The Faecal Microbiome of the Wild European Badger Meles meles: A Comparison Against Other Wild Omnivorous Mammals from Across the Globe

Abstract

Here we investigate the faecal microbiome of wild European badgers Meles meles using samples collected at post-mortem as part of the All Wales Badger Found Dead study. This is the first published characterisation of the badger microbiome. We initially undertook a sex-matched age comparison between the adult and cub microbiomes, based on sequencing the V3–V4 region of the 16S rRNA gene. Analysis used the QIIME 2 pipeline utilising DADA2 and the Silva database for taxonomy assignment. Fusobacteria appeared to be more abundant in the microbiomes of the cubs than the adults although no significant difference was seen in alpha or beta diversity between the adult and cub badger microbiomes. Comparisons were also made against other wild, omnivorous, mammals’ faecal microbiomes using publicly available data. Significant differences were seen in both alpha and beta diversity between the microbiomes from different species. As a wildlife species of interest to the disease bovine tuberculosis, knowledge of the faecal microbiome could assist in identification of infected badgers. Our work here suggests that, if comparisons were made between the faeces of bTB infected and non-infected badgers, age may not have a significant impact on the microbiome.

Metabolomic changes in the peripheral blood of wild trapped badgers correlate with bovine tuberculosis (Mycobacterium bovis) infection status

“…Faecal microbiome analysis of live trapped badgers would be useful to help corroborate any shifts in gut microbiota associated with altered tyrosine metabolism, which could be the cause of signi cant differences in gut derived metabolites (such as the phenylsulfates) observed in this study. A previous study of the faecal microbiome of badgers, involving samples collected from road-killed badgers showed that in bTB negative badgers the microbiome was distinct from that observed in other wild, omnivorous mammals [41].…”