To Improve Your Gut Microbiome, Spend More Time in Nature

Microbes found in green spaces can transfer into your body, increasing bacterial diversity and potentially boosting the strength of the immune system.

Microbes in our gut can have a profound impact on our health, but research is showing that those surrounding us in our environment—what’s known as the natural environmental microbiome—can have a big impact too. This suggests that we should all spend a lot more time interacting with nature, both outdoors and indoors.

I was first introduced to this emerging area of science by Professor Gretchen Daily from Stanford University. She mentioned a Finnish research project that showed how letting kindergarten-aged children play in a yard that contained “dirt” from the forest floor resulted in a significant positive impact on their gut microbiome. Seventy-nine young children took part, all living in urban environments and spending the majority of their days at different daycare centers around Finland. The only difference between them was that these daycare centers had three different types of outdoor spaces.

The first type was a fairly standard outdoor play area, comprised of concrete, gravel, and some plastic matting. The second was the type typically found in daycare environments that are already nature-orientated, with grass, soil, and planted areas for the children to play in. These two acted as a control against which to compare the third experimental space, where the concrete and gravel were covered with segments of forest floor and soil from the local coniferous forest.

The children were encouraged to play in only one of the three types of yard each day over the 28 days of the experiment (note that some kindergartens have multiple play areas). Before and after periods of play, the children’s skin and gut microbiota were measured using genetic sequencing of bacteria taken from skin swabs and stool samples, along with changes to T cells and cytokines in their blood. These cells and proteins play a critical role in preventing autoimmunity and autoimmune diseases; their levels are often used as an indication of how well the immune system is functioning.

Remarkable results emerged. The children who played in the experimental yard showed a large increase in the diversity of microbiota on their skin and in their gut in comparison to the children playing in the urban and nature-orientated areas. Importantly, these were the “good” types of microbiota—those associated with health benefits. There was also a significant increase in the children’s immunity markers, indicative of them having gained enhanced immunoregulatory pathways—which is indicative of a reduced risk of immune-mediated diseases such as inflammatory bowel disease and rheumatoid arthritis.

The importance of this study cannot be overstated. It implies that even short-term exposure to nature’s microbial diversity has the potential to radically alter the diversity of microbiota on our skin and in our gut. In addition, it suggests that the altered gut microbiota can modulate the function of our immune system.

A Healthy Microbiome Is Made, Not Born

Everyone has a distinctive community of microbes in their gut—a person’s ethnicity, the food they consume, antibiotic use, body size, and the amount they exercise all leave a clear signature on their gut microbial diversity. The role of these microbiota communities is significant. Our organs can only synthesize 11 of the 20 essential amino acids that we need, so the rest, along with 13 essential vitamins, are retrieved and synthesized by our gut microbes.

And these microbial communities don’t just help our gut extract nutrients from food. Microbes also produce some of the most important compounds for our health, including immuno-suppressants, anti-cancer, and anti-inflammatory compounds. They appear to be associated with the functioning of our immune system, central nervous system, and associated health outcomes, so much so that clear correlations have been found between particular gut microbiota—so called “sick” microbiomes—and certain illnesses. Those with a distinctive gut microbial signature include irritable bowel syndrome, inflammatory bowel disease, celiac disease, and colorectal cancer as well as nonintestinal disorders such as obesity and type 2 diabetes.

Our environment—broadly meaning our diet, lifestyle, antibiotic use, and so on—appears to have a stronger influence on our gut microbiome than our genetic background. Less than 8 percent of our gut composition is thought to be due to genetic inheritance. The implications of this are profound: it suggests that by changing our environment we may be able to prevent and/or improve certain debilitating illnesses. But how do we go about changing our gut microbiota for the better?

There are at least nine different approaches proposed by the medical profession. Some are more medically intrusive than others—fecal transplants and phage therapy—while nonclinical interventions such as eating a Mediterranean region or fermented foods such as sauerkraut are easier and more palatable.

Yet still missing is the advice for us to interact more with nature and its associated microbiome—especially when some of this evidence now suggests that exposure to nature-derived microbiota could in fact be far more useful and effective than taking orally administered probiotics.

Let the Right Ones In

Like us, all terrestrial plants and soils are inhabited by a diverse, complex, and interactive community of microorganisms. These microbiomes play an essential role in nutrient uptake and growth in plants, improving resilience against pathogens and sustaining plant growth under stress. The microbiomes of plants and soil share very similar bacteria communities to our own, being composed of five major bacterial phyla that are also found in the human gut and skin.

When we spend time interacting with the environmental microbiome, new evidence suggests it passes onto our skin and into our gut through ingestion and greatly improves our own gut microbiota and associated health benefits. This hypothesis, called the “biodiversity hypothesis” was first proposed over two decades ago. Leena von Hertzen and Tari Haahtela, medical scientists at the Helsinki University Central Hospital, and Ilkka Hanski, a biodiversity scientist in the Helsinki Department of Biosciences, suggested that by spending time in and around naturally biodiverse environments, we increase the diversity of microbiota in our own bodies, gaining a larger and more diverse arsenal of microbiota better able to deal with day-to-day digestive functions, and protection from various health conditions, particularly autoimmune diseases.

Over the past 20 years, a series of studies have set out to test the biodiversity—or breaking it down into three sub-hypotheses. First, that there are significant differences between the microbial diversity of natural environments and urban environments. Second, that this microbial diversity transfers into our bodies when we are close to nature, altering our own microbiota. And third, that the presence of nature-derived microbial diversity in our bodies triggers changes in our immune and allergic pathways, which result in positive health outcomes.

The first assumption to be proved broadly correct was that there are significant differences in microbial diversity and abundance between natural and urban environments. Using genetic tools to identify the bacterial communities present, microbial diversity has been measured in the air, soil, and on the leaves of plants across an array of different landscapes, including natural environments such as forests, herbaceous borders, and grasslands, and compared to those typically found in urban areas such as lawns, building sites, parklands, revegetated open woodlands, and remnant open woodlands. These measurements have spanned sites in the US, Canada, Australia, UK, Finland, and India. Without exception, they show that the more natural and biodiverse the environment, the more diverse and abundant the microbiota

Experiments have also taken place indoors to assess what happens if we bring nature into our homes. One of my favorites is a study that looked at what happened to the air in a cleaned room when a spider plant (Chlorophytum comosum) was placed in it for six months. After this time the microbial diversity of the surrounding floor and walls had a significant increase in beneficial plant bacteria (abundance and diversity). This was despite the fact that diversity on the leaves remained the same, suggesting that the plant was actively contributing to the microbial diversity in the room.

The second assumption that needed to be tested was that these nature-derived microbial communities are transferred and ingested into our bodies. Ilkka Hanski, of the biodiversity hypothesis fame, took skin swabs from 118 teenagers living in a variety of different urban and semi-rural environments in Finland, to measure their skin microbial diversity. Clear results emerged: Those who lived in environments with higher levels of biodiversity—trees, shrubs, and flowering plants—had a far greater diversity and abundance of microbes on their skin.

Similarly, Anirudra Parajuli and colleagues, also from the University of Helsinki, found in a study involving 48 elderly Finnish participants that the stool samples of those that lived in urban apartment houses with little surrounding vegetation showed much lower abundance and diversity of “healthy” gut microbiota compared to those in accommodation with gardens within 200 meters.

But how do we know that it is not some other feature, such as diet or pets, that is responsible for this difference? Several more recent studies appear to fill this important knowledge gap. One involved participants interacting with organic soil, an important distinction because soils containing chemical fertilizers have very different and less “good” microbiota). After having their hand microbiota measured using skin swabs and genetic analysis, the participants rubbed their hands for 20 seconds in different soil and plant-based materials including composts, forest turfs, moss material, and material from peat bogs. They then washed their hands in water but without soap for five seconds and dried them on a paper towel. Skin swabs were then taken again for genetic analysis. Researchers found a significant difference in the participants’ skin microbiota after touching the soil materials. In effect, the environmental microbiome signature had transferred onto the participants’ skin.

It is not hard to extrapolate from here that the environmental microbiome could also easily be inhaled and ingested—and indeed this is what was found in two other experiments. Caitlin Selway and colleagues from the University of Adelaide measured the microbiota in participants’ nasal cavities before and after they had spent time in urban green spaces in Australia, the UK, and India, where researchers had already measured the microbial diversity in the soil, air, and leaves. What they showed was a clear increase in the diversity of microbiota in participants’ noses and on their skin after they spent time in these biodiverse urban green spaces. Even though such studies involve only small numbers of participants and must therefore be treated as preliminary, they certainly start to suggest that when we interact in naturally biodiverse landscapes, our bodies adopt the microbial signature of the surrounding environment.

A Natural Immunity Booster

But what about the third assumption—that this change to our microbiota triggers important changes that impact our health? Again, some tantalizing findings have emerged. In the Finnish study involving teenagers, Hanski and colleagues screened their blood for specific antibodies known to be indicative of levels of allergies, and a strong relationship emerged. Those who had the lowest levels of allergy markers in their blood lived in the more biodiverse areas. Similarly, the study involving elderly Finnish participants showed that those who lived in areas surrounded by more diverse vegetation had a reduced abundance in their gut of bacteria that are known to be pathogenic. They also had a reduced occurrence of certain gut microbiota often associated with inflammatory bowel disease.

Both these studies suggest that exposure to environmental microbiota may modulate our gut microbial ecology, and this may then influence our immune system. I say “may” because until very recently, these studies, and similar ones, show associations rather than a direct link. Many of them also lack blind controls where participants are placed in either a placebo or intervention group and the results are compared.

In the past two years, however, studies have started to address these issues.

One of the most important has been carried out by Maja Roslund and colleagues, again from the University of Helsinki. Building on the knowledge gained in the experiment outlined at the beginning, Roslund and her team ran a placebo-controlled double-blinded test of the biodiversity hypothesis of immune-mediated diseases—meaning not only was there a control placebo and intervention group, but that no one involved in the experiment or its day-to-day delivery of the experiment knew which group was which.

The participants were 3- to 5-year-old children in kindergarten who played over a 28-day period in one of two types of sandpits for up to two hours per day. One had been enriched with a microbially diverse soil mixture; the other was microbially poor with no soil. Bacterial communities in the sand, skin, and stools of the children were measured before the experiment and on day 14 and day 28. Blood samples were also taken from the children before and on day 14, and the number of types of T cell were measured. Depending on their type, these can play a critical role in either reducing or enhancing our auto-immune responses. Interleukin-10 (Il-10) is known to be a key player in bringing about an anti-inflammatory response—so we want as much of this in our blood as possible. On the other hand, interleukin-17 (Il-17) causes a pro-inflammatory response and is associated with diseases such as inflammatory bowel disease, rheumatoid arthritis, and multiple sclerosis.

Knowing the details about these T cells is important to appreciate the full significance of this experiment’s findings. Children who played in the sandpit containing soil had a significant shift in their skin microbial diversity to become much closer in composition to the soil. And importantly, their blood plasma showed a large increase in Il-10 levels and a decline in Il-17. In the placebo group there was no such change in either microbial diversity or T cell type.The children who played in the soil-enhanced sand also had higher skin microbial diversity through the duration of the experiment (day 28), suggesting that as long as the intervention is in place, the benefits will be obtained.

This is clearly a very new field of science, with gaps yet to be filled. Possibly one of the most important things to understand is whether interacting with nature-derived microbiota can help people who already have autoimmune and other serious diseases. All the experiments carried out to date have been on healthy participants.

We also need to understand how long we should interact with these nature-derived microbiota to gain and maintain their benefits. Clearly short-term interaction brings about changes. But do we need to do this each day to retain the benefits? A hint that we need to keep “topping up” our environmental microbiota can be seen in the study where the Finnish participants were handling soils. Thirty-five days after the experiment, changes to their microbiota were no longer observed. This suggests that when we stop interacting with nature-derived microbiota, our own not-so-healthy microbiota reestablishes itself.

Excerpt adapted from Good Nature: Why Seeing, Smelling, Hearing, and Touching Plants is Good for Our Health by Kathy Willis. Published by Pegasus Books on December 3, 2024.

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