Dozens of gut bacteria have evolved in parallel with human evolution—and many of them are now highly dependent on it. This is the result of a genetic analysis in which the genome of people from Africa, Asia and Europe was compared with that of their respective intestinal flora.
For 36 of the 59 species of bacteria and archaea (archaebacteria) examined, the lineage history agreed surprisingly well with that of humans. This is what an international research team led by Ruth Ley from the Max Planck Institute for Biology in Tübingen reports in the journal Science. “We didn’t know until now that our gut microbes have followed our evolutionary history so closely,” Ley is quoted as saying in a statement from her institute. The biologist emphasizes that the results fundamentally changed the way we look at human intestinal bacteria.
It is true that individual microbes such as the stomach germ and colon cancer pathogen Helicobacter pylori were known to have been with humans since their time in Africa tens of thousands of years ago. But the fact that so many bacteria share their evolutionary history with humans surprised the scientists. This is because people’s diet has changed significantly over time, the population has spread across different climatic zones around the world, and modern lifestyles could also have disrupted the composition of the intestinal flora.
The team – including researchers from the Institute for Tropical Medicine at the University of Tübingen and partner organizations in Vietnam and Gabon – first collected stool and saliva samples, including those from many mothers with their small children. In addition, there was already existing data from people in Cameroon, South Korea and Great Britain.
Overall, the researchers analyzed genetic data from 1,225 people from Africa, Asia and Europe. The researchers drew up family trees based on more than 20,000 variants in the genome. As expected, people from one continent had similar genomes indicating a common ancestry. Likewise, Ley and colleagues created family trees of 59 species of bacteria and archaea. They in turn compared this with the history of human origins.
36 species showed parallels to human evolution in their development. “It is also noteworthy that those strains that have followed our evolutionary history most closely are now most dependent on the intestinal environment,” reports Ley. These bacteria have a reduced genome and are very sensitive to changes in temperature and oxygen levels, making it difficult to survive outside the human gut. They are also more sensitive to antibiotics than other intestinal bacteria.
“Many traits characteristic of the parallel diversified species likely adapted to the niche of an animal gut – not necessarily human,” the team writes. “Whether humans have reversely adapted to these microbial species or strains remains to be investigated.”
In a Science commentary, Andrew Moeller of Cornell University in Ithaca, New York, writes, “The results underscore that gut bacterial communities are not random assemblages of bacteria, but rather reflect the diverse ancestry of human populations.” Moeller sees this in bacteria that live in symbiosis with insects. As with the intestinal bacteria, which are heavily dependent on humans, these insect bacteria also show a greatly reduced genome, which is reduced to core sets of essential functions.