Cargando…

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

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 (wi...

Descripción completa

Detalles Bibliográficos
Autores principales: Dietrich, Muriel, Markotter, Wanda
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392341/
https://www.ncbi.nlm.nih.gov/pubmed/30847068
http://dx.doi.org/10.1002/ece3.4842
_version_ 1783398460726181888
author Dietrich, Muriel
Markotter, Wanda
author_facet Dietrich, Muriel
Markotter, Wanda
author_sort Dietrich, Muriel
collection PubMed
description 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.
format Online
Article
Text
id pubmed-6392341
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher John Wiley and Sons Inc.
record_format MEDLINE/PubMed
spelling pubmed-63923412019-03-07 Studying the microbiota of bats: Accuracy of direct and indirect samplings Dietrich, Muriel Markotter, Wanda Ecol Evol Original Research 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. John Wiley and Sons Inc. 2019-01-24 /pmc/articles/PMC6392341/ /pubmed/30847068 http://dx.doi.org/10.1002/ece3.4842 Text en © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Dietrich, Muriel
Markotter, Wanda
Studying the microbiota of bats: Accuracy of direct and indirect samplings
title Studying the microbiota of bats: Accuracy of direct and indirect samplings
title_full Studying the microbiota of bats: Accuracy of direct and indirect samplings
title_fullStr Studying the microbiota of bats: Accuracy of direct and indirect samplings
title_full_unstemmed Studying the microbiota of bats: Accuracy of direct and indirect samplings
title_short Studying the microbiota of bats: Accuracy of direct and indirect samplings
title_sort studying the microbiota of bats: accuracy of direct and indirect samplings
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392341/
https://www.ncbi.nlm.nih.gov/pubmed/30847068
http://dx.doi.org/10.1002/ece3.4842
work_keys_str_mv AT dietrichmuriel studyingthemicrobiotaofbatsaccuracyofdirectandindirectsamplings
AT markotterwanda studyingthemicrobiotaofbatsaccuracyofdirectandindirectsamplings