when the first humans moved out of Africa, they brought their gut microbes with them. It turns out that these microbes also evolved alongside them.
The human gut microbiome is made up of hundreds to thousands of species of bacteria and archaea. Within a given species of microbe, different strains carry different genes that can affect its health and the diseases it is susceptible to.
There is a pronounced variation in the microbial composition and diversity of the gut microbiome among people living in different countries around the world. Although researchers are beginning to understand what factors affect the composition of the microbiome, such as diet, there is still limited understanding of why different groups have different strains of the same species of microbes in their guts.
We are researchers who study microbial evolution and microbiomes. Our recently published study found that microbes not only diversified with their early modern human hosts as they traveled around the world, but also followed human evolution by restricting themselves to life in the gut.
Microbes share an evolutionary history with humans
We hypothesized that as humans spread across the globe and diversified genetically, so did the microbial species in their guts. In other words, gut microbes and their human hosts “co-diversified” and evolved together, just as humans diversified so that people in Asia look different from people in Europe, so did their microbiomes.
To assess this, we needed to match human genome and microbiome data from people around the world. However, the data sets that provided both microbiome data and genome information for people were limited when we began this study. Most of the publicly available data came from North America and Western Europe, and we needed data that was more representative of populations around the world.
So our research team used existing data from Cameroon, South Korea, and the UK, and also recruited mothers and their young children in Gabon, Vietnam, and Germany. We collected saliva samples from adults to determine their genotype, or genetic characteristics, and fecal samples to sequence the genomes of their gut microbes.
For our analysis, we used data from 839 adults and 386 children. To assess the evolutionary histories of humans and gut microbes, we created phylogenetic trees for each person and also for 59 strains of the most common microbial species.
When we compared human trees to microbial trees, we discovered a gradient of how well they matched. Some bacterial trees did not match human trees at all, while others matched very well, indicating that these species co-diversified with humans. Some microbial species, in fact, have been on the evolutionary path for more than hundreds of thousands of years.
We also found that microbes that co-evolved with people have a unique set of genes and traits compared to microbes that have not co-diversified with people. Microbes that were associated with humans have smaller genomes and higher sensitivity to oxygen and temperature, mostly unable to tolerate conditions below human body temperature.
In contrast, gut microbes with weaker links to human evolution have traits and genes characteristic of free-living bacteria in the external environment. This finding suggests that co-diversified microbes are highly dependent on the environmental conditions of the human body and must be rapidly transmitted from one person to another, either from generation to generation or between people living in the same communities.
Confirming this mode of transmission, we found that mothers and their children had the same strains of microbes in their intestines. Microbes that did not co-diversify, by contrast, were more likely to survive well outside the body and can be more widely transmitted through water and soil.
Gut microbes and personalized medicine
Our discovery that gut microbes co-evolved with their human hosts offers another way of looking at the human gut microbiome. Gut microbes have been passed between people for hundreds or thousands of generations, so as humans changed, so did their gut microbes. As a result, some gut microbes behave as if they were part of the human genome: they are packages of genes that are passed down between generations and shared by related individuals.
Personalized medicine and genetic testing are beginning to make treatments more specific and effective for the individual. Knowing which microbes have had long-term associations with people can help researchers develop microbiome-based treatments specific to each population. Doctors are already using locally sourced probiotics derived from the gut microbes of community members to treat malnutrition.
Our findings also help scientists better understand how microbes make the ecological and evolutionary transition from “free-living” in the environment to depending on conditions in the human gut. Codiversified microbes have traits and genes that are reminiscent of bacterial symbionts that live within insect hosts. These shared features suggest that other animal hosts may also have gut microbes that co-diversified with them through evolution.
Paying special attention to microbes that share human evolutionary history can help improve understanding of the role they play in human well-being.
This article was originally published on The conversation by Taichi A. Suzuki and Ruth Ley at the Max Planck Institute for Biology. Read the original article here.