The microbiome of Microtus agrestis

The microbiome is well-known to drive variation in host states (e.g., behaviour, or immunity) that would be expected to modulate the spread of infectious disease - but the role of microbiotal interactions in generating dynamically important superspreaders is poorly understood. Superspreaders are individuals with a strongly disproportionate contribution to pathogen transmission, and they come in two forms. Supershedders transmit infection to more individuals because they shed higher levels of a pathogen. Supercontacters transmit infection to more individuals because they have a larger number of social contacts. We explore associations between the gut microbiota and these two forms of superspreading in a wild rodent model – Bartonella spp. bacteraemia in the field vole (Microtus agrestis). We find evidence that, first, individuals fall into distinct shedding and contacting clusters, and second, that supercontacters have lower and more variable gut microbial alpha-diversity than low-contacters. We also show evidence that both supershedders and supercontacters have distinct gut microbial composition, and identify OTUs which are differentially abundant in the gut microbiota of these two classes of individuals. We find that the Muribaculaceae are associated with differences in both shedding and contacting, and discuss potential mechanisms by which they may be acting on these host traits. The data here relates to amplicon sequencing of the 16S rRNA gene (V4 region) on an Illumina platform with 2x250bp reads. --leftPrimer GTGCCAGCMGCCGCGGTAA --rightPrimer GGACTACHVGGGTWTCTAAT