Our Gut Microbiome Evolved with Us
New research shows our gut microbes coevolved with us over thousands of generations, kinda like our genes.
Hiya!
Even though I’m fully vaccinated and boosted and got my flu shot, I still got sick last week — along with everyone else in the house, which effectively canceled our Thanksgiving. It ripped through and toppled us like dominoes one day after each other. All tests said negative for Covid, so it was just the flu, but let me tell you, it was terrible.
It was the type where you can’t even watch television because you can’t focus on anything other than how awful you feel, not to mention any movement on a screen makes you hurl your guts out.
But it was while I was doing exactly that — my head hung on the toilet, drenched in sweat, wondering if this is how it all ends — that my mind turned to my gut microbiome. In between dry heaves, I wondered if science has learned anything more about our guts and the microbes within them since I last wrote about them. (Inspiration really can strike anywhere.) Now, here we are because it turns out science has indeed.
Gut Microbes Recap
If you didn’t know, our gastrointestinal (GI) tract is home to a shit-ton of microbiomes, which are mainly made of bacteria. By “a shit-ton,” I mean that you have over two pounds of microorganisms living in your GI tract — that’s more than 100 trillion of them, which is over twice the number of cells making up our bodies. So… if you think about it, this means we’re more bacteria than cells.
Woah.
And while these microbiomes may be microscopically tiny, they have a significant influence on our mental and physical health. They form our gut-brain, or second brain, which works in conjunction with the brain in our skull. I wrote about the gut-brain before and the leading theory that our appendix is a safe haven for “good bacteria.”
While exciting, scientists are still learning about the connection and communication between the brain and microbes and how our microbes influence our health and behaviors. We’ve mostly thought diet has the largest role in how our gut microbes function and in determining which strains we have, but experts recently learned that some of our gut microbiomes were inherited and coevolved with our ancestors.
Recent Research
Postdoctoral researcher at the Max Planck Institute in Germany, Taichi A. Suzuki, who will be starting as an assistant professor at Arizona State University in 2023, recently published a study in Science showing that some of the precious microbes in our guts were passed down to us from our ancient ancestors — one generation after another over hundreds to thousands of years.
See, not only do we have a boatload of microbiomes, as we discussed, but there’s also lots of variation in diversity and composition between the microbiome strains of people living in different areas around the world.
We know a lot of these differences are because of things like the foods we eat — the contents of which can dramatically influence how well our microbes function — but there’s limited knowledge outside of that to explain the differences in strains between the same species of microbes in different groups of people.
In other words, you know how people in Asia look different than people in Europe or Africa, or South America because their ancestors evolved different physical traits to help them survive their environments? And that even though they look different, they’re all still Homo sapiens? Well, their microbiome followed a similar path, but that’s not all.
Suzuki wrote an article in the Conversation about his discovery, and in it, he explains:
“Our recently published study found that not only did microbes diversify with their early modern human hosts as they traveled across the globe, they followed human evolution by restricting themselves to life in the gut.”
Meaning much of our gut microbiome coevolved with us, adapting as our ancestors did — but they did it with such dedication that they sacrificed the ability to survive outside our bodies. Now they’re as much a part of us as our genes are.
The Study
Suzuki and his team paired human genome and microbiome data from people around the world. They gathered data sets (made from saliva and fecal samples) from individuals in Cameroon, North America, South Korea, the United Kingdom, and Western Europe. They also recruited and gathered data from mothers and their young children in Gabon, Germany, and Vietnam. In the end, they had data from a total of 836 adults and 386 children.
They used the samples to create phylogenetic trees—like a family tree — for each person and for 59 strains of the most commonly shared microbial species. After comparing the trees, they found a gradient in how well the trees of the humans matched the trees of the microbes.
Amazingly, some microbial species matched very well and have been hitching a ride through the ancestral line for hundreds of thousands of years. These microbes have smaller genomes, are more sensitive to temperature and oxygen levels, and often can’t survive outside the human body for long.
All of this suggests some of our gut microbes are passed quickly among people living in the same communities and are transmitted generationally from mother to child, where they wouldn’t need to be exposed to elements beyond the body. The latter the researchers confirmed when they compared the samples from the mothers and their young children and found the same strains of microbes.
Though the trees weren’t all such great matches. In fact, some didn’t match at all, indicating these microbes have stronger ties to free-living bacteria in the external environment and probably weren’t from long past generations.
Suzuki’s findings open the door for more research into our gut microbes and their influence on us over generations. But his findings could also influence medicine. After all, doctors are already treating malnutrition in some people by transplanting probiotics from community members’ gut microbiomes.
His discoveries are especially significant since the pandemic considering experts recently discovered that Covid-19 disrupts our microbiome by “allowing pathogenic bacteria to colonize the gut, and by altering the gut lining to let these bacteria more easily spread from the gut to the bloodstream.” Oof that makes me want to eat a vegetable or something. Let’s hope research spurs forward quickly.
Perspective Shift
When I first learned about our gut-brain, I started paying closer attention to my food choices. I’m far from perfect, but considering the impact our microbiome has on our mental and physical well-being, I figure I can at least try to make the environment as hospitable as possible.
But Suzuki’s research takes things to the next level. Learning more about these ancient microbe strains that wove with human evolution could help us understand their role in our well-being. Do they affect us any differently than the non-ancient microbes?
I mean, you know how some people seem to have “old souls”? Well, what if their gut microbes are actually the wise ones? Doubtful, probably. But it’s fun to wonder.
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