{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T07:24:52Z","timestamp":1773300292349,"version":"3.50.1"},"reference-count":30,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2019,1,24]],"date-time":"2019-01-24T00:00:00Z","timestamp":1548288000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["5 NU2GGH001874-02-00"],"award-info":[{"award-number":["5 NU2GGH001874-02-00"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Ecology and Evolution"],"published-print":{"date-parts":[[2019,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Given the recurrent bat\u2010associated 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\u2010throughput 16S rRNA sequencing of urine and feces samples from <jats:italic>Rousettus aegyptiacus<\/jats:italic>, a cave\u2010dwelling 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\u2010 and beta\u2010diversity of urinary and fecal microbiotas. In particular, increased alpha\u2010diversity and more overlapping composition between urine and feces samples was seen when direct sampling was used, suggesting that cross\u2010contamination 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\u2010associated 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.<\/jats:p>","DOI":"10.1002\/ece3.4842","type":"journal-article","created":{"date-parts":[[2019,1,25]],"date-time":"2019-01-25T05:10:04Z","timestamp":1548393004000},"page":"1730-1735","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Studying the microbiota of bats: Accuracy of direct and indirect samplings"],"prefix":"10.1002","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2665-7970","authenticated-orcid":false,"given":"Muriel","family":"Dietrich","sequence":"first","affiliation":[{"name":"Department of Medical Virology, Faculty of Health Sciences, Centre for Viral Zoonoses University of Pretoria Pretoria South Africa"},{"name":"UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), INSERM U1187, CNRS UMR 9192, IRD UMR 249 Universit\u00e9 de la R\u00e9union Sainte\u2010Clotilde Reunion Island  France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wanda","family":"Markotter","sequence":"additional","affiliation":[{"name":"Department of Medical Virology, Faculty of Health Sciences, Centre for Viral Zoonoses University of Pretoria Pretoria South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2019,1,24]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky379"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.01753"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep36948"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.micres.2015.10.006"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1201366"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00017-06"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00447"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gdata.2015.04.001"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fnw284"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1098\/rsos.180041"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.12766"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid1703.100526"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr381"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.4084"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v014.i09"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0191301"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1744-7429.2003.tb00606.x"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.4174"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01043-13"},{"key":"e_1_2_9_21_1","unstructured":"Oksanen J. 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