No one likes a rodent’s nest, and for good reason. Beyond sheltering mice, rats and other creatures we aren’t fond of, they kindle car fires, harbor bloodsucking bugs and infest the walls, ceilings and attics of homeowners.

But for paleoecologists studying the prehistoric natural world, ancient, urine-soaked rat nests can be a treasure trove, not unlike owl pellets dissections that you might have done during a school trip to a natural history museum. Since the 1960s, scientists have examined thousands of fossil rat nests, or middens, to learn about regional changes in climate and ecosystems over time.

Today, with advanced molecular technology, scientists can even tease apart the owners of millenniums-old DNA preserved in those middens. Until now, they’ve targeted small genetic fragments from specific organisms such as plants or viruses. But in a study published Tuesday in Ecology and Evolution, paleoecologists show that an expansive approach can be used to sequence all kinds of DNA found in a single midden — the scientific equivalent of moving from spear fishing to casting a broad net.

“It’s just wild that it works,” said Michael Tessler, an evolutionary biologist at the American Museum of Natural History and one of the study’s authors. “There’s a very rich picture that takes a lot of work to paint — but is now paintable.”

For a variety of reasons, rat middens make excellent stockpiles of ancient DNA. Nest building materials, such as bones, twigs, insects and plant fragments, are biologically diverse but come from within a 100-meter radius of the pack rat that built them. Those rodents also constructed their middens in dry caves or rock shelters, where both the animals and, later, DNA are protected from moisture and wind. And because rodents breed, sleep, eat and urinate in their nests, their urine eventually crystallizes into a shellac, cementing the midden into an impenetrable, well-preserved mass.

“It ends up very rocklike,” said Robert Harbert, a co-author of the journal article and a biologist at Stonehill College in Massachusetts, “and whatever’s inside of them is embedded in this crystalline matrix of 20,000-year-old rat urine.”

For the latest study, they extracted DNA from 25 middens, the oldest of which dates back 48,000 years. Then they tried to identify as many genetic scraps as possible.

More than half of the midden DNA they identified was bacterial and there was some evidence of ancient viruses. And documenting such a variety of invisible microorganisms from a single sample is an important advance, Dr. Harbert said.

Previously, paleoecologists either visually examined fossils or ran molecular tests seeking specific genes. In 2018, for example, researchers homed in on plant pathogen DNA in fossil middens from Chile’s Atacama Desert, and another team found the oldest known papillomavirus in a 27,000-year-old midden in the Grand Canyon.

“They went in looking for those genes,” Dr. Harbert said. “We cast that very wide net, and we’re seeing evidence of organisms we would’ve never been able to identify before.”

They also tracked plant life in Idaho’s City of Rocks National Reserve over time. DNA from grass and sunflower families dominated the oldest middens, suggesting a treeless shrub land landscape tens of thousands of years ago. But in samples from 1,000 to 5,000 years ago, the scenery changed to woodlands, with DNA profiles shifting to include pines, junipers and mountain mahoganies.

“We see massive migrations of plants across thousands of kilometers,” as glaciers retreated, Dr. Harbert said. “This is probably the best system that we have for observing how populations of organisms responded to massive global climate change.”

Ancient DNA research efforts still face hurdles. Incomplete reference databases often complicate identification, as can the breakdown of DNA over time and the risk of contamination from modern DNA. And while these studies offer a window into the past, it is safe to assume some of the landscape remains out of view.

But the new study demonstrates that there is much more to learn from ancient rodent nests.

“Pack rats are definitely a pest, and you wouldn’t consider they have value when they’re filling your grill,” Dr. Tessler said. “But these little rodents can have such extraordinary impacts on our view of the world once we let in the information that they have to lend to us.”