Million-year-old microbes found in mammoths reveal new purpose for DNA

For decades, scientists thought the noncoding parts of DNA were useless leftovers. Today, that view has completely changed.

A pair of groundbreaking studies published in Cell show how much these hidden instructions matter—not only for living organisms today but also for creatures that vanished long ago. Together, they reveal a world where DNA is not just about making proteins but also about orchestrating when, where, and how life unfolds.

A large research team has mapped out the DNA switches that decide how genes are turned on and off in both human and mouse cells. These switches, known as enhancers, silencers, and insulators, were found to form an intricate network around every gene. The maps showed that a single gene could be surrounded by more than a dozen of these regulatory elements, each adding to the final outcome.

This redundancy may sound wasteful, but it actually provides security. If one switch is broken, others keep the system running. Experiments proved this point: when researchers deleted certain enhancers, the gene didn’t completely shut down, it only lost some strength. That safety net may explain why living cells are so good at resisting errors.

To test these ideas, scientists used CRISPR-based editing tools. They cut out or altered specific enhancers and measured the results. Sometimes, deleting one caused a sharp drop in activity. Other times, the effect was barely noticeable. What mattered most was where the enhancer was located and how tightly it bound transcription factors—the proteins that read DNA.

The research revealed surprising teamwork among enhancers. Some worked in groups, creating stronger effects than they could alone. Others stayed quiet until a partner was removed, stepping in as a backup. This cooperative web helps explain why organisms can adapt to challenges, from environmental changes to harmful mutations.

The team then built machine learning models to see if they could predict gene expression from these regulatory codes alone. By training the models on DNA sequence patterns, binding sites, and how DNA folds in the cell, they were able to forecast how strongly many genes would be expressed across different tissues.

The results weren’t perfect, but they were a leap forward. The long-term goal is clear: one day doctors might scan someone’s genome and predict not only disease risk but also how their cells will react to treatment.

The medical impact of this work could be enormous. Many diseases come not from broken protein-coding genes but from mutations in the regulatory DNA that controls them. Even a tiny change in one enhancer can raise the chance of diabetes, cancer, or developmental disorders. Understanding these elements may allow doctors to diagnose conditions earlier and design therapies aimed at the true cause.

It may also explain why the same drug helps one patient but fails in another. Even when protein-coding genes are nearly identical, regulatory DNA can vary greatly between individuals. That difference may hold the key to more precise and personalized medicine.

The research also sheds light on how species evolved. Humans and chimpanzees share almost all their protein-coding genes, yet we are clearly different. Regulatory DNA is thought to be the main reason. The scientists compared data from humans and mice and discovered that some enhancers have been conserved for millions of years, while others are unique to each species. These changes likely helped shape the traits that distinguish one species from another.

While one group of scientists was exploring living genomes, another was pushing back the clock over a million years. At the Centre for Palaeogenetics in Stockholm, researchers recovered microbial DNA from woolly and steppe mammoths. They analyzed 483 specimens, including a 1.1-million-year-old tooth, and found preserved traces of ancient bacteria.

“We were stunned to see that a mammoth’s remains could still hold fragments of its microbiome after so long,” said Benjamin Guinet, a postdoctoral fellow and lead author. The team identified six groups of bacteria that seemed to live closely with the animals, including relatives of Pasteurella and Streptococcus. Some may have caused disease. One bacterium resembled a modern pathogen responsible for deadly outbreaks in African elephants, suggesting mammoths may have faced similar risks.

In an especially remarkable find, the researchers reconstructed partial genomes of Erysipelothrix bacteria from that 1.1-million-year-old mammoth. That is the oldest known host-associated microbial DNA ever recovered. “Because microbes evolve quickly, following their trail over a million years was like chasing a moving target,” explained Tom van der Valk, a senior author of the study. Their success shows that fossils hold far more than just host DNA—they can preserve entire ecosystems of microscopic life.

The microbes persisted across different times and locations, suggesting long-term partnerships between mammoths and their microbial communities. Some may have supported digestion, while others could have contributed to disease and even extinction.

The work opens a new frontier. Scientists can now study not only the genomes of extinct animals but also the bacteria that lived with them. This gives a richer picture of their biology and environment. “It’s like uncovering an ancient diary,” said Love Dalén, Professor of Evolutionary Genomics at the Centre for Palaeogenetics. “You can see not just the mammoth’s story, but the lives of the tiny organisms that shared it.”

These studies carry enormous promise for the future. Mapping regulatory DNA in living species could change how medicine is practiced. By understanding the switches that control genes, doctors may be able to design more personalized treatments, detect disease earlier, and even prevent illness before it begins. The same knowledge could also help farmers breed crops and livestock with greater precision and fewer side effects.

The mammoth findings add a new dimension. By showing that microbial DNA can survive more than a million years, researchers can now reconstruct ancient ecosystems and learn how microbes influenced the survival—or extinction—of species. This could improve our understanding of modern pathogens, help protect endangered species, and guide conservation biology.

Together, the two projects remind us that DNA is more than just a string of letters. It is a layered code, shaped by both regulation and relationships with other life. Learning to read it could unlock healthier futures for people and deeper insights into the history of life on Earth.

Note: The article above provided above by The Brighter Side of News.

Like these kind of feel good stories? Get The Brighter Side of News' newsletter.