Experimental validation of small mammal gut microbiota sampling from faeces and from caecum after death.

In a controlled experiment profiling microbial 16S-rRNA in 52 house mice (Mus musculus) from 8 families and 4 genetic backgrounds, we studied the effects of live and snap trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared caecal microbiota of individuals sampled 16-18 hours after death and those enclosed in live traps with caged controls, as well as caecal and faecal GM collected from mice in live-traps.