Monday 19 September 2022

Evolution News - How Our Gut Microbes Have Co-Evolved With Us.

human migration out of Africa
Gut microbes spread over the globe along with humans.

© MPI for Biology, Tübingen
Gut microbes and humans on a joint evolutionary journey | Max-Planck-Gesellschaft

When non-African humans came out of Africa, we didn't come alone. In addition to our ectoparasites such as lice, fleas, bedbugs, etc, we also brought some more fellow travellers. We brought our gut microbiota along with us.

And, like us, they have continued to evolve and diversify, co-evolving in lockstep with us, according to the findings by a group of researchers from the Max Planck Institute for Biology, Tübingen, Germany and several research institutes at the University of Tübingen, Germany. By constructing phylogenetic trees for both us and 59 species of microbes found in our gut biota, they showed that there is a close match between theirs and our trees. The more dependent the species of microbe is on us, the more closely our trees match.

This will shock Creationists, but they also found that the more dependent on us our microbes have become, the smaller their genomes. In other words, their evolution has been by loss of genetic information, similar to what we see in other obligate parasites such as parasitic worms. So close is the match for some microbes that it prompted one of the researchers to remark that they behave like part of the human genome.

According to the Max Planck Institute’s press release:
The human gut microbiome is composed of thousands of different bacteria and archaea that vary widely 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: the microorganisms co-evolved in the human gut environment over hundreds of thousands of years. In addition, some microbes exhibit genomic and functional features making them dependent on their host. Now published in Science, the researchers present the results of their study conducted with data from 1225 individuals out of Africa, Asia and Europe.

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.

The research team conjectured that specific species and strains have been with people as humanity diversified and spread over the globe. To test if microbes evolved and diversified simultaneously with their human hosts, researchers from the Max Planck Institute for Biology, the Institute for Tropical Medicine, and the Cluster of Excellence CMFI at the University of Tübingen systematically compared for the first time the evolutionary histories of humans and of gut microbes. The researchers created phylogenetic trees for 1225 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.

We didn`t know that any of our gut microbes followed our evolutionary history this closely.

It is also remarkable that the strains that followed our history most closely are now those who rely most on the gut environment.

This fundamentally changes how we view the human gut microbiome.

Ruth Ley, corresponding author
Head of the department for Microbiome Science
Max Planck Institute for Biology, Tübingen, Germany
Over 60 percent of the investigated species matched with the evolutionary history of their human host, meaning that these microbes co-diversified over ~100,000 years in the human gut when people fanned out of Africa across the continents.

Gut microbes became dependent on their hosts

Some of the gut microbes behave like they are part of the human genome. 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.

Taichi A. Suzuki, co-first author
Department of Microbiome Science
Max Planck Institute for Biology, Tübingen, Germany.
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 similar to free living bacteria.

To obtain data from a diverse subset of the global population, the research team analyzed the gut microbes and genomes of 1225 individuals in Europe, Asia, and Africa. The stool and saliva samples were collected with the help of researchers from the Institute for Tropical Medicine at the University of Tübingen and their partners in Vietnam and Gabon. In addition, researchers around the globe supported the study by providing similar datasets from participants recruited in Cameroon, South Korea, and the UK.
The team explain more in their paper, published in Science, sadly behind a paywall. However, the abstract is available here and is reprinted below with the kind permission of the publishers.

The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.

Given that we are dependent on a healthy gut microbiome just as much as they are dependent on us, it's hardly surprising that this co-dependency has come about by co-evolution, and vice versa, and that the genomes of our more dependent microbes can be used to show the relationships and origins of different human groups in just the same way that our own genomes can.

And of course, this co-dependency/co-evolution didn't begin as Homo sapiens migrated out of Africa and spread across the globe. It will have been going on in our remote ancestors back in the time of the first multicellular organisms with a digestive tract, probably in the pre-Cambrian or Early Cambrian Era. The microbes in their gut were the direct ancestors of our own gut microbiome, just as the first chordates they evolved into were our direct ancestors.

Just another strand to the story of human evolution.

Thank you for sharing!

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