A multi-disciplinary international research team, comprising University of Cape Town’s biological anthropologist associate professor Victoria Gibbon has made a major scientific breakthrough.
The team discovered “unexpected clues about human evolution and health after reconstructing the oral microbiomes of Neanderthals, primates, and humans, including the oldest oral microbiome ever sequenced from a 100 000-year-old Neanderthal”.
Theteam is led by scientists from the Max Planck Institute for the Science of Human History. The study which has been published in the Proceedings of the National Academy of Sciences is titled: “The evolution and changing ecology of the African hominid oral microbiome.”
Gibbon said the study investigates the evolutionary history of the hominid oral microbiome by analyzing the fossilised dental plaque of humans and Neanderthals spanning the past 100 000 years and comparing it to those of wild chimpanzees, gorillas, and howler monkeys.
“In recent years, the human microbiome has become a popular topic, using bacterial DNA obtained from tooth plaque from South African people who lived thousands of years ago has contributed to the better understanding of human history, human evolution and our early diets,” said Gibbon.
This global collaboration, she said, has allowed for sequencing of plaque from individuals dating back to 100 000 years in hominin history. The study has shown that the shift to diet based predominately on starch occurred much earlier than previously thought and long before the advent of agriculture within humans, Gibbons observed.
She added: “This study is the first of many of its kind to follow. The ability to analyse the diets of ancient peoples at this level has the potential to answer many questions around past peoples and their lifeways across Africa and within South Africa. The research outcomes from the study are exciting but they are just the beginning.”
Researchers from 41 institutions in 13 countries were involved making it one of the largest and most ambitious study of the ancient oral microbiome to date. According to the study their analysis of dental calculus from more than 120 individuals representing key points in primate and human evolution has revealed surprising findings about early human behavior and provided novel insights into the evolution of the hominid microbiome.
Although there were oral microbiome differences, researchers identified ten core bacterial types maintained within the human lineage for over 40 million years. They also discovered similarities between Neanderthals and humans. This includes an apparent Homo-specific acquisition of starch digestion capability in oral streptococci, suggesting that the bacteria adapted to a dietary change that occurred in a common ancestor.
Working with DNA dating hundreds of thousands of years back presented some challenges as the researchers, like archaeologists, had to “painstakingly piece together the broken fragments of ancient genomes in order to reconstruct a complete picture of the past”.
In addition, researchers had to develop new tools and computational approaches to genetically analyse billions of DNA fragments and identify the long-dead bacterial communities preserved in archaeological dental calculus. With these new tools, researchers reconstructed the 100 000-year-old oral microbiome of a Neanderthal from Pešturina Cave in Serbia.
According to the study, one of the biggest surprises was the discovery that a subgroup of Streptococcus bacteria present in both modern humans and Neanderthals appears to have specially adapted to consume starch early in Homo evolution. Starchy foods, such as roots, tubers, and seeds, are rich sources of energy, and previous studies have argued that a transition to eating starchy foods may have helped our ancestors to grow the large brains that characterise our species.
Although humans share many oral bacteria with other primates, there are also a few small differences, mostly at the level of bacterial strains. A closer look at the differences by the researchers revealed that ancient humans living in Ice Age Europe shared some bacterial strains with Neanderthals. Because the oral microbiome is typically acquired in early childhood from caregivers, this sharing may reflect earlier human-Neanderthal pairings and child rearing, observed the study.
It was further observed that within the fossilised dental plaque, researchers identified ten groups of bacteria that have been members of the primate oral microbiome for over 40 million years. Many of these bacteria are known to have important beneficial functions in the mouth and may help promote healthy gums and teeth. A surprising number of these bacteria, however, are so understudied that they even lack species names.
Said Floyd Dewhirst, senior member of staff at the Forsyth Institute and a co-author on the study: “That many of the most important taxa are poorly characterised is a surprise to oral microbiologists who have been working on these bugs for years.”