Why is it so hard to find DNA in bird poop

For years, scientists talked about the problem. They swapped stories of failed projects, came up with explanations and hinted at it in published studies. Only this May did a team of microbiome researchers finally publish a paper asking the question directly:

Why is it so hard to find DNA in bird poop?

"There's all kinds of things you can do with feces, and mammalian feces work really well for these applications," said Kevin Kohl, associate professor in the Kenneth P. Dietrich School of Arts and Sciences' Department of Biology and lead author of the study. "But bird feces seem to have this mysterious problem."

And it is a problem. Scooping some poop and searching for DNA is perhaps the best way to glimpse the community of bacteria, fungi and other microorganisms that live within an animal's gut without disturbing it. That same fecal DNA can help identify what the animal has been eating, too.

As researchers discover new ways gut microbes influence their hosts - like how they can affect their host's diet and help animals adapt to climate change, both discoveries made in Kohl's lab - such forms of investigation are gaining more importance.

"Poop is amazing," Kohl said. "Feces are this instant readout of the gut microbiome, and more and more, we're realizing that these microbial communities play really large roles for the health and physiology of animals."

Standard procedure for microbiome researchers is to freeze a feces sample, shake it together with granite beads and chemicals that break up cells, and extract and sequence the DNA. Do that with, say, human stool, and the community of microbes you'll identify will be a fairly accurate representation of what's present in that person's gut.

But time and time again, when researchers take the same steps with bird droppings, they come up with sparse, inconsistent results - if they get any results at all. It got to the point where Kohl convened a series of discussions on the issue in 2019 and a symposium in 2021. While many of the experts gathered agreed it was a problem, one that had caused many of them to abandon projects or find alternative methods, they didn't come up with a clear plan of action. Years later, with the publication of their paper in the journal Animal Microbiome, the problem remains.

"We're still asking the same question that we were then," said Kohl. "No one has really made any headway on improving things or even on what the cause has been."

Not that there's a lack of explanations. The most commonly cited one is that an acid present in bird droppings gets in the way of the technique used to sequence DNA (though Kohl's literature search showed that the idea is untested). It could also be that enzymes in birds' guts chop up the DNA before scientists can test it, or even that birds don't have strong links to their gut microbes at all: They may move too much and food may not spend enough time in their short, flight-optimized intestines for microbes to get a foothold.

In other words, scientists don't even know enough to determine whether a failure to find DNA points to a problem with their methods or a deeper biological reality about birds and how they coexist with microbes.

There are a few reasons problems like these might persist for years, Kohl said. The projects abandoned because of poor DNA yields will never get published and shared, so they might as well be invisible to someone reading the scientific literature. And even for scientists experiencing the problem themselves, there often aren't strong incentives to investigate deeper. The effort involved in making improvements to research methods doesn't exactly rake in the big funding and publications.

"No one wants to devote all of their time to just refining methods, checking and troubleshooting," Kohl said. "We want to ask the bigger questions."

By hosting conversations and publishing papers that bring those conversations into the scientific record - making the intangibles tangible, as he puts it - Kohl hopes to push the methods forward while also pursuing his broader, more comparative research. And maybe with time, he and his colleagues will get a peek inside the black box of bird poop, too.

"I am also trying to prompt my own field, that this is something we do have to care about," he said. "This could have big implications for our understanding."

Artwork courtesy of Elizabeth Rudzki