Researchers studied how moving from rural villages to cities affects the bacteria living in your stomach and intestines. They compared indigenous communities in the Amazon rainforest with urban populations in nearby Leticia, Colombia. They found that city living changes which bacteria live in your gut—some helpful bacteria from eating natural foods decreased, while other bacteria increased. Interestingly, people living in rural areas had more parasites, but these parasites were actually linked to having more diverse gut bacteria. The study suggests that these changes in gut bacteria from urbanization might increase the risk of diseases like diabetes and autoimmune conditions later in life.
The Quick Take
- What they studied: How moving from rural villages to cities changes the bacteria and parasites living in people’s digestive systems
- Who participated: Indigenous and non-indigenous people living in rural and urban areas of Leticia in the Colombian Amazon. The exact number of participants wasn’t specified in the abstract, but researchers collected samples from both communities.
- Key finding: City dwellers had fewer beneficial bacteria types associated with eating natural, unprocessed foods, but more of other bacteria types. Rural residents had more parasitic worms, but these were connected to having more diverse gut bacteria overall.
- What it means for you: If you’re moving from a rural to an urban area, your gut bacteria will likely change. This shift may increase your risk of developing chronic diseases like diabetes or autoimmune conditions later in life. However, this is preliminary research and more studies are needed to confirm these connections.
The Research Details
This was a cross-sectional study, which means researchers took a snapshot in time by comparing two different groups—urban and rural populations in Leticia, Colombia. They collected stool samples from people in both areas and analyzed the bacteria and parasites present. The researchers used genetic testing to identify which bacteria were living in each person’s gut and counted how many different types existed. They also tested for parasitic worms and single-celled parasites that can live in the intestines.
The study took advantage of a unique situation: two communities living very close to each other geographically but with very different lifestyles. The rural area is mostly indigenous people living traditionally, while the urban area is mostly non-indigenous people living modern city lives. This allowed researchers to see how urbanization specifically affects gut bacteria, separate from other geographic factors.
Researchers also used computer analysis to predict what functions the bacteria might perform based on their genetic makeup, looking specifically at how they process fats and use oxygen.
This research approach is important because it looks at a population that hasn’t been studied much before—indigenous communities in the Amazon during urbanization. Most previous research on how cities change gut bacteria has focused on wealthy countries. By studying this transition happening in real time in Colombia, researchers can understand how urbanization affects people in developing countries, which is crucial since billions of people worldwide are moving to cities.
This study provides valuable real-world observations, but readers should know it’s a snapshot rather than a long-term follow-up. The researchers didn’t track the same people over time to see how their bacteria changed as they moved to the city. The sample size wasn’t specified in the abstract, so we don’t know how many people were studied. The study shows associations (connections) between urbanization and bacterial changes, but cannot prove that urbanization directly causes these changes. Published in mSphere, a peer-reviewed scientific journal, which means experts reviewed the work before publication.
What the Results Show
The most striking finding was that urban residents had fewer bacteria from families like Lachnospiraceae, Spirochaetaceae, and Succinivibrionaceae—bacteria that thrive when people eat natural, unprocessed foods. Interestingly, Prevotellaceae bacteria, which are also associated with traditional diets, were actually more abundant in urban areas, suggesting a complex shift rather than a simple decline.
Parasitic worms (soil-transmitted helminths) were found mainly in rural residents, which makes sense because rural areas have less sanitation infrastructure. However, single-celled parasites were found in both urban and rural populations equally. This was surprising and suggests that urbanization doesn’t eliminate all parasites.
A key discovery was that people with parasitic infections had more diverse and richer gut bacteria overall. This seems counterintuitive—you might think parasites would harm bacteria—but it suggests parasites and bacteria may coexist in ways we don’t fully understand yet.
The computer analysis of bacterial genes showed that urban and rural bacteria had different capabilities, particularly in how they process unsaturated fats and use oxygen. This suggests the bacteria are adapting to different food sources and living conditions in urban versus rural environments.
The study revealed that the shift in bacterial composition appears to be moving toward a state that might increase vulnerability to chronic diseases. The loss of certain bacteria families associated with traditional diets is particularly concerning because these bacteria may help protect against conditions like diabetes, obesity, and autoimmune diseases. The presence of parasites in rural populations, while often considered negative, may actually be maintaining higher bacterial diversity that could be protective. The differences in metabolic pathways suggest urban bacteria are less equipped to handle certain nutrients from traditional foods.
This research confirms what other studies have shown in wealthy countries—that urbanization reduces gut bacterial diversity. However, it adds important new information by showing this happens in the Amazon context and by revealing the unexpected connection between parasites and bacterial diversity. Previous research has suggested that the loss of parasites during urbanization might contribute to increased autoimmune diseases, and this study provides evidence supporting that theory. The findings align with the ‘hygiene hypothesis,’ which proposes that reduced exposure to parasites and microbes in modern urban life may increase disease risk.
The study is a snapshot in time, not a long-term follow-up, so we can’t see how individual people’s bacteria change as they urbanize. The sample size wasn’t specified, making it unclear how many people were studied and whether results are reliable. The study shows associations but cannot prove urbanization causes the bacterial changes—other factors like diet, water quality, or healthcare access could be responsible. The research was conducted in one specific location (Leticia), so results may not apply to other urbanizing areas. The study didn’t measure actual health outcomes, so we don’t have direct evidence that these bacterial changes lead to disease.
The Bottom Line
Based on this research, people moving to urban areas should be aware that their gut bacteria will likely change. To minimize potential negative effects, try to maintain a diet rich in unprocessed, fiber-rich foods similar to traditional diets. This may help preserve beneficial bacteria. However, these are preliminary findings, and more research is needed before making specific dietary recommendations. The study does not suggest that people should try to maintain parasitic infections—the health risks of parasites outweigh any bacterial diversity benefits. Healthcare providers in urbanizing areas should monitor for increased rates of chronic diseases and consider preventive strategies.
This research is most relevant to indigenous communities and people in developing countries experiencing rapid urbanization. Healthcare workers and public health officials in these regions should pay attention to these findings. People with family histories of diabetes, autoimmune diseases, or other chronic conditions may want to be especially mindful of maintaining diverse diets. This research is less immediately relevant to people already living in established urban areas in wealthy countries, though the findings may eventually apply to them as well.
Changes in gut bacteria can happen relatively quickly—within weeks to months of dietary changes. However, the development of chronic diseases like diabetes or autoimmune conditions typically takes years or decades. You wouldn’t expect to see health problems immediately after moving to a city, but maintaining healthy eating habits now may reduce disease risk over the long term (5-20+ years).
Want to Apply This Research?
- Track daily fiber intake and the number of different plant-based foods consumed. Aim to eat at least 30 different plant species per week, including vegetables, fruits, legumes, and whole grains. Log these in your nutrition app to monitor whether you’re maintaining dietary diversity as you transition to urban living.
- If you’re moving to or living in an urban area, use your nutrition app to intentionally include more whole grains, legumes, vegetables, and fruits—foods that feed beneficial gut bacteria. Set weekly goals to try new plant-based foods and track your progress. Replace processed foods with whole foods when possible.
- Over 3-6 months, monitor how you feel—energy levels, digestion, and any changes in weight or health markers. If possible, work with a healthcare provider to track inflammatory markers or metabolic health indicators annually. Use the app to identify patterns between your diet diversity and how you feel, adjusting your eating habits accordingly.
This research is preliminary and shows associations, not proven cause-and-effect relationships. The findings are based on a single study in one geographic location and may not apply to all populations. This information is not a substitute for professional medical advice. If you have concerns about your digestive health, parasitic infections, or chronic disease risk, consult with a qualified healthcare provider. Do not attempt to self-treat parasitic infections or make major dietary changes without medical guidance. The study does not recommend maintaining parasitic infections for any reason—parasites pose serious health risks and should be treated if detected.