Guano exposed: Impact of aerobic conditions on bat fecal microbiota

Abstract

Bats and their associated guano microbiota provide important terrestrial and subterranean ecosystem services and serve as a reservoir for a wide range of epizootic and zoonotic diseases. Unfortunately, large‐scale studies of bats and their guano microbiotas are limited by the time and cost of sample collection, which requires specially trained individuals to work at night to capture bats when they are most active. Indirectly surveying bat gut microbiota through guano deposits could be a more cost‐effective alternative, but it must first be established whether the postdefecation exposure to an aerobic environment has a large impact on the guano microbial community. A number of recent studies on mammalian feces have shown that the impact of aerobic exposure is highly species specific; therefore, it is difficult to predict how exposure will affect the bat guano microbiota without empirical data. In our study, we collected fresh guano samples from 24 individuals of 10 bat species that are common throughout the arid environments of the American southwest and subjected the samples to 0, 1, and 12 hr of exposure. The biodiversity decreased rapidly after the shift from an anaerobic to an aerobic environment—much faster than previously reported in mammalian species. However, the relative composition of the core guano microbiota remained stable and, using highly sensitive targeted PCR methods, we found that pathogens present in the original, non‐exposed samples could still be recovered after 12 hr of exposure. These results suggest that with careful sample analysis protocols, a more efficient passive collection strategy is feasible; for example, guano could be collected on tarps placed near the roost entrance. Such passive collection methods would greatly reduce the cost of sample collection by allowing more sites or roosts to be surveyed with a fraction of trained personnel, time, and effort investments needed.

Special Features of Bat Microbiota Differ From Those of Terrestrial Mammals

“…All animals included this study displayed no apparent clinical signs of illness based on their normal behavior as well as smooth fur appearance. The sampling process, in brief, was performed by spreading an aseptic plastic cloth under bat colonies and waiting until sufficient fecal samples to be collected (normally 1-2 h) (Fofanov and Furstenau, 2018). Samples were frozen in liquid nitrogen immediately after collection.…”

A fecal sequel: Testing the limits of a genetic assay for bat species identification

“…Successful sequencing has been found to be higher for fresher feces [9, 10], and for samples collected in conditions such as cold temperatures [11, 12], dry climates with protection from precipitation [13], and low UV exposure [14]. Further, DNA response to these variables has been found to be taxon-specific (e.g., accurate genotyping after 2 months in feral horses [15], errors after 7 days in coyotes [16]) and target-specific (from bat guano: change in bacterial community composition after 1 hour [17], identification of bat species at 3 months [3]). DNA concentration can also vary by collection/preservation method [15, 18] and by the order the feces traveled through the intestines [19].…”

Studying the microbiota of bats: Accuracy of direct and indirect samplings

“…A possible explanation is the potential degradation of material collected inside the cave, especially for feces droppings, as we cannot exactly tell the time since defection for these samples (even if we tried to minimize it by collecting the freshest droppings). A recent study showed indeed that a rapid reduction in fecal microbiota diversity can be expected after 1 hr post‐defecation, especially for anaerobic bacteria (Fofanov et al, ). For our indirect urine samples, material degradation should be limited as these samples were collected rapidly (within 20 min).…”