Story at a glance

  • The diversity of our gut microbiomes depends on what foods we put into our bodies.
  • Researchers want to know what the gut microbiomes were like in humans prior to industrialization.
  • They examined ancient DNA from ancient dried feces found at a paleontology site.

The gut microbiome is an essential part of the human body’s digestive and immune systems. With modern diets, the species makeup and diversity of the gut microbiome has changed and adapted. Researchers who are hoping to understand what the gut microbiome was like prior to industrialization don’t have many existing populations to study that would be reliably similar. So one group of researchers turned to ancient ruins to find their answers.

The food we eat has a direct effect on our gut microbiome because we are also feeding them when we eat. For example, microbes that prefer feeding on vegetation and fiber will not survive well on a mainly meat diet.

“In ancient cultures, the foods you're eating are very diverse and can support a more eclectic collection of microbes,” said Aleksandar Kostic, is a Joslin Assistant Investigator and an Assistant Professor of Microbiology at Harvard Medical School, in a press release. “But as you move toward industrialization and more of a grocery-store diet, you lose a lot of nutrients that help to support a more diverse microbiome.”

The researchers extracted and studied ancient microbe DNA from Indigenous human paleofeces, meaning desiccated excrement. They found that the ancient microbe genomes had relatively higher amounts of transposases, which are sections of DNA sequence that can change location within the genome.

“We think this could be a strategy for the microbes to adapt in an environment that shifts a lot more than the modern industrialized microbiome, where we eat the same things and live the same life more or less year-round,” Kostic said. “Whereas in a more traditional environment, things change and microbes need to adapt. They might use this much larger collection of transposases to grab and collect genes that will help them adapt to the different environments.”


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The ancient microbes also had fewer genes associated with antibiotic resistance, as well as fewer genes that make proteins that break down the layer of mucus in the intestine, which can lead to inflammation.

The experts hope that this line of research will provide insight on how the gut microbes evolved with humans and whether they were passed vertically from one generation to another or if the main place evolution took place was outside the body in the environment.

This research was also informed by the perspectives from Native American Indigenous communities in the Southwest region.

The authors write in the paper published in Nature, “We acknowledge and appreciate those individuals whose genetics and microbes were analysed for this research, as well as present-day individuals with associated genetic or cultural heritage.”

The researchers plan to continue studying these ancient microbes and hope that one day they can try inserting parts of the ancient genomes into current bacterial species to learn more about the ancient species.


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Published on May 13, 2021