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Neanderthal Gut Microbes Overlap With Microbiome of Modern Humans

NEW YORK – An international team has started characterizing the Neanderthal gut microbiome using DNA from feces-rich sediment samples from a Spanish site where the ancient hominins lived roughly 45,000 to 60,700 years ago, uncovering some of the same commensal bugs that inhabit the gut of modern humans.

"These components included so-called 'old friends' and beneficial commensal inhabitants of modern human guts, providing insights into their relevance to the biology of the Homo lineage," co-senior and -corresponding authors Marco Candela, a University of Bologna researcher, and Stephanie Schnorr, a researcher affiliated with the Konrad Lorenz Institute for Evolution and Cognition Research and the University of Nevada, and their colleagues wrote.

Using shotgun metagenomic sequencing, the researchers searched for ancient gut microbe sequences in more than a dozen Middle Paleolithic sediment samples from locations at the El Salt site in Spain where fossilized stool and fecal lipid markers have been found in the past. After weeding out potential modern DNA contaminants using insights into DNA damage to the ancient genetic material, they were left with more than 6,800 sequences per sample, on average, which they compared to publicly available bacterial genome sequences to pinpoint hundreds of species in the ancient samples.

The team's findings, published in Communications Biology on Friday, suggest that the Neanderthal gut was home to some of the same commensal bacteria found in the modern human gut microbiome — a set that included bacterial genera such as Blautia, Ruminococcus, Faecalibacterium, and Bifidobacterium, known for their ability to ferment indigestible carbohydrate into short-chain fatty acids.

"[T]he presence of short-chain fatty acid producers … provides a unique perspective on their relevance as keystone taxa to the biology and health of the Homo lineage," the authors suggested. "While the former are known to allow extra energy to be extracted from dietary fiber, strengthening the relevance of plant foods in human evolution, Bifidobacterium could have provided benefits to archaic human mothers and infants as a protective and immunomodulatory microorganism."

In their follow-up analyses, the investigators considered potential ties between the apparent ancient gut microbes and the metabolites documented in the El Salt sediment samples, and attempted to tease out microbes specific to the Neanderthal gut rather than the oral microbiome, the microbiome of other animals, or the environment.

Along with clues to the ongoing relationships between hominins and the microbes residing in their gut, the team suggested that the Neanderthal findings may provide hints for those pursuing probiotics or other microbiome-based therapeutic strategies. 

"[W]e propose the existence of a core human gut microbiome with recognizable coherence between Neanderthals and modern humans, whose existence would pre-date the split between these two lineages, i.e., in the early Middle Pleistocene," the authors reported. "Although the risk of fractional contamination by modern DNA can never be ruled out and our data must be taken with some caution, the identification of this ancient human gut microbiome core supports the existence of evolutionary symbiosis with strong potential to have a major impact on our health."