In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for faecal microbiome research, comparing microbiota of noninvasively collected faecal samples to those collected from trapped common cranes at the same sites over the same periods. We found significant differences in faecal microbial composition (alpha and beta diversity), which likely did not result from noninvasive sample exposure to soil contaminants, as assessed by comparing bacterial oxygen use profiles. Differences might result from trapped birds' exposure to sedatives or stress. We conclude that if all samples are collected in the same manner, comparative analyses are valid, and noninvasive sampling may better represent host faecal microbiota because there are no trapping effects. Experiments with fresh and delayed sample collection can elucidate effects of environmental exposures on microbiota. Further, controlled tests of stressing or sedation may unravel how trapping affects wildlife microbiota.
Bibliographical noteFunding Information:
This research was funded by BSF grant 904/2015 to RN and WG, NSF grant 1617982 to WG, RCKB, and PLK, and ISF grant 2525/16, the JNF/KKL grants 14–093–01‐6 and 19–12814‐1931, the Adelina and Massimo Della Pergola Chair of Life Sciences and the Minerva Center for Movement Ecology to RN.
© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
- avian microbiome
- common crane
- microbial community characterization
- noninvasive sampling