Can Our Connection to the Natural World Shape Our Microbiome?

Women walking her dog outdoors

Connection. This word carries so much weight, especially now in the time of COVID-19. Is it true that all forms of life are interconnected, and what does that mean? Humans and other microbial communities in nature have been evolving together for billions of years, but how connected are we, truly, to the landscape outside of our bodies? Can urbanized lifestyles, exposure to pollution, and the consumption of nutrient-depleted and synthetic foods contribute to dysbiotic health patterns? These are just some of the questions scientists are beginning to explore as they expand their understanding of the environment-microbiome health axis and examine what happens inside the body when humans are disconnected from their natural surroundings.

This branch of research centers around a hypothesis that is based on the idea that humans have co-evolved with microbiota in biodiverse environments, and that this relationship is vital to the evolution and progression of resilient immune systems.1,2 In fact, one study estimates that approximately 22-36% of the inter-person microbiome variability is associated with environmental factors and only 1.9-9% with genetics.3 This supports the view that humans are ‘holobionts’—a host plus trillions of micro-organisms working symbiotically to form a functional ecological unit.1,2 Called Microbioscape Research, this field of study examines the environmental microbiome and its relationship with people and nature.1 It also aims to understand the social implications and functional ecology of these communities, with a focus on their importance for people, place, and nature.1

Recent research suggests that growing up in microbe-rich environments, such as traditional farms, may have protective health effects on children.4 For example, an individual’s proximity to greenspaces and their associated microbiota may play a role in developing non-communicable diseases.1 In 2015, researchers showed that greenspace proximity was inversely associated with atopic sensitization in children.5 Four study cohorts, comprising children and adolescents, were used to analyze the prevalence of atopic sensitization (by measuring serum IgE specific to inhalant allergens) from five land-use types—forest, agricultural land, built areas, wetlands, and water bodies.5 The amount of green environment (forest and agricultural land) around the homes of study subjects were inversely associated with the risk of atopic sensitization in children.5 For example, land-use pattern explained 20% of the variation in the relative abundance of Proteobacteria on the skin of healthy individuals, supporting the hypothesis of a strong environmental effect on the commensal microbiota.5 Another team found that residents living with higher surrounding biodiversity supported a higher diversity of immunoregulatory gammaproteobacteria.1,6

However, these beneficial health effects may be minimized if land use becomes more urbanized. Some researchers speculate that if early-life exposure to environmental microbes increases gut microbiota diversity by influencing patterns of gut microbial assembly, then soil biodiversity loss due to land-use changes such as urbanization could be considered a public health threat.4

An interesting 2018 study investigated whether land use type around Finnish homes affected the diversity, richness, and abundance of bacterial communities indoors.7 Researchers evaluated debris deposited on doormats in 30 rural and 26 urban households; bacterial community composition was characterized for four different land use types (built area, forest, transitional, and open area) within 200 m and 2,000 m radiuses from each household. The diversity of total bacterial, Proteobacterial, Actinobacterial, Bacteroidetes, and Firmicutes communities decreased as the percentage of built area increased. Additionally, the relative abundance of potentially pathogenic bacterial families and genera increased as the percentage of built area increased. Interestingly, having domestic animals (including pets) only altered the association between the richness of Gammaproteobacteria and diversity of Firmicutes with the built area coverage, suggesting that animal ownership minimally affects transfer of environmental microbiota indoors from the living environment.7

Urban-dwelling groups may be less exposed to diverse microbiota from natural environments due to a range of socioeconomic factors like lack of access to quality greenspaces.1 People with lower socioeconomic status also tend to eat higher proportions of ultra-processed foods and may face additional barriers to accessing affordable fruit and vegetables.1

Clinical Implications

The bulk of the research into the Microbioscape builds upon studies signifying the importance of the microbiome in human health—from processing nutrients to the modulation of inflammatory diseases1,8,9 and mood disorders.10 Dysbiosis of the gut microbiome of infants has been linked to an increased risk of asthma and allergic diseases.11 Some data points to the correlation between early-life risk factors (including mode of delivery, lack of animals in the home, early-life antibiotic use) and changes in the structure of the gut microbiome that disrupt immune regulation.11,3 Lack of microbial diversity in the urban environment may also lead to changes in the type, degree, and timing of microbial stimulation in early life.11 Dysbiosis has also been linked to an increased predisposition to chronic allergic conditions.11 This is known as the “microflora hypothesis.”11

As literature supporting the symbiotic relationship between humans, biodiverse environments, and microbial communities continues to grow, so too do strategies designed to benefit people and nature.1,2 For example, there is a continued interest in the role of nature-based health interventions (NBIs) like “green prescribing,” which can include therapeutic horticulture, biodiversity conservation activities, or activities like exercise in greenspaces.12 Some researchers are looking at whether green infrastructure, like urban parks and community allotments, could be designed and managed to generate microbiome-associated health benefits. Others are examining the possibility of “rewilding” environmental microbiomes by restoring urban ecosystems and their microbial communities to a state that benefits human health.1

A number of studies suggest potential benefits of NBIs to facilitate health and well-being through the “structured promotion of nature-based experiences.”13-15 These include the development of public greenspace and nature prescriptions, where doctors or other health practitioners prescribe nature-based experiences for patients living with specific health conditions.15 A range of NBIs have been examined in the peer-reviewed scientific literature, including green prescriptions, wilderness therapy, green gyms, and outdoor exercise groups.15 It is important to note that many factors influence both the effectiveness and the success of NBIs; further longitudinal studies are needed.12,15


Today, over half the world’s population lives in an urban setting; the United Nations projects that 66% of us will live in a built city environment within two decades.11 How will this shape and contribute to overall health? Will the integration of nature-based interventions in therapeutic settings change the trajectory of disease? As our understanding of the connection between humans, their microbes, and the environment continues to evolve, we may begin to see all life through a holistic and symbiotic perspective and learn to integrate strategies that honor the interconnectedness of all things.

Learn More About Functional Medicine

For more information about the microbiome, please read the following IFM-authored articles:

Intestinal Permeability and Inflammatory Triggers

Optimizing the Pediatric Microbiome

Microbiome Health and Cardiometabolic Conditions

New call-to-action


  1. Robinson JM, Jorgensen A. Rekindling old friendships in new landscapes: the environment-microbiome-health axis in the realms of landscape research. People Nat. 2020;2:339-349. doi:1002/pan3.10082
  2. Robinson JM, Mills JG, Breed MF. Walking ecosystems in microbiome-inspired green infrastructure: an ecological perspective on enhancing personal and planetary health. Challenges. 2018;9(2):40. doi:3390/challe9020040
  3. Dong TS, Gupta A. Influence of early life, diet, and the environment on the microbiome. Clin Gastroenterol Hepatol. 2019;17(2):231-242. doi:1016/j.cgh.2018.08.067
  4. Tasnim N, Abulizi N, Pither J, Hart MM, Gibson DL. Linking the gut microbial ecosystem with the environment: does gut health depend on where we live? Front Microbiol. 2017;8:1935. doi:3389/fmicb.2017.01935
  5. Ruokolainen L, von Hertzen L, Fyhrquist N, et al. Green areas around homes reduce atopic sensitization in children. Allergy. 2015;70(2):196-202. doi:1111/all.12545
  6. Hanski, I, von Hertzen L, Fyhrquist N, et al. Environmental biodiversity, human microbiota, and allergy are interrelated. Proc Natl Acad Sci U S A. 2012;109(21):8334-8339. doi:1073/pnas.1205624109
  7. Parajuli A, Grönroos M, Siter N, et al. Urbanization reduces transfer of diverse environmental microbiota indoors. Front Microbl. 2018;9:84. doi:3389/fmicb.2018.00084
  8. Bicknell B, Liebert A, Johnstone D, Kiat H. Photobiomodulation of the microbiome: implications for metabolic and inflammatory diseases. Lasers Med Sci. 2019;34(2):317-327. doi:1007/s10103-018-2594-6
  9. Koppel N, Maini Rekdal V, Balskus EP. Chemical transformation of xenobiotics by the human gut microbiota. Science. 2017;356(6344):1246-1257. doi:1126/science.aag2770
  10. Lucas G. Gut thinking: the gut microbiome and mental health beyond the head. Microb Ecol Health Dis. 2018;29(2):1548250. doi:1080/16512235.2018.1548250
  11. Sbihi H, Boutin RC, Cutler C, Suen M, Finlay BB, Turvey SE. Thinking bigger: how early-life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease. Allergy. 2016;74(11):2103-2115. doi:1111/all.13812
  12. Robinson JM, Breed MF. Green prescriptions and their co-benefits: integrative strategies for public and environmental health. Challenges. 2019;10(1):9. doi:3390/challe10010009
  13. Seltenrich N. Just what the doctor ordered: using parks to improve children’s health. Environ Health Perspect.2015;123(10):A254-A259. doi:1289/ehp.123-a254
  14. Maier J, Jette S. Promoting nature-based activity for people with mental illness through the US “Exercise Is Medicine” initiative. Am J Public Health.2016;106(5):796-799. doi:2105/ajph.2016.303047
  15. Shanahan DF, Astell-Burt T, Barber EA, et al. Nature-based interventions for improving health and wellbeing: the purpose, the people and the outcomes. Sports. 2019;7(6):141. doi:3390/sports7060141

Related Insights