Introduction
Outdoors vs. indoors
Effects on human microbiome composition
Health implications
Potential interventions
Conclusions
References
Further reading

We spend most of our lives indoors, surrounded by invisible microbial communities. Scientists are investigating how our homes change the microorganisms we encounter and what that could mean for our health.

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Introduction

Exposure to natural environments influences the composition of the human microbiome, while bacteria and fungi enter buildings through people or pets, outdoor air, surface contact, or water systems. The global shift toward indoor living has altered patterns of microbial exposure, with implications for host-microbiome interactions.1,2,4

Outdoors vs. indoors

Outdoor environments can have greater microbial richness and diversity than some indoor spaces. For example, certain bacteria, fungi, and other microorganisms that are typically abundant in soil, water, and plants may be less prevalent in built spaces.1,2 Comparisons across studies are complicated by differences in sampling and sequencing methods.2

The indoor microbiome is influenced by microbial communities of the occupants and their habits, alongside ventilation and other environmental inputs. In a study of one newly commissioned building, human-associated genera including Escherichia, Klebsiella, and Pseudomonas became more abundant after commissioning. These genera should not be assumed to dominate every indoor environment.3

Several factors contribute to these differences, some of which include building design, ventilation, occupancy, plumbing systems, cleaning practices, and proximity to green spaces. In one longitudinal study, indoor microbial communities became less similar to outdoor communities after a building was commissioned, when occupancy and cleaning patterns also changed. Environmental conditions, including temperature and humidity, can influence indoor microbial composition.1,3,4

People living in densely developed urban areas may have limited contact with nature, potentially reducing exposure to some microorganisms present in the outdoor environment. It remains uncertain whether these exposure differences translate into measurable improvements or harms to human health.1,4,5

Effects on human microbiome composition

Staying predominantly indoors may change patterns of microbial exposure relevant to microbial communities across the skin, gut, and respiratory tract. Differences detected on building surfaces do not, by themselves, establish corresponding changes in human microbial communities.2,3 In the gastrointestinal tract, urbanization-related changes in diet, medication use, and environmental exposure are associated with changes in gut microbiota, but indoor residence alone has not been shown to directly reduce diversity or weaken immunity. Diet and physical activity can affect gut microorganisms involved in producing short-chain fatty acids (SCFAs), which contribute to metabolic and immune signaling.4,5,6

The skin microbiome may vary with differences in outdoor exposure, but evidence does not establish that time spent indoors independently increases sensitivity to irritants and allergens. Early-life exposures are particularly relevant to immune maturation, as microbial interactions during this period may help shape immune regulation. Reduced interactions with environmental microorganisms during early development have been proposed as a possible contributor to allergic and immune-mediated conditions, but causal pathways in humans remain uncertain.1,4,5

These findings suggest that early environmental exposure may contribute to the development of long-term immune function. Exposure to natural outdoor environments during early childhood, including time spent in green spaces, gardening, and outdoor physical activity, has been associated with broader microbial contact and potential benefits for immune system development. In this context, outdoor play may facilitate interactions with environmental microbial reservoirs in air, soil, and water, but such contact has not been shown consistently to increase human microbiome diversity or improve clinical immune outcomes.1,4

Exploring the Relationship Between Air Conditioning and Microbiome DiversityPlay

Health implications

Urbanization-related changes in diet, lifestyle, and environmental exposure have been associated with a greater risk of developing allergic, autoimmune, and metabolic disorders, but their separate contributions remain difficult to distinguish. Microbial imbalances in the intestinal microbiome, a condition otherwise known as gut dysbiosis, are linked to alterations in metabolic and immune signaling. Proposed mechanisms include disruption of the gut’s protective lining, altered microbial metabolite profiles, and downstream modulation of host immune signaling pathways, potentially contributing to chronic inflammation.1,5

These observations align with the hygiene hypothesis, which proposes that differences in early-life contact with certain microorganisms may influence immune system maturation and increase the risk of developing immune-mediated diseases. Current microbial-exposure hypotheses focus on the types and timing of contact, rather than suggesting that routine hygiene should be abandoned.

Limited contact with soil, plants, and animals among urban dwellers may reduce opportunities for environmental microbial exposure, while appropriate cleaning and disinfection remain important for infection prevention.1,4,5 Indoor microbial hazards also include respiratory problems associated with dampness and mould, and infections caused by pathogens such as Legionella, which can multiply in plumbing and spread through contaminated water aerosols.1

Homes that differ in ventilation systems and proximity to green spaces may contain different microbial communities from those in more open spaces that include plants and natural vegetation. Individuals who engage in frequent contact with animals and soil may experience different microbial exposures; some studies of early-life farm or dog contact have reported lower rates of allergic sensitization or asthma, without establishing that greater microbial richness explains the association. Together, these findings warrant further research into whether outdoor exposures can alter disease risk through changes in the human microbiome.1,4

Potential interventions

At the individual level, possible approaches include behavioral and environmental modifications that change environmental microbial contact and indoor microbial diversity. Cleaning and disinfection should be selected according to infection risk, rather than avoided solely to increase microbial diversity. For general dust removal, a damp cloth with water or mild detergent may be sufficient, while contaminated food-contact surfaces and other higher-risk areas may require appropriate disinfection.1

At the household scale, environmental and behavioral factors may modulate exposure to environmental microbiota. Increased natural ventilation and regular outdoor physical activity may serve as potential pathways for intermittent microbial exchange between indoor and outdoor environments; the effects of ventilation also depend on outdoor air quality, allergen levels, and building conditions.1,2

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Lifestyle changes can alter microbial diversity and richness in built spaces. Pet ownership, particularly dog ownership, has been associated with greater household microbial diversity, though direct health benefits for every occupant have not been established. Increasing the consumption of plant-based foods like fruits and vegetables, while limiting the intake of ultra-processed and refined foods with added sugar and preservatives, can influence gut microbiota, an outcome distinct from microbial diversity on indoor surfaces. In a small study of 13 adolescents, 10 provided paired stool samples; gut microbial diversity increased after a four-week camp combining dietary changes, exercise, and outdoor activities, but the separate effects could not be determined.1,5,6 The study found no statistically significant difference in overall gut microbial community structure before and after the camp.6

At the architectural level, incorporating ventilation and filtration systems with sensor technology to assess indoor conditions such as humidity and airflow could improve the management of microbial exposure, but health benefits attributable to increased indoor microbial diversity remain unproven. This may involve designing homes that incorporate sustainable practices like the use of natural, moisture-regulating materials and smart heating, ventilation, and air conditioning (HVAC) systems that control moisture and air exchange while maintaining indoor air quality.1,4

Compared with some treated wood and non-wood surfaces, untreated wood supports more diverse microbial communities under the conditions examined in one study; this finding does not establish better hygiene or health outcomes. Researchers are also exploring building-design and environmental-management approaches that might safely influence microbial exposure. Introducing microorganisms into household plumbing is not an established health intervention.1,4,7

Conclusions

Scientists and environmentalists are increasingly recognizing indoor environments as active microbial communities that can influence human microbial exposure. Current research investigates how building design, outdoor microbial inputs, and occupants affect indoor microorganisms while maintaining infection prevention and indoor air quality.1,4

Emerging evidence indicates that architectural and environmental features may influence patterns of microbial exposure, with appropriate designs likely to vary across settings and usage conditions.1,4,7 Designing healthy indoor environments requires approaches that balance hygiene and moisture control with opportunities for safe environmental microbial exposure. It remains uncertain whether deliberately increasing indoor microbial diversity improves health.1,4

References

National Academies of Sciences, Engineering, and Medicine. (2017). Microbiomes of the built environment: A research agenda for indoor microbiology, human health, and buildings. National Academies Press. DOI: 10.17226/23647.
https://www.ncbi.nlm.nih.gov/books/NBK458819/
Adams, R.I., Bateman, A.C., Bik, H. M., et al. (2015). Microbiota of the indoor environment: a meta-analysis. Microbiome 3; 49 . DOI: 10.1186/s40168-015-0108-3. https://link.springer.com/article/10.1186/s40168-015-0108-3
Young, G. R., Sherry, A., & Smith, D. L. (2023). Built environment microbiomes transition from outdoor to human-associated communities after construction and commissioning. Scientific Reports 13(1); 15854. DOI: 10.1038/s41598-023-42427-0. https://www.nature.com/articles/s41598-023-42427-0
Gilbert, J. A. & Hartmann, E. M. (2024). The indoors microbiome and human health. Nature Reviews Microbiology 22; 742–755. DOI: 10.1038/s41579-024-01077-3. https://www.nature.com/articles/s41579-024-01077-3
Huang, Z., Li, Y., Park, H., et al. (2023). Unveiling and harnessing the human gut microbiome in the rising burden of non-communicable diseases during urbanization. Gut Microbes 15(1); 2237645. DOI: 10.1080/19490976.2023.2237645. https://www.tandfonline.com/doi/full/10.1080/19490976.2023.2237645
Kang, J., Choi, Y., Keum, G. B., et al. (2025). Effect of Diet and Lifestyle Changes on Gut Microbial Diversity in Healthy Adolescents. Journal of Microbiology and Biotechnology, 35, e2503018. DOI: 10.4014/jmb.2503.03018. https://www.jmb.or.kr/journal/view.html?doi=10.4014/jmb.2503.03018
Kettunen, E., Ahlblad, J., Kurkilahti, M., et al. (2026). From antimicrobial activity to microbial ecology: Untreated and treated wood surfaces shape bacterial survival and community diversity in indoor environments. Journal of Hazardous Materials Advances 22; 101090. DOI: 10.1016/j.hazadv.2026.101090. https://www.sciencedirect.com/science/article/pii/S2772416626000896

Further Reading

Last Updated: Oct 13, 2026