Gut Microbes and Humans Evolved Together

Scientists in Germany have compared the evolution of gut microbes and their human hosts over hundreds of thousands of years and found that, in most cases, they share a parallel evolutionary history. In addition, some microbes exhibit genomic and functional features making them dependent on their host.

The human gut microbiome is composed of thousands of different bacteria and archaea that vary widely between populations and individuals. Many microbe species in the human gut can be found across populations from all over the world. However, within a microbe species the microbe strains vary remarkably between individuals and populations. Despite their importance for human health, little was known so far about the origins of these strains. Moreover, most of these strains live almost exclusively in the human gut. This raises the question of where the microorganisms in the human gut come from.

To help inform this search, a research team from the Max Planck Institute for Biology, the Institute for Tropical Medicine, and the Cluster of Excellence CMFI at the University of Tübingen studied stool and saliva samples from 1,225 people of African, Asian, and European origin. They hypothesized that specific species and strains have been with people as humanity diversified and spread over the globe. They created phylogenetic trees for the human study participants as well as for 59 microbial species found within their guts and used statistical tests to investigate how well these trees match.

The work, reported recently in Science, found that over 60% of the investigated species matched with the evolutionary history of their human host, meaning that these microbes co-diversified in the human gut when people fanned out of Africa across the continents. “We didn`t know that any of our gut microbes followed our evolutionary history this closely,” says Ruth Ley, head of the department for Microbiome Science at the Max Planck Institute for Biology, Tübingen and deputy spokesperson of the CMFI. “It is also remarkable that the strains that followed our history most closely are now those who rely most on the gut environment,” Ley adds.

Indeed, some of the microbe strains that evolved together with humans are heavily dependent on the human gut environment: they possess smaller genomes and are more sensitive to oxygen levels and temperature–traits making it difficult to survive outside the human body.

In contrast, microorganisms that showed weaker association with the human history showed more characteristics like free living bacteria. “Some of the gut microbes behave like they are part of the human genome,” says Taichi Suzuki of Max Planck. “You can imagine that those microbes are on a gradient from ‘free-living’ to reliant on the human body environment. We have seen that some human gut bacteria are further along the gradient towards irreversible host dependence than previously thought. This fundamentally changes how we view the human gut microbiome.”

The findings help to further understand population-specific microbes that have long been associated with the local human population and could inform development of microbiome-based disease therapies.