Study: Humanity Is Losing Gut Microbes Passed Down Through Generations

Some bacterial species living in the human gut may have accompanied our ancestors for tens of thousands of years. As people migrated around the world and formed families, they appear to have passed these microbes down from generation to generation. A new study has identified evidence of this shared history in two communities living far apart: the Tsimane people of the Bolivian Amazon and the Hadza people of northern Tanzania, PlanetToday reports. Despite the vast distance separating them, both groups harbor many of the same bacterial species in their guts. Their ancestors may have carried these microbes long before the communities came to live on different continents.

Many of these bacteria are now rare or entirely absent among people in industrialized countries. Scientists want to understand exactly what has been lost and whether this loss matters for human health.

The human gut is home to a community of tiny living organisms, including bacteria. Together, these microbes form what scientists call the gut microbiome. Diet and interactions with other people help shape this community. However, some of its members may have a history that stretches far beyond an individual person's lifetime.

Microbiologist Justin Sonnenburg and his colleagues investigated this possibility by comparing the Tsimane and Hadza populations. The Tsimane grow crops, fish, and gather wild foods, while the Hadza rely on hunting and gathering.

Both populations still harbor numerous microbes that researchers rarely find in industrialized countries. Studying these organisms may help scientists identify which bacteria lived in the human gut in the distant past.

The researchers found many similar microbial species in the two remote communities. They collected 133 stool samples from 85 Tsimane individuals and analyzed the microbial DNA in the samples to identify the organisms living in their guts.

Using this DNA, the team assembled 12,746 microbial genomes. A genome is the complete set of genetic instructions contained in an organism. The researchers compared this information with previously collected data from 137 Hadza individuals. Of the 1,408 microbial species identified in the Tsimane samples, 1,231 were also present in the Hadza samples.

This means that the Hadza carried most of the species found in the Tsimane. However, 848 of these shared species were rare or absent among people living in industrialized countries.

Finding the same species in both communities was only the first step. The researchers still needed to determine how these microbes had come to inhabit both populations. Perhaps both groups had acquired them relatively recently from the environment or from other people. Alternatively, the bacteria might have remained in their ancestors for thousands of years.

To distinguish between these possibilities, the team examined different variants of each bacterial species, known as strains. Strains can be thought of as members of the same species that have small differences in their genetic makeup. If two strains have nearly identical DNA, they probably share a relatively recent common ancestor. Greater differences may indicate that they have been separated for a longer period.

The researchers examined 636 species for which they had sufficient DNA data from both groups. They looked for pairs of strains that were likely to have shared a common ancestor within approximately the past 5,000 years. Almost all these closely related pairs came from within a single community. Nearly 94% consisted of two strains from either the Tsimane or the Hadza.

For 545 of the 636 species, the researchers found no evidence of recent strain exchange between the communities. Thus, although both groups carried the same species, they generally had different variants of those species. This pattern supported the idea of an ancient connection: the bacteria appear to have persisted in each population while their strains evolved independently over time.

To estimate how long the two groups of strains had been separated, the team examined DNA that bacteria had exchanged with one another. Following such an exchange, both strains contain the same long stretch of genetic instructions. This segment does not remain unchanged indefinitely. Over time, new genetic changes break it down, so the length of the remaining shared segment provides an approximate indication of when the exchange occurred.

The analysis suggested that the last exchange of DNA between bacterial lineages in the Tsimane and Hadza occurred approximately 17,000 years ago. European and North American strains exchanged DNA much more recently, around 1,100 years ago, while the estimated date for Asian and North American strains was approximately 4,600 years ago. This suggests that gut bacteria continue to move between industrialized regions, whereas the exchange between these two communities largely ceased long ago.

The earlier date roughly corresponds to the period when humans were settling the Americas. A separate analysis based on genetic differences in 15 species produced a similar estimate, although this pattern did not hold for every species.

Three bacterial species showed evidence of more recent strain exchange between the Tsimane and Hadza: Escherichia coli, Akkermansia muciniphila, and Bacteroides ovatus. All three are also widespread among populations in industrialized countries. The researchers compared an additional 8,855 microbial genomes from Europe, Asia, and North America and found close relatives of these strains there as well. They suggest that contact with people from outside these communities may have introduced these strains into both populations.

Other bacteria had a different history. They were found in guts around the world, yet strains from the Tsimane and Hadza still showed signs of ancient separation. Widespread distribution does not necessarily mean that a species spread recently.

Researchers use the term VANISH to describe a group of microbes that remain common in non-industrialized populations but are rare in industrialized societies. Many species found in the Tsimane and Hadza belong to this group. The findings suggest that their distant common ancestors already carried many of these bacteria.

If so, people living in industrialized countries may have lost microbes that once accompanied humans for thousands of generations. Sonnenburg explained that the state of his own gut may reflect more recent events.

“The microbes that inhabit my gut are unlikely to be the very same microbes that were passed down from generation to generation by my great-great-grandparents,” Sonnenburg said. “More likely, they are a product of my current lifestyle and my interactions with the people around me in our neighborhood.”

This question remains unanswered. The study examined microbial DNA but did not investigate whether people carrying these bacteria were healthier. The authors discuss earlier evidence linking the loss of VANISH microbes to certain chronic diseases.

However, an association does not prove that losing these bacteria causes disease, and this study cannot show that replacing them would improve health. The timeline also has limitations because it depends on estimates of how quickly bacterial DNA changes. The dates provide useful clues rather than exact answers.

Restoring these microbial populations will require further research and the involvement of Indigenous communities that continue to harbor them.