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

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.

Automated summary

In ecological and conservation studies, responsible researchers aim to gather rich data with minimal disturbance to wildlife and ecosystems. This study compared the microbiota of noninvasively collected fecal samples to those collected from trapped common cranes to assess the use of noninvasive sampling for fecal microbiome research. The results showed significant differences in microbial composition between the samples, potentially due to the effects of trapping on the birds' microbiota. It was concluded that noninvasive sampling may better represent the host fecal microbiota without trapping effects.