Comparing invasive and noninvasive faecal sampling in wildlife microbiome studies: A case study on wild common cranes

Sondra Turjeman*, Sasha Pekarsky*, Ammon Corl, Pauline L. Kamath, Wayne M. Getz, Rauri C.K. Bowie, Yuri Markin, Ran Nathan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


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.

Original languageAmerican English
Pages (from-to)359-367
Number of pages9
JournalMolecular Ecology Resources
Issue number2
StatePublished - Feb 2023

Bibliographical note

Publisher Copyright:
© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.


  • avian microbiome
  • common crane
  • microbial community characterization
  • noninvasive sampling
  • stress
  • trapping


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