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For the first time, scientists have analyzed metabolism-related molecules from the fossilized bones of animals that lived 1.3 to 3 million years ago, revealing insights about both the animals and their environments.
The metabolic clues about the animals’ health and diets enabled researchers to paint a picture of their living conditions, including the temperature, soil, rainfall, and vegetation.
Their findings, published in Nature, reveal warmer and wetter conditions across these environments compared to today.
Studying metabolites—the molecules produced and used in digestion and other chemical processes in the body—can provide information about health and disease, as well as external factors like diet and environmental exposures.
While metabolomic research is increasingly used in studying human diseases and drugs, few scientists have explored its use in understanding the prehistoric world. Instead, they largely focus on DNA in fossils, which is primarily used for establishing genetic relationships.
“I’ve always had an interest in metabolism, including the metabolic rate of bone, and wanted to know if it would be possible to apply metabolomics to fossils to study early life. It turns out that bone, including fossilized bone, is filled with metabolites,” said Timothy Bromage, professor of molecular pathobiology at NYU College of Dentistry and affiliated professor in NYU’s Department of Anthropology, who led this study with an international team of researchers.
Measuring metabolites
In recent years, paleontologists learned that collagen—the protein that provides structure to bones, skin, and connective tissues—can be preserved in ancient bones, including those of dinosaurs.
“I thought, if collagen is preserved in a fossil bone, then maybe other biomolecules are protected in the bone microenvironment as well,” said Bromage, who directs the Hard Tissue Research Unit at NYU College of Dentistry.
The surfaces of bones are spongy and surrounded by capillary networks, exchanging oxygen and nutrients between the bloodstream and bones. Bromage suspected that, during the process of bone formation, metabolites carried in the bloodstream enter and become trapped in tiny niches in bone.
To test this idea, the researchers employed mass spectrometry, an analytical technique that converts molecules into ions, to see if they could extract metabolites from bone. Using present-day mouse bones, they identified nearly 2,200 metabolites for analysis. The technology also analyzed proteins to detect collagen in some bone samples.
The researchers then turned to animal fossils from 1.3 million to 3 million years ago, collected for prior paleontological research at sites in Tanzania, Malawi, and South Africa where early humans lived.
Focusing on species with living counterparts near these sites today, they used the same analytical methods on fossilized bone fragments from rodents (mouse, ground squirrel, gerbil), as well as an antelope, pig, and elephant.
The analyses yielded thousands of metabolites, many of which were shared with modern-day animals.
The stories fossils tell
Many of the metabolites the researchers found in the fossilized bones represent normal biological functions, including the metabolism of amino acids, carbohydrates, and vitamins and minerals. Several pointed to genes associated with estrogen, suggesting that some of the animals were female.
Other metabolites revealed the animals’ response to disease. Notably, in the bone of a 1.8-million-year-old ground squirrel from the Olduvai Gorge in Tanzania, the researchers found evidence that the squirrel was infected with a parasitic disease known as sleeping sickness in humans, caused by the Trypanosoma brucei parasite and transmitted by the tsetse fly.
“What we discovered in the bone of the squirrel is a metabolite that is unique to the biology of that parasite, which releases the metabolite into the bloodstream of its host. We also saw the squirrel’s metabolomic anti-inflammatory response, presumably due to the parasite,” said Bromage.
The researchers could also deduce what plants the animals ate. While data on plant metabolites are much more limited than those documented in human and animal health, they identified the metabolites of several regionally specific plants, including forms of aloe and asparagus.
“What that means is that, in the case of the squirrel, it nibbled on aloe and took those metabolites into its own bloodstream,” explained Bromage.
“Because the environmental conditions of aloe are very specific, we now know more about the temperature, rainfall, soil conditions, and tree canopy, essentially reconstructing the squirrel’s environment. We can build a story around each of the animals.”
The reconstructed environments corroborate what other research has found about these settings millions of years ago—for instance, that the Olduvai Gorge Bed in Tanzania was freshwater woodland and grassland, while the Olduvai Gorge Upper Bed was dry woodland and marsh. Across all of the sites studied, the conditions in which the animals lived were wetter and warmer than the regions are today.
“Using metabolic analyses to study fossils may enable us to reconstruct the environment of the prehistoric world with a new level of detail, as though we were field ecologists in a natural environment today,” said Bromage.
Reference:
Timothy Bromage, Palaeometabolomes yield biologic and ecologic profiles at early human sites, Nature (2025). DOI: 10.1038/s41586-025-09843-w.
Note: The above post is reprinted from materials provided by New York University.
