See:
https://www.archaeology.org/news/943...l-fecal-matter

"an international team of scientists led by Marco Candela of the University of Bologna analyzed 50,000-year-old Neanderthal fecal matter uncovered in El Salt, an archaeological site in Spain, and found it contained microorganisms similar to those still found in the modern human gut. “This finding allows us to state that these ancient microorganisms populated the intestine of our species before the separation between Sapiens and Neanderthals, which occurred about 700,000 years ago,” said team member Silvia Turroni of the University of Bologna. Microorganisms in the gut are thought to help regulate metabolism and the immune system. The study could therefore help scientists understand which species in the microbiota have been essential to human health and developed a diet supportive of microbiota diversity, Candela explained. To read more about the study of ancient microbial DNA, go to "Worlds Within Us."

My only question is, couldn't we have gotten it from the Neanderthal admixture instead? To prove their hypothesis, did they test modern people with no Neanderthal ancestry.

The whole field of microbiology in the human gut has lately become a topic of study for me. As a result I've started taking a supplement.