"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.