Abstract:
Given the recurrent bat‐associated disease outbreaks in humans and recent advances
in metagenomics sequencing, the microbiota of bats is increasingly being studied.
However, obtaining biological samples directly from wild individuals may represent a
challenge, and thus, indirect passive sampling (without capturing bats) is sometimes
used as an alternative. Currently, it is not known whether the bacterial community
assessed using this approach provides an accurate representation of the bat microbiota.
This study was designed to compare the use of direct sampling (based on bat
capture and handling) and indirect sampling (collection of bat's excretions under bat
colonies) in assessing bacterial communities in bats. Using high‐throughput 16S rRNA
sequencing of urine and feces samples from Rousettus aegyptiacus, a cave‐dwelling
fruit bat species, we found evidence of niche specialization among different excreta
samples, independent of the sampling approach. However, sampling approach influenced
both the alpha‐ and beta‐diversity of urinary and fecal microbiotas. In particular,
increased alpha‐diversity and more overlapping composition between urine and
feces samples was seen when direct sampling was used, suggesting that cross‐contamination
may occur when collecting samples directly from bats in hand. In contrast,
results from indirect sampling in the cave may be biased by environmental contamination.
Our methodological comparison suggested some influence of the sampling
approach on the bat‐associated microbiota, but both approaches were able to capture
differences among excreta samples. Assessment of these techniques opens an
avenue to use more indirect sampling, in order to explore microbial community dynamics
in bats.
