How Urban Microbes Shape Our Health and Sustainability
In the concrete jungle where we spend 87% of our lives, an unseen ecosystem holds the key to our future well-being 7 .
Beneath the sleek surfaces of our modern cities, behind the glass facades of contemporary architecture, and within the very air we breathe in urban centers, exists an invisible world that profoundly influences our health, well-being, and the sustainability of our urban habitats.
This is the world of the urban microbiome—the complex communities of bacteria, fungi, viruses, and other microorganisms that inhabit our built environments. As we march toward a future where 70% of humanity will live in cities by 2050, understanding and harnessing these microscopic allies may be the key to creating healthier, more sustainable urban ecosystems 9 . The cities of tomorrow may be designed not just for human inhabitants, but for the trillions of microorganisms that literally help shape our world.
70% of humanity in cities by 2050 9
Complex communities of microorganisms in built environments
Creating healthier urban ecosystems through microbial understanding
The relationship between humans and microbes is ancient, stretching back over our entire evolutionary history. "Humans have evolved in direct and intimate contact with their environment and the microbes that it contains, over a period of 2 million years," note researchers in Environmental Research 5 . Our physiology has become intrinsically linked to environmental microbiota, with these microscopic communities playing crucial roles in training our immune systems, protecting against pathogens, and maintaining our overall health.
Autoimmune diseases and non-communicable diseases have reached unprecedented and alarming levels in urban populations, with research suggesting that inadequate exposure to microbial diversity plays a significant role 1 .
Urbanization has dramatically altered this ancient relationship. While modern sanitation has undoubtedly protected us from many harmful pathogens, there's increasing evidence that these same health-protective improvements may have unintended consequences.
The problem isn't just about losing contact with beneficial microbes—it's also about what replaces them. Built environments develop distinct microbial communities that differ dramatically from outdoor environments. As one study revealed, after buildings are commissioned and occupied, indoor environments become significantly enriched with human-associated bacteria including Escherichia, Pseudomonas, and Klebsiella species, while losing the diversity of outdoor soil microbes 7 .
First proposed in 1989, this theory suggests that highly sanitized environments in early childhood may prevent proper development of the immune system, increasing susceptibility to allergic and autoimmune diseases 1 .
An extension of the hygiene hypothesis, this 2012 theory proposes that co-evolution with specific microorganisms throughout human history has made them essential for proper immune function 1 .
An emerging approach that incorporates understanding of microbial communities into urban planning and architectural design to promote health-supporting microbiomes 1 .
What happens to microbial communities when a new building is born? A groundbreaking study published in Scientific Reports in 2023 provided unprecedented insights by tracking the microbial development of a new building from construction through commissioning and use 7 .
Researchers conducted a 36-month longitudinal study of The OME, an experimental building in Newcastle upon Tyne, England. Their approach was comprehensive:
This meticulous tracking of microbial colonization from the very beginning of a building's life represented a novel approach in microbiome research.
The findings revealed a dramatic microbial transformation as the building transitioned from construction to active use:
| Metric | Before Commissioning | After Commissioning | Change |
|---|---|---|---|
| Bacterial Richness | Higher | Significantly reduced (P < 0.001) | Decreased |
| Community Structure | Similar to outdoor | Significantly altered (R² = 0.14) | Diverged from outdoor |
| Community Stability | Lower outdoor stability | Higher outdoor stability | Increased divergence |
| Environmental Selection | 0.3% | 10.5% | 10.2% increase |
Table 1: Microbial Diversity Changes Before and After Building Commissioning
Perhaps most strikingly, the influence of outdoor microbiota on indoor communities plummeted from 17% to just 0.004% following commissioning, indicating that human activity and building use quickly override outdoor environmental influences in shaping the indoor microbiome 7 .
| Surface Type | Dominant Microbial Genera | Probable Sources |
|---|---|---|
| Outdoor Soil | Solirubrobacterales, Kaistobacter, Nocardioidaceae | Environmental, soil-associated |
| Indoor Floors | Escherichia, Pseudomonas, Klebsiella | Human-associated, enteric commensals |
| Shelving & Windowsills | Mixed environmental and human-associated | Both outdoor and human sources |
| Sinks & Splashbacks | Pseudomonas, Escherichia | Human-associated, moisture-loving |
Table 2: Microbial Community Composition by Surface Type
Seasonal patterns emerged as well, with temperature and humidity significantly affecting microbial diversity. Lowest alpha diversity occurred at temperatures between 10-20°C and relative humidity of 50-60%, while highest diversity aligned with conditions closer to ideal growth conditions for many host-associated microbes (30°C and 80% humidity) 7 .
Outdoor environmental microbes dominate, high bacterial richness
Human-associated bacteria begin to colonize surfaces
Rapid shift to human-associated microbiome, reduced diversity
Stable indoor microbiome with minimal outdoor influence
Studying urban microbiomes requires sophisticated tools that have only recently become accessible to researchers. The field has evolved rapidly from basic observations to high-resolution molecular analysis.
| Tool/Technique | Function | Application in Urban Settings |
|---|---|---|
| 16S rRNA Sequencing | Identifies bacterial communities via specific gene region | Profiling surface microbiomes in built environments |
| Shotgun Metagenomics | Sequences all genetic material in a sample | Identifying functional potential of urban microbiomes |
| Metatranscriptomics | Analyzes expressed genes in community | Understanding active microbial functions in cities |
| Metabolomics | Identifies and quantifies metabolic products | Linking microbial activity to health outcomes |
| Culture-Based Methods | Grows microorganisms in lab conditions | Isolating specific strains for functional testing |
Table 3: Essential Tools for Urban Microbiome Research
Each method provides complementary insights. While 16S sequencing efficiently identifies "who's there," metagenomics reveals "what they could do," and metatranscriptomics shows "what they're actually doing" in the urban environment 6 .
Identifies bacterial communities via specific gene region
Grows microorganisms in lab conditions for isolation
Recent advances in strain-level identification have been particularly important, as not all strains within a species are equally functional. For example, while some Escherichia coli strains are harmless gut commensals, others can be deadly pathogens 6 . This resolution matters tremendously when assessing urban microbiomes for health risks or benefits.
The growing understanding of urban microbiomes points toward a revolutionary approach to city planning: bioinformed design that consciously shapes microbial communities to support human and ecosystem health 1 . This represents a paradigm shift from viewing microbes solely as threats to be eliminated, toward recognizing them as potential allies to be cultivated.
The World Health Organization recommends at least one public green space of 0.5 hectares within 300m of every residence. Larger spaces are more likely to support functioning ecosystems that provide diverse aerobiomes 5 .
Rather than highly manicured landscapes, some degree of rewilding can support more diverse microbial communities. Soil biodiversity is particularly important, as urban soils host immense microbial diversity that can suppress pathogens, remediate contaminants, and potentially enhance human immune function 5 9 .
Green roofs, vertical gardens, and living walls do more than just beautify—they introduce diverse microbial communities into the urban matrix. The Bosco Verticale in Milan, Italy, exemplifies this approach, with its vertical forest potentially creating a net gain in ecological services 8 .
Indoor microbiome health can be enhanced through operable windows, indoor plants, and careful consideration of how function, form, and organization affect microbial communities 5 .
One significant concern in urban ecosystems is microbial homogenization—the reduction in beta diversity (differences between sites) across urban environments 9 . While individual urban locations may have high alpha diversity (richness at a single site), the similarities between microbial communities in different cities are increasing due to common anthropogenic influences. This reduction in microbial heterogeneity may limit the immune-training opportunities for urban residents.
Despite progress, significant challenges remain in fully understanding and harnessing urban microbiomes. The field must overcome:
Differentiating between active and dormant microbial communities, understanding strain-level functional differences, and integrating multi-omics approaches present substantial analytical challenges 6 .
With varied sampling and analysis methods across studies, comparing results and building comprehensive models remains difficult 3 .
Ensuring equitable access to microbiome-supporting green spaces across socioeconomic groups represents both an ethical imperative and practical challenge 5 .
Nevertheless, the potential rewards are tremendous. By viewing cities as living laboratories and embracing our role as co-inhabitants with microbial communities, we can reimagine urban ecosystems that work with nature rather than against it. The future of sustainable cities may depend not just on visible green infrastructure, but on the invisible microbial networks that literally bring our urban environments to life.
As we continue to unravel the complex relationships between urban design, microbial ecology, and human health, one thing becomes clear: the cities of the future must be designed for all their inhabitants, seen and unseen. Our well-being depends on it.