Genomic tools reveal health insights for endangered Indiana bats

How do wildlife researchers know when an endangered population is sick? They can detect infectious microbes in animal waste, but the presence of a microbe doesn’t always equate to impactful symptomatic infections. In a new study, University of Illinois Urbana-Champaign researchers have used advanced molecular tools to survey the health status of endangered Indiana bats, identifying microbiome changes resulting from parasitic infections.

The findings are published in the journal Microbial Genomics.

“In conservation medicine, sick patients will rarely schedule a follow-up visit, so tracking the impact of a disease in real time is a challenge. We take a big picture view of microbial interactions at the population level to infer the burden of a disease over time from a snapshot,” said lead study author Andrew Bennett, a postdoctoral researcher in the Department of Natural Resources and Environmental Sciences, part of the College of Agricultural, Consumer and Environmental Sciences at Illinois.

Bennett and his colleagues temporarily captured Indiana bats at the entrance of a Missouri hibernation site, gently holding them long enough to collect a single fecal sample. They brought these samples back to a lab where they extracted DNA and identified the presence of gut microbes and parasites using a process called multiplex metabarcoding. They also documented changes in the makeup of the gut microbiome that corresponded with the amount of parasites present.

What they found was Eimeria, a protozoan parasite that hangs out in the gut and causes coccidiosis, a disease that leads to economic losses in many livestock animals. Bennett says Eimeria can be present at low levels in the gut without causing problems, but research in other animals has shown that stress can cause Eimeria to proliferate, invading and damaging gut tissue and leading to secondary bacterial infections.

“This is where our work adds value. Before, if we just detected Eimeria, we wouldn’t necessarily be able to say whether it was causing problems,” Bennett said. “But by analyzing changes in the microbiome that are associated with Eimeria load in these bats, we gain a non-invasive marker that can help us assess their gut health.”

The analysis revealed that bats with high loads of Eimeria had a corresponding proliferation of Clostridium bacteria, particularly those associated with severe tissue damage in other species.

Study co-author Joy O’Keefe, associate professor in NRES and wildlife Extension specialist, says they can still only guess at symptoms infected bats might be experiencing and whether Eimeria infection significantly affects survival or population size.

“We don’t know exactly what the stressors are that would drive bats to experience more ill effects from Eimeria, but this is the first step to allowing us to start making those investigations,” she said. “This also gives us a baseline that we can relate to other things, like management practices, the number of bats in a roost, and behaviors that bats are exhibiting.”

Study co-author Cory Suski, professor in NRES, points out that molecular tools add a level of sophistication to ecological research, as well as a great deal of insightful information.

“So much of conservation is just counting individuals. If there are a lot, we think they must be doing well,” he said. “So this is a way to ask some deeper questions and get information that goes beyond just counting without having to do crazy stuff or take animals into captivity.”

O’Keefe hopes the research community will use the same approach on other endangered bat species in North America to paint a comparative picture of their health.