Ethnic differences in gut microbiota composition and functional capacity persist over six years in the HELIUS multi-ethnic longitudinal cohort

Inside the human gut, a vast and invisible ecosystem of bacteria, viruses, and fungi works tirelessly to help digest food, train the immune system, and protect against illness. This community, known as the microbiome, is not the same for everyone. It varies significantly from person to person, shaped by a complex mix of genetics, diet, lifestyle, and where one lives. For decades, scientists have observed that people from different ethnic backgrounds often carry distinct collections of these microbes, even when they live in the same city and eat similar foods. This difference is more than just a biological curiosity; it may help explain why certain ethnic groups face higher risks of heart disease and diabetes. However, a critical question remained unanswered: if people from different backgrounds live together in the same urban environment for many years, do their gut microbes eventually blend together, or do they remain distinct?

To answer this, researchers turned to a long-term study in Amsterdam called HELIUS, which follows thousands of people from six different ethnic groups: Dutch, African Surinamese, South-Asian Surinamese, Ghanaian, Turkish, and Moroccan. The team collected stool samples from nearly 2,000 participants at the start of the study and again six years later. By analyzing the genetic material in these samples, they could track exactly how the microbial communities changed over time. They looked at the types of bacteria present, the specific strains of those bacteria, and the functional tools the microbes use to break down food and resist antibiotics. The goal was to see if living in the same Western city for half a decade was enough to erase the deep-rooted differences between these groups.

The findings reveal that while the gut microbiome is dynamic and constantly shifting, the differences between ethnic groups are remarkably stubborn. Over the six-year period, the researchers observed that the microbes of some groups, particularly those of Moroccan origin, changed more than others, while the Dutch and South-Asian Surinamese groups remained relatively stable. Despite these individual shifts, the distinct microbial signatures of each ethnic group persisted. Even after living in Amsterdam for decades, the gut bacteria of a South-Asian Surinamese participant remained clearly different from those of a Dutch participant. The study calculated that if these differences were to fade away at the rate observed, it would take roughly twenty years for the groups to become half as different as they were at the start. This suggests that the forces shaping the microbiome—likely a mix of long-held cultural dietary habits, family traditions, and perhaps factors like housing or early-life exposures—are far stronger than the influence of a shared urban environment over a six-year span.

The researchers also discovered that what drives change in an individual's gut is less about their ethnicity and more about their health and medication use. Participants who developed type 2 diabetes or started taking certain medications, such as drugs for high blood pressure or diabetes, showed much larger shifts in their microbial communities over time. For instance, people with diabetes experienced a more dramatic turnover in their gut bacteria compared to those without the condition. This indicates that while ethnicity sets the stage for what a person's gut looks like, major health events and medical treatments are the actors that cause the most significant changes in the play.

Digging deeper into the specific types of bacteria, the team focused on a species called Alistipes putredinis, which showed the most interesting pattern of change. At the beginning of the study, this bacterium was common in Dutch participants but much less common in South-Asian Surinamese participants. Over six years, the South-Asian Surinamese group began to acquire this bacterium more frequently, causing their levels to move closer to those of the Dutch group. However, this convergence was limited to the presence of the species itself. When the researchers looked at the genetic makeup of the bacteria within that species—the specific strains—they found that the strains remained distinct. The South-Asian Surinamese participants acquired new strains, but these strains did not replace the existing ones in a way that erased the ethnic differences. Instead, the two groups continued to harbor different genetic versions of the same bacteria.

The study also examined the functional capabilities of these microbes, specifically looking at the enzymes they produce to break down food. The Dutch participants generally had a higher capacity to break down complex plant fibers, while the South-Asian Surinamese participants showed different patterns. Over time, some of these functional differences narrowed slightly, but the overall gap remained wide. Similarly, when looking at antibiotic resistance genes—the genetic instructions that allow bacteria to survive exposure to antibiotics—the total amount of these genes dropped in both groups over the six years, likely reflecting a general decrease in antibiotic use in the Netherlands. However, the specific types of resistance genes present remained different between the groups, with the Dutch participants retaining a more diverse set of resistance genes than their South-Asian Surinamese counterparts.

Ultimately, this research paints a picture of the human gut microbiome as a resilient system that carries the imprint of a person's background for a very long time. While living in a modern city and sharing the same food supply can nudge the microbiome in new directions, it does not quickly erase the deep-seated differences established by culture, genetics, and history. The study suggests that for the foreseeable future, the gut microbiomes of different ethnic groups living in the same city will remain distinct. This has important implications for medical research, reminding scientists that when studying gut health or developing treatments for diseases like diabetes, they must account for these persistent ethnic differences rather than assuming that a shared environment will make everyone's biology the same. The gut microbiome, it turns out, is a long-term memory of who we are and where we come from.