants around your home and open your windows regularly to bring natural light and fresh air into the building.

Just like humans, all plants have their own unique microbial cloud. Plants help detoxify harmful substances found in the air of your home and may add diversity to your home’s microbiome.1,14

5. Consider getting a dog.

If your living situation and lifestyle permit you to have a pet, getting a dog is definitely worth considering. Not just because getting a dog can boost your activity levels (daily walks are part of the package) and give you someone to play with, but because pets bring microbes into your home—and potentially all the way into your gut. Don’t be afraid to let your dog kiss you or lick your face.

A recent study found that “the presence of dogs had a significant effect on bacterial community composition in multiple locations within homes as the homes occupied by dogs harbored more diverse communities and higher relative abundances of dog-associated bacterial taxa.”2 Other studies have shown that children who grow up with dogs have a reduced risk of allergic sensitization to multiple allergens.3,7,13

Keep in mind: While microbial exchange with a dog that carries a healthy microbiota can enhance your health and well-being, microbial transfer from a sick dog with a damaged microbiota and/or pathogenic infections can undermine your health. In other words, make sure your dog is eating a healthy diet and spends plenty of time outdoors.

6. If you live or work in a “sick” building, remedy the problem or get out now!

I can’t emphasize this point enough. Indoor air quality is a lot more important than most people think.

As previously mentioned, humans evolved to live in nature, not in closed buildings. The types of microorganisms found in modern buildings are different from those our Paleolithic ancestors were exposed to on a daily basis.

A wide range of airborne substances, including microorganisms and microbially produced compounds, found in houses, office buildings, schools and other areas may negatively impact your health.5,12 While a building with good air quality and healthy occupants can contribute to making you healthy, a building with poor air quality and/or unhealthy occupants can make you very sick.

Some experts have argued that as many as 50 percent of buildings may be contaminated with toxic mold.8 You can eat as much fermented food and as many fiber-rich vegetables as you want, but it’s not going to make you healthy if you’re breathing in mold toxins day in and day out!

7. Eat fresh, raw, minimally washed/cleaned vegetables and fruits from a trusted source (like a farmers market or backyard garden).

Our primal ancestors lived in close contact with Mother Earth and were regularly exposed to bacteria associated with food, untreated water and “dirt.” Certainly, they might have come in contact with pathogenic organisms, but exposure to a variety of microbes during the early years of life would have strengthened their microbiome and immune system, thereby giving them a better defense against pathogens than what most of us have today.

Our world has changed dramatically since then: We’ve damaged our soil with pesticides, herbicides and other man-made chemicals, rarely a day goes by when we don’t hear about new outbreaks of food-borne illness, and a lot of people have a dysbiotic microbiota. In other words, we shouldn’t necessarily try to emulate every aspect of our primal forebears’ lifestyle by eating raw animal foods or being careless about food hygiene. That said, there’s no reason to triple-wash fruits and vegetables you get from the backyard garden or farmers market.

When you eat lettuce, apples and other plant foods, you’re not just getting a solid dose of prebiotics, simple carbohydrates, micronutrients and phytochemicals, but you’re also ingesting food-borne microorganisms that may take up residence in your gut and/or transfer genes to bacteria living in gut biofilms.9 In other words, by consuming raw fruits and vegetables, you’re potentially increasing the biodiversity of your gut microbiota.

8. Pick up bacteria from healthy people.

All humans have their own unique microbial cloud, which we bring with us everywhere we go.10 Studies have shown that the individuals with whom we interact shape our microbial communities, and that cohabiting family members share microbiota with one another and with their dogs.17

Some of the microorganisms we’re exposed to have little to no impact on us, while others may exploit an available niche and take up permanent residence in our body.

Health is contagious. From the perspective of achieving a healthy microbiome, it’s much better to live together with healthy people who eat nutrient-dense, whole-foods diets than it is to live with sick individuals. As crazy as it may sound, having a healthy boyfriend or girlfriend may be one of the best ways to maintain a diverse, resilient microbiome, as bacteria are continually shared through activities like kissing, hugging and sex.

9. Stay away from foods, drugs, and activities that negatively impact the microbiome.

One of the key concepts of Darwinian/evolutionary medicine is that many chronic diseases arise because there’s a mismatch between our genome and our current environment.

What has become increasingly clear over the past decade is that many of the negative health effects associated with a “modern” lifestyle result from a perturbation of the microbiome. Basically, the microbiome acts as a bridge between our environment and our human self. When we place ourselves in an environment for which we are poorly adapted—as we’ve done in the modern, industrialized world—a mismatch between our genome and our microbiome is likely to occur.

For millions of years, hominins evolved in diverse ancestral environments that differed markedly from modern environments in several respects. During this time, we not only evolved bodies that were adapted to certain types of physical activity patterns, diets and circadian rhythms, but also to harboring certain types of microbiomes. With the Agricultural Revolution—and even more so the Industrial Revolution and the modern age—profound changes to our environment triggered equally profound changes in our microbiomes.4,6,11

Overuse of antibiotics, widespread consumption of highly processed foods, excessive hygiene, C-sections and a myriad of other factors have molded modern microbiota that are very different from those of our ancient ancestors.4,6,11 We’ve not only lost many microbial “old friends,” but have also altered the overall community structure. In the blink of an eye—from an evolutionary perspective—we’ve dramatically shifted the balance between man and microbes.

To achieve a healthier microbiota, it’s not only important to focus on the kinds of activities/behaviors you should do more of, but also which ones you should avoid. If your goal is to achieve a diverse, resilient microbiota, you should definitely stay away from antibiotics and other drugs, unless you absolutely need to take them. When it comes to diet, consumption of highly processed foods obviously shouldn’t be a daily occurrence. Also, it’s important to keep in mind that many dietary supplements perturb the gut microbiota. Finally, excessive hygiene and regular use of antibacterial gels are definitely not a good idea if the goal is to achieve a healthy microbiota.

10. If all else fails, consider getting one or more microbiota transplantations.

For people with severe gut dysbiosis, a fecal microbiota transplantation (FMT)—or perhaps in a couple of years, the use of advanced probiotic drugs—might be necessary to fix a broken ecosystem.

Finally, it’s important to note that although there are now thousands of research papers on the human microbiome listed on PubMed, there’s still a lot we don’t know about the trillions of critters that inhabit our bodies. For example, although everyone can benefit from the steps mentioned in this article, it may be that genetic/epigenetic factors hinder some people from completely repairing their microbiota, even if they perform several FMTs and/or use advanced microbiome modulators.


  1. Claudio L. “Planting healthier indoor air.” Environmental Health Perspectives. 119.10 (2011): A426–7.
  2. Dunn RR, Fierer N, Henley JB, Leff JW, Menninger HL. “Home life: factors structuring the bacterial diversity found within and between homes.” PLoS One. 8.5 (2013): e64133. DOI: 10.1371/journal.pone.0064133.
  3. Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, et al. “Man’s best friend? The effect of pet ownership on house dust microbial communities.” Journal of Allergy and Clinical Immunology. 126.2 (2010): 410–2, 12.e1-3. DOI: 10.1016/j.jaci.2010.05.042.
  4. Garnas E. “Are Gut Bacteria Making You Fat? Part II: Ancestral Vs. Westernized Microbiome.” Paleo Magazine. 5 Aug 2014.
  5. Gray MR, Thrasher JD, Crago R, Madison RA, Arnold L, et al. “Mixed mold mycotoxicosis: immunological changes in humans following exposure in water-damaged buildings.” Archives of Environmental Health. 58.7 (2003): 410–20.
  6. Hold GL. “Western lifestyle: a ‘master’ manipulator of the intestinal microbiota?” Gut. 63.1 (2014): 5–6. DOI: 10.1136/gutjnl-2013-304969.
  7. Huang YJ, Boushey HA. “The Microbiome in Asthma.” Journal of Allergy and Clinical Immunology. 135.1 (2015): 25–30. DOI: 10.1016/j.jaci.2014.11.011.
  8. Kresser C. “RHR: Dr. Ritchie Shoemaker on Chronic Inflammatory Response Syndrome.” 13 Aug 2015.
  9. Leff JW, and Fierer N. “Bacterial communities associated with the surfaces of fresh fruits and vegetables.” PLoS One. 8.3 (2013): e59310. DOI: 10.1371/journal.pone.0059310.
  10. Meadow JF, Altrichter AE, Bateman AC, Stenson J, Brown GZ, et al. “Humans Differ in Their Personal Microbial Cloud.” PeerJ. 3 (2015): e1258. DOI: 10.7717/peerj.1258.
  11. Moeller AH1, Li Y2, Mpoudi Ngole E3, Ahuka-Mundeke S4, Lonsdorf EV, et al. “Rapid changes in the gut microbiome during human evolution.” Proceedings of the National Academy of Sciences. 111.46 (2014): 16431–5. DOI: 10.1073/pnas.1419136111.
  12. Norback D. “An update on sick building syndrome.” Current Opinion in Allergy and Clinical Immunology. 9.1 (2009): 55–9. DOI: 10.1097/ACI.0b013e32831f8f08.
  13. Ownby DR, Johnson CC, Peterson EL. “Exposure to dogs and cats in the first year of life and risk of allergic sensitization at 6 to 7 years of age.” Journal of the American Medical Association. 288.8 (2002): 963–72.
  14. Pegas PN, Alves CA, Nunes T, Bate-Epey EF, Evtyugina M, Pio CA. “Could houseplants improve indoor air quality in schools?” Journal of Toxicology and Environmental Health, Part A. 75.22–23 (2012): 1371-80. DOI: 10.1080/15287394.2012.721169.
  15. Rook GA. “99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: darwinian medicine and the ‘hygiene’ or ‘old friends’ hypothesis.” Clinical & Experimental Immunology. 160.1 (2010): 70–9. DOI: 10.1111/j.1365-2249.2010.04133.x.
  16. Rook GA. “Regulation of the immune system by biodiversity from the natural environment: an ecosystem service essential to health.” Proceedings of the National Academy of Sciences. 110.46 (2013): 18360–7. DOI: 10.1073/pnas.1313731110.
  17. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, et al. “Cohabiting family members share microbiota with one another and with their dogs.” eLife. 2 (2013): e00458. DOI: 10.7554/eLife.00458.
  18. Sonnenburg ED, Sonnenburg JL. “Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates.” Cell Metabolism. 20.5 (2014): 779–86. DOI: 10.1016/j.cmet.2014.07.003.