Our hominid cousins, the Neanderthals, have contributed much to our evolution as a species, and now an international team of researchers led by investigators at the University of Bologna just found a new contribution after analyzing 50,000-year-old fecal samples—gut microbes. The fecal samples were unearthed at the archaeological site of El Salt, near Alicante (Spain). The data from their analyses led the scientists to propose the hypothesis that ancestral components of human microbiota have been living in the human gastrointestinal tract since before the separation between Homo sapiens and Neanderthals that occurred more than 700,000 years ago. The findings from this new study were published today in Communications Biology through an article titled, “Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.”

“These results allow us to understand which components of the human gut microbiota are essential for our health, as they are integral elements of our biology also from an evolutionary point of view,” explained senior study investigator Marco Candela, PhD, a professor in the department of pharmacy and biotechnology at the University of Bologna. “Nowadays, there is a progressive reduction of our microbiota diversity due to the context of our modern life: this research group’s findings could guide us in devising diet- and lifestyle-tailored solutions to counteract this phenomenon.”

The gut microbiota is the collection of trillions of symbiont microorganisms that populate our gastrointestinal tract. It represents an essential component of our biology and carries out crucial functions in our bodies, such as regulating our metabolism and immune system and protecting us from pathogenic microorganisms. Recently, studies have shown how some features of modernity—such as the consumption of processed food, drug use, life in hyper-sanitized environments—lead to a critical reduction of biodiversity in the gut microbiota. This depletion is mainly due to the loss of a set of microorganisms.

“The process of depletion of the gut microbiota in modern western urban populations could represent a significant wake-up call,” noted lead study investigator Simone Rampelli, PhD, a researcher at the University of Bologna. “This depletion process would become particularly alarming if it involved the loss of those microbiota components that are crucial to our physiology.”

Indeed, there are some alarming signs. For example, in the West, we are witnessing a dramatic increase in cases of chronic inflammatory diseases, such as inflammatory bowel disease, metabolic syndrome, type 2 diabetes, and colorectal cancer.

How can we identify the components of the gut microbiota that are more important for our health? And how can we protect them with targeted solutions? This was the starting point behind the idea of identifying the ancestral traits of our microbiota—i.e., the core of the human gut microbiota, which has remained consistent throughout our evolutionary history. Technology nowadays allows us to successfully rise to this challenge thanks to a new scientific field, paleomicrobiology, which studies ancient microorganisms from archaeological remains through DNA sequencing.

The research group analyzed ancient DNA samples collected in El Salt (Spain), a site where many Neanderthals lived. To be more precise, they analyzed the ancient DNA extracted from 50,000-year-old sedimentary feces (the oldest sample of fecal material available to date). In this way, they managed to piece together the composition of the microorganisms populating the intestine of Neanderthals. By comparing the composition of the Neanderthals’ microbiota to ours, many similarities arose.

“To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya,” the authors write. “According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium, and Bifidobacterium already populated the intestinal microbiome of Homo sapiens since as far back as the last common ancestor between humans and Neanderthals.”

“Through the analysis of ancient DNA, we were able to isolate a core of microorganisms shared with modern Homo sapiens,” added co-lead study investigator Silvia Turroni, PhD, a researcher at the University of Bologna. “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.”

Interestingly, these ancestral components of the human gut microbiota include many well-known bacteria that are fundamental to our health. Indeed, by producing short-chain fatty acids from dietary fiber, these bacteria regulate our metabolic and immune balance. There is also the Bifidobacterium: a microorganism playing a key role in regulating our immune defenses, especially in early childhood.

Researchers identified some of those “old friends” in the Neanderthal gut microbiota. This confirms the researchers’ hypotheses about the ancestral nature of these components and their recent depletion in the human gut microbiota due to our modern life context.

“In the current modernization scenario, in which there is a progressive reduction of microbiota diversity, this information could guide integrated diet- and lifestyle-tailored strategies to safeguard the microorganisms that are fundamental to our health,” concluded Candela. “To this end, promoting lifestyles that are sustainable for our gut microbiota is of the utmost importance, as it will help maintain the configurations that are compatible with our biology.”