Rural vs. Urban: How Your Environment Shapes Your Gut

Studies show that people living in urban environments tend to have less diverse gut bacteria and more variation between individuals, often linked to Westernized diets and modern habits like altered sleep and higher stress. Rural populations however, often have more diverse gut microbiomes, influenced by traditional diets and closer contact with natural environments. These differences not only affect individual health but can also be seen across generations. 

People in urban areas can eat whatever they want whenever they want, because multiple food types are available, whereas people in rural areas have to eat what is seasonally available.

Increased contact between humans, animals, and the environment also promotes the exchange of both pathogenic and commensal microbes. While most research focuses on pathogens, commensals likely follow similar transmission routes, albeit less frequently. Domesticated and wild animals, as well as environmental vectors like soil, water, and air, facilitate microbial movement, which can influence human health. Practices such as farming, live animal trade, and cultural behaviors (e.g., hygiene, food preparation) further shape exposure. As global trade, travel, and urbanization rise, microbial transmission across species is expected to grow. This interspecies exchange, especially in populations with mixed traditional and industrial lifestyles, may play a key role in shaping the human microbiome and could help explain global health disparities.

A large-scale study from the Chinese Healthy Gut Project reveals that urbanization significantly influences the gut microbiome. Researchers found that people living in more urbanized environments tend to have less diverse gut bacteria within individuals but more variation between individuals. Urban living was also associated with a shift toward a Bacteroides-dominant microbiome, a pattern linked to Westernized diets and lifestyles (Ren et al., 2023). These findings suggest that modern urban habits, like altered sleep patterns, increased alcohol consumption, and higher stress levels, may disrupt the gut microbiota, potentially impacting long-term health.

Interestingly, close contact between animals and humans, such as on farms or in households with pets, enables microbial transmission, with studies showing that veterinarians and farm workers can acquire microbes and resistance genes from livestock. Even without direct selection, urban-adapted animals like dogs, sparrows, and gulls exhibit lower microbial diversity in urban areas, reflecting shared environmental pressures ​​(Kuthyar & Reese., 2021). Shared environments and interactions across species can shape microbial communities in ways that likely influence human health.

The three main gut microbiome enterotypes—Bac-1, Bac-2, and Bac-3—reflect distinct dietary patterns and lifestyles. Bac-1 is commonly found in urban populations and is associated with a Westernized diet, with Bacteroidota as the dominant phylum. In contrast, Bac-2 is more typical of rural populations whose diets are rich in fiber and plant-based foods, leading to a microbiome dominated by Prevotella (Costea et al., 2018).

In a recent study examining the impact of urbanization on the gut microbiome, researchers compared rural and urban Fula communities in Senegal. The rural group, living in Widou Thiengoli, maintained a largely pre-industrial, pastoralist lifestyle with limited access to modern infrastructure and a simple, dairy-based diet. In contrast, the urban group in Dakar had access to electricity, healthcare, and a more diverse, globalized diet. By analyzing stool samples from 30 mother-infant pairs in each group at two time points, the study found notable differences in gut microbiome composition and diversity. Urban mothers showed slightly higher alpha diversity, and increased Bifidobacterium-rich Actinobacteriota levels over time in both groups, suggesting microbiome recovery postpartum. Interestingly, colonization by Entamoeba coli, a non-pathogenic amoeba more common in the rural group, was linked to higher microbial diversity (Morandini et al., 2023). These findings show how urbanization, through changes in lifestyle, diet, and environmental exposure, shapes the gut microbiome across generations.

A study conducted in Finland investigated how urban land use influences indoor microbial diversity, supporting the hypothesis that urbanization limits exposure to environmental microbiota. Researchers collected and analyzed microbial debris from standardized doormats in 30 rural and 26 urban households, using 16S rRNA gene sequencing. Results showed that increased built environment coverage around homes was associated with reduced bacterial diversity and richness, particularly among Proteobacteria and Actinobacteria. In contrast, the relative abundance of potentially pathogenic taxa increased with urbanization (Parajuli et al., 2018). These findings reinforce concerns that urbanization restricts environmental microbial exposure, potentially contributing to immune-related health issues.

This study comparing gut microbiomes across Indian populations found that rural communities, particularly those in sea-level Ballabhgarh and high-altitude Leh, show distinct and beneficial microbial patterns. Rural Ballabhgarh residents exhibited higher microbial diversity and more consistent microbiome profiles across individuals, suggesting a stable and resilient gut environment. Meanwhile, the rural high-altitude community in Leh had a microbiome enriched in Bacteroidetes and lower in Proteobacteria, often associated with inflammation, indicating a potentially healthier gut composition (Das et al., 2018). These rural microbiomes contrast with more urban-influenced patterns, highlighting how geography and traditional diets in rural settings may promote more favorable gut microbial traits.

No matter where you may live, spending time in green spaces like parks or gardens may also support a healthier gut and skin microbiome. A large international study found that people living in greener areas had greater microbial richness in both their gut and on their skin. They also had higher levels of beneficial bacteria such as Lactobacillus and Bifidobacterium. These microbes are known for their roles in digestion and immune support (Zhang et al., 2023). Even brief, regular exposure to natural environments could help enrich your microbiota and strengthen your body's defenses.