Bat Roostmates Share More Than Just Space: Exploring the Invisible World of the Gut Microbiome

As the sun sets over Ontario on a warm summer evening, hundreds of bats leave their roosts to forage on the buffet of insects swarming the night sky. You might not know it, but living inside these voracious insect-eaters is a complex, dynamic ecosystem – a microbial world constantly at work, but invisible to the naked eye.

But what shapes this invisible world – the gut microbiome – and how?

That’s what four researchers from the Department of Integrative Biology recently set out to identify and describe in big brown bats and little brown bats. The study was led by Dr. Eleonore Lebeuf-Taylor, a recent PhD graduate working with Dr. Karl Cottenie, along with collaborators Alexandria Cosby, PhD candidate, and Dr. Quinn Webber.

“The gut microbiome is composed of the microbes living inside the gastrointestinal tract of animals, mostly bacteria,” explains Lebeuf-Taylor. “Their environment is inside that host, so whatever is going on in the host’s body, or whatever traits the host might have, will affect what kind of microbes live in there.”

The team studied bat fecal samples collected from six different bat maternity colonies in southern Ontario. Maternity colonies form in spring and early summer, and are made up almost entirely of adult female bats and their pups. The colonies ranged in size from a few dozen bats to around 150, and were roosting in bat boxes, barns, and garages.

DNA was extracted from the fecal samples to find out which microbes lived in the bats’ guts, and how many types were present.

Despite having similar names, big brown bats and little brown bats are not closely related. The researchers found that the two species each hosted distinct gut microbiomes, even when living in similar environments and eating similar diets. Lebeuf-Taylor notes that the little brown bat samples came from a single roost, so the difference may be due at least in part to the roost and not the species; more sampling is necessary to confirm.

The data also show that the bat gut microbiome changes over the course of the summer, but it isn’t clear if this is a result of changes in the types of microbes in the environment, or physiological changes in the female bats as they give birth and rear their pups.

“On one hand, if the big brown bat gut microbiome is mostly formed by whatever microbes are in the environment, it suggests there is not a tight association between host and microbiome,” says Lebeuf-Taylor. “On the other hand, if their physiology is changing over the summer and this is driving changes in the microbiomes, that suggests a much tighter association.”

The strength of the association between host and microbiome remains one of the big questions in microbiome research.

The team also found that the microbiome was more similar for bats within roosts than between roosts. “Finding a similarity in an internal microbiome when there doesn’t seem to be an exchange of internal fluids was a surprise,” says Lebeuf-Taylor. “We think that there is some sort of microbe exchange happening within each maternity colony.”

This exchange could happen when the bats defecate in the roost, and some of that fecal matter may splatter on the walls or on other bats. The bats may take up those bacteria again through grooming.

“We don’t know which microbes are being transmitted in which environments – inside or outside of the roost – but it’s more likely that ones that are adapted to the gut would be transmitted within the roost,” explains Lebeuf-Taylor.

“We have a general sense that the microbiome is really important for host health, but we don’t know how important or how tight that association is across species,” explains Lebeuf-Taylor. “We need to gather data from many different species in wild settings, not only in a lab, but actually out in nature.”

Real-world context is critical to understanding the gut microbiome, because it can be affected by so many things. 

“We can think of the microbes living in and on different hosts as analogous to animals living on different islands,” explains Lebeuf-Taylor. “Islands that are closer to each other will be more similar. Bigger islands might have more diversity. But unlike islands, hosts move around, they’re changing, they might interact. We have islands, but they’re on the move.”

This work sets the stage for exploring how the invisible microbial world of bats is shaped by individual social interactions, and how gut microbiome influences colony health—insights that could also shine a spotlight on microbial diversity and health far beyond the context of bats.

This research was funded by Vanier Canada Graduate Scholarships awarded to E. Lebeuf-Taylor and A. Cosby, and Natural Sciences and Engineering Research Council (NSERC) Discovery Grants awarded to Q. Webber and K. Cottenie.

Read the full study in the journal PLoS One.

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