Characterization of the avian postmortem gut microbiome across space and time using 16S rRNA sequencing

Abstract

The advent of high-throughput sequencing technologies, such as 16S rRNA amplicon sequencing, has enabled the characterization of microbial communities across diverse ecosystems including animal carrion. Although most studies on postmortem microbial communities focus on its application to human death scene analysis, this technique holds great potential for wildlife crime investigations. We conducted a pilot study to characterize the spatial heterogeneity and temporal shifts between the perimortem (i.e., at time of death) and postmortem (i.e., after death) microbiomes associated with the gut tracts of decomposing European Starling (Sturnus vulgaris) nestlings over three days. We observed significant differences in microbial community structure among perimortem gut tract regions. The microbial communities converged across all gut tract regions within the first 24 h of death and remained stable between 24 and 72 h postmortem. A random forest classifier identified Lactococcus, Serratia, and Clostridium as the top three taxonomic predictors for predicting perimortem or postmortem microbial communities. Our findings provide preliminary data for considering the potential forensic utility of incorporating the postmortem gut microbiome in avian wildlife crimes.

Keywords

• Gut microbiome
• Wildlife forensics
• Birds, Sturnus vulgaris