12 Evidence-Based Steps to a Healthier Microbiome

Girl with saladThe trillions of microorganisms that live in and on your body have a profound impact on your mood, behaviour, and overall health. By taking better care of your microbiome, you can dramatically reduce your risk of chronic disease, boost your brain function, and slow down age-related physical and mental decline. Few, if any, people in contemporary industrialized societies harbour a truly healthy microbiota, so chances are high that you will benefit from the tips in this article.

Before we jump in, I think it’s important to mention that there’s still a lot we don’t know about the human microbiome. In the coming decades, our understanding of man-microbe interactions and how we should eat and live to attain a diverse, balanced microbiota is undoubtedly going to improve. That said, there is already lot we do know, and as long as we adhere to an evolution-based diet and lifestyle template when we make our choices about how to eat and live, we are on safe grounds.

1. Eat a diet that promotes a healthy, diverse gastrointestinal microbiota

beef-shrimp-vegetablesThe structure and make-up of the microbial communities living in your gastrointestinal tract are largely determined by your diet (1, 2)

A modern processed and fiber-depleted diet selects for a gut microbiota that is incompatible with the human genetic make-up, whereas a diet that has characteristics similar to that of the preagricultural diets that conditioned the human genome contributes to shaping a fit, well-functioning body and a microbiota that lives in harmony with its human host (3, 4, 5, 6, 7, 8).

Does this mean that everyone should eat a strict Paleo diet? Not necessarily. In my mind, there’s no doubt that the Paleolithic template is the best starting point for designing a healthy diet. That said, we have to keep in mind that contemporary humans don’t live or exercise like hunter-gatherers, and hence, our nutritional requirements may differ somewhat from that of Paleolithic people (e.g., people who perform a lot of anaerobic exercise typically benefit from including some grains in their diet).

Furthermore, the foods we have available to us today are different from the ones our primal forebears consumed. Perhaps most importantly in the context of diet-microbiome interactions, modern fruits and vegetables tend to be markedly lower in fiber and higher in sugar than their wild counterparts; a difference produced by artificial selection. Our hunter-gatherer forebears probably ate upward of 70 grams of dietary fiber per day, an intake level that can be very difficult to attain on a strict, contemporary Paleo diet.

Some people may find that they are able to attain good gut health on a strict contemporary Paleo diet, as long as they deliberately seek out and eat fruits and vegetables that are especially fiber-rich; however, others might find that they need to include small-moderate quantities of fiber-heavy, low-glycemic index grains and/or legumes such as oats, lentils, or buckwheat in their diet in order to achieve good colonic health.

It’s important to note that a healthy diet will only get you so far. To really be able to achieve good health, you also need a microbiota that is adapted to the diet you’re eating. If you already harbour a diverse microbiota, diet changes may be all that is needed; however, if your microbiota is rid of diversity, you also have to acquire new microbes.

Key points:

  • Be consistent
    An inconsistent, disordered diet can wreak havoc on the gut microbiota. If you’re constantly changing what you eat  and trying new dishes and spices all the time, your gut microbiome will never have time to properly adapt to your diet. It’s better to gradually change your diet by the seasons, than to change it day-by-day.
  • Stay away from foods that negatively impact the gut microbiome
    It’s particularly important to limit the consumption of highly processed foods and foods that have a very high concentration of fat (e.g., GHEE, high-fat cream) or sugar (e.g., soft drinks, fruit nectars).
  • Feed your colonic microbiota
    The average intake of dietary fiber 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, something that can result in an irreversible depletion of gut bacteria (9, 10, 11). 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, Jerusalem artichokes, and onions.

2. Stay away from drugs, dietary supplements, body-care products, and activities that negatively impact the microbiome

antibioticsOveruse of antibiotics, widespread consumption of highly processed foods, excessive hygiene, c-sections, and a myriad of other factors have shaped modern microbiotas that are very different from those of our ancient ancestors. We’ve not only lost many microbial old friends, but 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 what kind of activities/behaviours you should do more of, but also which ones you should avoid.

Following are a list of some of the drugs, activities, dietary supplements, and body-care products that may perturb the microbiota:

  • Antibiotics decrease microbial diversity in the gut and promote a range of adverse health effects (12, 13). If you have to take antibiotics, you should take steps to rebuild your microbiota after the antibiotic treatment is completed. Many other pharmaceutical drugs elicit similar – although less potent – effects (14).
  • Whey protein supplements may destabilize the gut microbiota.
  • Multivitamin supplements may interfere with quorum sensing in gut biofilms (15).
  • Probiotic supplements (the ones that are on the market today) don’t provide the range of microorganisms needed to build a diverse, healthy gut microbiota, and the vast majority contain bacteria that are incapable of colonizing the gut. Moreover, some (many?) probiotic supplements and probiotic-enriched drinks may block the development of a diverse, healthy gut microbiota. That said, in a not so distant future, “probiotics” that contain a wider spectrum of microorganisms and are a lot more effective than today’s supplements may make their way onto the market.
  • Antibacterial lotions can decrease the microbial diversity of the skin microbiota and may impair the skin’s protective barrier.
  • Smoking alters the lung microbiota (16, 17).
  • Excessive use of liquid soaps, body washes, and other similar products may disturb the skin microbiota and/or decrease your exposure to beneficial microorganisms. 

3. Spend more time in nature

man-in-natureHumans evolved to live in nature, not in closed buildings. Today, most people spend more than 90% 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, huge office buildings, and vehicles. This is problematic for a number of reasons, one of which being that we’ve lost contact with some microorganisms that co-evolved with humans for millions of years (18, 19).

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.

Here’s what Dr. Graham Rook, a leading researcher in the microbiome field, had to say about the importance of adequate exposure to microorganisms found in the natural environment:

What are the microbial exposures that result from proximity to the natural environment or farms or that fall onto settle plates in a child’s bedroom? First, the air itself contains large numbers of microorganisms, some of which may actively metabolize and replicate in the air (87). Particulate matter in the air such as pollen carries a load of bacteria (88). Many airborne particles are more than 5 μm and will therefore be deposited in the upper airways, so that after being carried up the trachea by the action of cilia, they will be swallowed. Therefore, airborne microorganisms end up on the skin, in the airways, and in the gut where they modulate the immune system.

When total numbers of organisms in air were counted (i.e., not only the cultivable ones) levels of 105/m3 or more were regularly encountered over a grassy field on clear sunny days, and estimates approaching 106/m3 have been reported above shrubs and some grasslands (reviewed in ref. 89). The air in facilities housing agricultural animals can contain still higher numbers, reaching 107–108 archaea and bacteria/m3 (90). (20)

4. Take better care of the microbiome in your home. If you live or work in a “sick”, mold-contaminated building, remedy the problem or get out now

houseplantsYour home has a microbiome too, which interacts with the one you carry with you.

The microbial communities found in modern buildings differ from those our Paleolithic ancestors were exposed to on a daily basis. A wide range of air-borne substances, including microorganisms and microbially-produced compounds, found in houses, office buildings, schools, etc. may negatively impact your health (21, 22, 23).

While a building with good air quality and healthy occupants can contribute to making you healthy, a building with an imbalanced microbiome may make you very sick.

Here’s what Dr. Graham Rook had to say about this topic in one of his research papers:

Humans evolved in a natural environment and in contact with animals. Until recently even our homes were constructed with timber, mud, animal hair, animal dung, thatch, and other natural products and were ventilated by outside air. By contrast, modern buildings are constructed with synthetic materials, plastics, and concrete, and the timber and cardboard are treated with adhesives and biocides, and the buildings are ventilated by air conditioning systems. When these modern structures degrade, become damp, or accumulate condensation in cavity walls, they do not become colonized with the bacterial strains with which we coevolved. They become habitats for unusual strains that we did not encounter during our evolutionary history, some of which synthesize toxic molecules that we are unable to inactivate (112, 113). Some examples of “sick building syndrome” have been tentatively attributed to prolonged exposure to these inappropriate airborne microbiota (112, 113). (20)

Some experts have argued that as many as 50% of buildings may be contaminated with toxic mold (24). Chronic exposure to mold-produced mycotoxins can result in a range of health problems, including chronic fatigue, depression, brain fog, sugar cravings, low libido, and muscle weakness. You can eat as much fiber-rich vegetables as you want, it’s not going to make you healthy if you’re breathing in mold toxins day in and day out!

Most of us are not going to move out of our city apartment 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.

Some ways to improve your home’s microbiome is to place plants around your house, replace harsh cleaning products with natural alternatives, and regularly open your windows 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 (25, 26, 27). A recent review paper had the following to say about the beneficial effects of plant-associated microbes on indoor microbiomes and human health:

Enclosed environments and their microbiomes—like private/public buildings, hospitals, and clean rooms, which are more or less separated from outside, are especially shaped by human influence and human associated microbes (Hospodsky et al., 2012; Dunn et al., 2013). Hence, microbial diversity is altered and partially reduced compared to the outdoor environment. A reduction in microbial diversity is well known to facilitate dominant proliferations of certain strains, which might bear the risk to have a negative effect toward our health. To increase microbial diversity in an indoor environment we could simply open our windows instead of using air-condition (Hanski et al., 2012; Kembel et al., 2012; Meadow et al., 2013). Alternatively, we could use potted houseplants in built environments as a source of microbial biodiversity and possibly beneficial microorganisms. (28)

5. Consider making and occasionally consuming fermented vegetables

kimchiFermented vegetables such as sauerkraut and kimchi are a rich source of bacteria, some of which may be able to colonize your gut and/or transfer genetic material to microbes that are already established in your intestine.

To date, no studies have investigated how traditionally fermented vegetables affect the gut microbiota (This may change in a not so distant future, because I’m planning to conduct a randomized controlled trial later this year, in which I’ll look into the effects of sauerkraut on the microbiota). However, research has shown that fermented vegetables such as Kimchi may promote fat loss, reduce cholesterol, and improve metabolic parameters, among other things (29, 30, 31).

My feeling and personal experience are that it’s better to consume homemade fermented vegetables occasionally, rather than every day, as I suspect that a chronic daily influx of “large” quantities of lactic acid bacteria could block the development of a normal, diverse gut microbiota. Our Paleolithic ancestors may have occasionally consumed smaller quantities of plant foods that had undergone natural fermentative processes, but they obviously didn’t eat significant quantities of fermented foods on a regular basis. That said, if you feel that daily consumption of fermented vegetables works great for you, then by all means keep doing what you’re doing.

My general suggestion is to consume fermented vegetables every now and then, as a way to increase the biodiversity of your microbiota. They are also useful for occasions when you feel that your microbiome is out of balance (e.g., following a meal that upset your gut).

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 decrease microbial diversity.

It’s important to note that the yoghurt and probiotic-containing products 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.

6. Consider getting a dog

dogIf 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 also 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.” (32). Other studies have shown that children who grow up with dogs have a reduced risk of allergic sensitization to multiple allergens (33, 34, 35).

Keep in mind: While swapping microbes 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 may undermine your health. In other words, make sure your dog is eating a healthy diet and spends plenty of time outdoors.

7. Eat fresh, raw vegetables and fruits from a trusted source (e.g., from the farmers’ market or backyard garden)

vegetablesOur primal ancestors lived in close contact with Mother Earth and were regularly exposed to bacteria associated with food, untreated water, and soil. Certainly, they occasionally came 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, such as by eating raw animal foods or being careless about food hygiene. That being said, there’s no reason to triple-wash fruits and vegetables you get from the backyard garden or farmer’s market.

When you eat raw lettuce, apples, and other plant foods, you’re not just getting a dose of prebiotics, simple carbohydrates, micronutrients, and phytochemicals, but you’re also ingesting food-borne microorganisms, some of which may take up residence in your gut and/or transfer genes to bacteria living in gut biofilms (36). In other words, by consuming raw fruits and vegetables you’re potentially increasing the biodiversity of your gut microbiota.

A 2013 review paper entitled Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables had the following to say about the impact of plant-associated microorganisms on human health:

Fresh produce, including apples, grapes, lettuce, peaches, peppers, spinach, sprouts, and tomatoes, are known to harbor large bacterial populations [1]–[7], but we are only just beginning to explore the diversity of these produce-associated communities. We do know that important human pathogens can be associated with produce (e.g., L. monocytogenes, E. coli, Salmonella), and since fresh produce is often consumed raw, such pathogens can cause widespread disease outbreaks [8]–[11]. In addition to directly causing disease, those microbes found in produce may have other, less direct, impacts on human health. Exposure to non-pathogenic microbes associated with plants may influence the development of allergies [12], and the consumption of raw produce may represent an important means by which new lineages of commensal bacteria are introduced into the human gastrointestinal system. (36)

8. Pick up bacteria from healthy people

kissingAll humans have their own unique microbial cloud, which we bring with us everywhere we go (37).

Studies have shown that individuals with whom we interact shape our microbial communities and that cohabiting family members share microbiota with one another and with their dogs (38). Some of the microorganisms we’re exposed 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 (39). From the perspective of achieving a healthy microbiota, 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/girlfriend may be one of the best ways to maintain a diverse, resilient microbiota, as bacteria are continually shared through kissing, hugging, and sex.

9. Manage your stress levels

meditationIt’s well established in the scientific literature that the bacteria in our gut affect our brain function, stress levels, and behaviour. What some people don’t know is that the highway between the gut and the brain also have many open lanes in the other direction – from the brain to the gut.

Animal studies have shown that chronic psychological stress can disrupt the balance of the microbiota, triggering unfavorable shifts in bacterial composition and diversity (40, 41, 42). It’s little doubt in my mind that these effects extend to humans as well; a belief that is supported by human studies showing that psychological stress can affect gut motility, epithelial barrier function, and inflammatory states (43, 44).

Completely avoiding chronic stress is very difficult, if not impossible. That said, there are a lot of things we can do to reduce our stress levels, such as managing our time better, reducing our use of the internet, and spending more time in nature.

10. Exercise (but not too much)

push-ups-outsideEveryone knows that it’s healthy to exercise. However, what most people don’t know is that some of the health effects associated with physical activity are mediated by the microbiota.

Both observational data and findings from human studies have suggested that people who move more tend to have a more diverse microbiome (45, 46). However, it wasn’t until recently that a cause-effect relationship was proved (46, 47, 48). In general, exercise seems to have positive effects on the microbiome, as long as it’s not excessive.

A balanced training routine that consists of regular strength training, plenty of low-moderate intensity activities (e.g., walking), and some occasional sprinting and/or rowing, will confer multifaceted fitness and could help you build a better microbiome.

More extreme forms of training, on the other hand, can have detrimental effects on health. For example, prolonged, high intensity endurance training may induce leaky gut and gastrointestinal distress in many people (49, 50). When taken to the extreme, bodybuilding-type training can also negatively affect gut health, because it substantially increases your caloric needs and food intake, something that may put excessive stress on your gastrointestinal system.

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

bacteriaStudies have shown that Fecal Microbiota Transplantation (FMT) is highly effective in the treatment of Clostridium difficile infection (51). FMT is also being investigated as a treatment for a variety of other health disorders.

For some people with a severely damaged microbiome, diet and lifestyle changes may not be sufficient to repair the microbiome. Microbiota transplantation can be effective in some of these cases.

However, it’s should be noted that some individuals seem to be unable ta build a diverse, well-functioning microbiota regardless of what they do. This could be due to inflammatory, gastrointestinal disease, insufficient priming of the immune system during the early years of life, and/or genetic/epigenetic factors. Future research will hopefully shed light on these issues.

12. Bonus tips for raising healthy children: Perform a vaginal birth (if you can) and breastfeed your child(ren)

breastfeedingThere’s solid evidence to show that children who are born via caesarean section have a different microbiota than those who are vaginally delivered, and are more likely to develop health problems such as obesity, asthma, allergic disorders, and type-1 diabetes when they get older (52, 53, 54). This isn’t surprising, as these children aren’t exposed to the acid-producing bacteria found in the human vagina; rather, they start their life by picking up bacteria from the skin of their mother and the nurses at the hospital.

Some women are unable to perform a vaginal birth and therefore have to deliver via c-section. In these instances, it may be beneficial to swab the baby with vaginal fluid from their mother.

As for the importance of breastfeeding, several studies have shown that formula-fed infants are at increased risk for infectious disease, childhood obesity, type 1 and type 2 diabetes, leukemia, and sudden infant death syndrome, among other things (55, 56, 57).

Breast milk has been specifically designed by natural selection to support the development and immune maturation of a growing child. Infant formulas, on the other hand, are designed by man, and don’t contain the same combination of nutrients and other health-enhancing substances as mother’s milk. Most importantly in the context of the microbiome, they don’t contain the same mix of microorganisms and prebiotic oligosaccharides.

Perhaps we are best off just doing things the way nature intended?

Pictures: No.1 by Freepik. The rest: Creative Commons pictures, some rights reserved. No. 2 by Julia Frost, no. 3 by Sheep Purple, no. 4 by Philipp Zleger, no. 5 by F. D. Richards, no. 6 by I Believe I Can Fry, no. 7 by Michael Gll, no. 8 by Moyan Brenn, no. 9 by Pedro Ribeiro Simões, no. 10 by Mitchell Joyce, no. 11 by Living Fitness, no. 12 by AJC ajcann.wordpress.com, no. 13 by paxye

Comments

  1. Jennifer says:

    Excellent points. Consuming a small amount of my caraway-sauerkraut a couple/few times a week definitely works best for me rather than worrying about eating some every single day, and not overly stressing/obsessing about optimum nutrition has helped me quite a bit — less stressful, and I finally realized that I do need some grains (traditionally sprouted grains in bread). In addition I have added diversity to my vegetable intake. Also, we have 3 dogs… they get me outside more often than I normally would be outside, and they make me laugh – a lot 🙂 Also, one of them makes me jog a little bit so my exercise regimen has expanded.. all good stuff.

    • I think you’re right in not eating sauerkraut every day, because as I state in the article, I suspect that daily consumption may block the development of a healthy gut microbiota (at least when it’s consumed in fairly large quantities). I’m planning to conduct a study (RCT) later this year looking into the effects of fermented vegetables on the microbiota (We just need to get the funding in place). That study will hopefully shed some light on these issues.

  2. Alessio says:

    I tried plantain flour as prebiotic and I found it really good, I feel to suggest it because I got leaner and my performance improved as well, I feel like my metabolism is speeding up, as far as feelings and placebo effect may be confounding variables.
    I occasionally have some fermented stuff like Kombucha as well.

    • Plantain flour? Alessio… What’s happening?? I thought you adhered to strict Paleo principles (i.e., only eating whole foods); this is outrageous 😛

  3. Alessio says:

    You’re right, I probably got crazy
    I mostly focus on a strict paleo template, however, thanks to you, I’ve been starting to wonder whether I’m properly feeding my buddies or I may need something more. I haven’t found any contraindication to plaintain flour since it’s mostly a source of resistant starch and I decided to give it a try, together with fermented veggies. I’m still against miraculous probiotic pills.
    I blame you for my madness

  4. Nan Deadorff-McClain says:

    Hi Eirik, I had never heard that high fat foods like Ghee are harmful to the microbiota. Would you be able to elaborate? I thought carbohydrates were the main issue.

    • Hi Nan!

      Several studies (e.g., 1, 2, 3, 4) have shown that foods with a very high fat density – especially those that are novel from an evolutionary perspective and high in saturated fat – contribute to the low-grade inflammation often seen after a high fat meal by rapidly increasing the production of chylomicrons that bind bacterial endotoxins and/or by promoting an environment where bad bacteria are able to thrive in the upper intestine.

      This inflammatory effect can probably be explained by the fact that many of the high-fat foods we consume in today’s society have a fatty acid profile that is very different from that of the foods our Paleolithic ancestors consumed. The severity of these effects depends on several factors, such as the state of the gut microbiota, intestinal barrier function, and quantity and type of food eaten.

Trackbacks

  1. […] in many of my previous articles, as well as discussed what we can do to reduce inflammation (Hints: Take better care of your microbiome, adhere to a Paleo-style diet), so that’s not something I’m going to do again here. […]

  2. […] adopting to a good diet is not going to be sufficient to make you healthy; you also need to take steps to repair your microbiome. […]

  3. […] of building a healthy microbiota, but to really be able to make some headway, you also need to add other tools to your tool box, such as fermented vegetables, fiber, and a healthy diet. If your gut microbiota is severely […]

  4. […] has yet to definitively determine the best way to develop and reestablish a diverse microbiome, these 12 steps look like our best options for […]

Leave a Reply

Follow

Get every new post delivered to your Inbox

Join other followers: