The human gut microbiome is made up of thousands of different bacteria and archaea that vary greatly between populations and individuals. Scientists from the Max Planck Institute for Biology in Tübingen have now discovered gut microbes that share a parallel evolutionary history with their human hosts: microorganisms co-evolved in the human gut environment over hundreds of thousands of years. In addition, some microbes exhibit genomic and functional traits that make them dependent on their host. It is now posted in SciencesThe researchers presented the results of their study, which was conducted with data from 1,225 individuals from Africa, Asia and Europe.
Many types of microbes can be found in the human gut across populations all over the world. However, microbial lineages within microbial species differ markedly between individuals and populations. Despite their importance to human health, little is known yet about the origins of these breeds. Moreover, most of these strains live almost exclusively in the human intestine. This raises the question about the source of microorganisms in the human gut.
The research team speculated that certain species and strains were with people as humanity diversified and spread across the globe. To test whether microbes evolved and diversified simultaneously with their human hosts, researchers from the Max Planck Institute for Biology, the Institute of Tropical Medicine, and the CMFI Excellence Group at the University of Tübingen systematically compared for the first time the evolutionary history of humans and gut microbes. The researchers created genetics trees for the 1,225 human study participants as well as the 59 microbial species found in their guts, and used statistical tests to check how well these trees matched.
More than 60 percent of the species examined matched the evolutionary history of their human host, meaning that these microbes diversified over the roughly 100,000 years in the human gut when people spread out of Africa across continents. “We didn’t know that any of the microbes in our gut followed our evolutionary history so closely,” said Ruth Lee, chair of the Department of Microbiome Sciences at the Max Planck Institute for Biology, Tübingen, where the study was conducted, and CMFI’s deputy spokesperson.
Gut microbes become dependent on their hosts
“It is also remarkable that the strains that have followed our history most closely are now those that are most dependent on the environment of the gut,” Lee adds. In fact, some of the strains of microbes that have co-evolved with humans are highly dependent on the human gut environment: they have smaller, more sensitive genomes to oxygen levels and temperature — traits that make it difficult to survive outside the human body. In contrast, microorganisms that showed a weaker association with human history exhibited more free-living bacteria-like properties. “Some gut microbes behave as if they were part of the human genome,” explains Taishi Suzuki, who co-authored the study with Liam FitzStevens. Suzuki adds, “You can imagine that these microbes range from ‘free-living’ to being dependent on the human body’s environment. We’ve seen that some human gut bacteria go along the gradient toward irreversible host dependence than previously thought.” Ley further says, “This fundamentally changes the way we look at the human gut microbiome.”
To obtain data from a diverse subset of the world’s population, the research team analyzed the gut microbes and genomes of 1,225 individuals in Europe, Asia and Africa. Stool and saliva samples were collected with the help of researchers from the Institute of Tropical Medicine at the University of Tübingen and their partners in Vietnam and Gabon. In addition, researchers around the world supported the study by providing similar data sets from recruited participants in Cameroon, South Korea, and the United Kingdom.
The study findings help increase understanding of the population-specific microbes that have long been associated with the local human population. With this knowledge, microbiome-based disease therapies can be adapted and optimized for a population-specific treatment.