Crap Tool ID's Species from Feces

Like a grocery scanner reading a barcode, the 'stool tool' reads DNA signatures from poop.

A new tool based on waste allows researchers to identify a species solely via the animal's poop.

The stool tool, described in the journal PLOS ONE, has so far been tested on bats, which leave behind large amounts of fecal material known as guano.

While many animals are easy to identify using just visual information, bats' nocturnal nature, ability to fly, frequent small size and other factors make them challenging to study in the wild. So they were excellent candidates for the Species From Feces tool.

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Lead author Faith Walker, who is director of the Bat Ecology & Genetics Lab at Northern Arizona University, explained how it works.

"Basically about 200 guano pellets are collected from across a bat roost and pooled into a single tube of DNA preservative," Walker told Discovery News. "DNA is then extracted, and after many steps it's placed into a next-generation sequencer, and a short (200 base pairs) DNA region that's really good at species-level identification is sequenced."

At that stage, the researchers have tens of thousands of bat "reads" or sequence data.

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"We (then) feed all these data into an analysis pipeline that basically compares our reads to a reference library that we built that contains all available bat sequences," she added. "In this way we can determine all the bat species that contributed to the sample."

In short, the stool tool works even if the clump of gathered poop was originally produced by multiple individuals.

The technology relies upon the DNA mini-barcode system that targets a small segment of mitochondrial DNA. This is DNA inherited only down the female line.

The particular genetic segment that the researchers chose to focus on, called COI, turns out to be very unique in each bat species. It also always traces back to the bats themselves, and not to their prey. That's important because feces is full of material that the individual ate.

The new reference library includes the conservation status for each bat as well as the regions/countries where it can be found.

The stool tool's applications highlight three primary goals.

The first is to identify bats located in a mine, cave, bridge, bat box or other location. Bats tend to hang out in dark places with low visibility for humans, so the tool allows researchers to study the flying mammals even when they cannot directly look at them.

The second application is to confirm the identification of captured bats that are difficult to distinguish from others. The DNA barcode device can read cheek swab samples as well as feces.

Finally, the stool tool is meant to identify IUCN Red List bat species. These are bats that are listed as threatened, endangered or otherwise at risk due to low population numbers. Many bats fall into those classifications, especially in the U.S., where the disease white nose syndrome has devastated various species.

The disease is caused by the fungus Pseudogymnoascus destructans, which colonizes the bat's skin. It has proven challenging to prevent and treat. Some species have died out at a rate greater than 90 percent within five years of white nose syndrome reaching their site.

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So far, the device can identify about a third of the world's bats, representing the majority of the bat species that have been "barcoded," or have had their unique COI signature determined. It works on both fresh and "aged" poop.

Walker and her team are now developing a portable version of the tool called Species From Feces Mobile. She said it allows scientists to "go to remote places in the world to genetically search caves and other roosts for critically endangered bats via guano, and sequence right there in the field with palm-sized sequencers."

Such a tool could also be developed for animals other than bats, but it would require an extensive matching database.