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

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.

Sex differences and individual variability in the captive Jamaican fruit bat (Artibeus jamaicensis) intestinal microbiome and metabolome

“…Despite these cohort-level differences, several dominant bacterial families in both cohorts, including Enterobacteriaceae, Moraxellaceae, and Streptococcaceae, comprise the microbiota of wild rousette and pteropid bats [51][52][53][54] , potentially signaling a pattern of dominance of a few families across multiple bat species. Several of these families, including Enterobacteriaceae and Moraxellaceae, belong to the Pseudomonadota phylum (renamed from Proteobacteria in 2021), the abundance of which may indicate microbial dysbiosis in humans 20,55 .…”

An overview of bats microbiota and its implication in transmissible diseases

“…Considering the difficulty to obtain samples directly from wild individuals, a comparison between directly and indirectly collected samples was made to determine whether indirect sampling would produce results similar to direct sampling ( Dietrich and Markotter, 2019 ). The results obtained showed that even if the sampling approach influenced the microbiota composition – i.e.…”

“…The results obtained showed that even if the sampling approach influenced the microbiota composition – i.e. cross-contamination in both methods or temporal sampling – niche specialization among excreta was well assessed by both methods ( Dietrich and Markotter, 2019 ). Furthermore, significant differences in alpha-diversity microbial composition between small and large intestine and feces samples was observed in two insectivorous species supporting that fecal samples cannot be used as microbial inventories in other gut regions ( Wu et al, 2019 ).…”

The microbiome of bat guano: for what is this knowledge important?

“…Bats ( Chiroptera ) are a diverse group of mammals with more than 1400 different species with abilities to inhabit various ecological niches and environments (Winter et al 2016 ; Gorbunova et al 2020 ). Although bats are geographically widespread, the ecology of their microbial communities and the role involved in bat health and behavior are scarce, especially on the microbiota residing in bat’s excreta accumulated in the form of guano, which could be potentially involved in pathogen transmission to humans (Dietrich et al 2018 ; Dietrich and Markotter 2019 ). Bats revealed versatile feeding behavior; they have a flying capacity and inherent characteristics which makes them as highly potent vectors and natural reservoir hosts for many pathogens.…”