Detection of Bartonella schoenbuchensis and a novel sigmavirus within the microbiome of deer keds (Lipoptena cervi) from the United Kingdom

Background Lipoptena cervi is a member of the Hippoboscidae family of insects and are hematophagous ectoparasites of cervid species, commonly referred to as deer keds. Lipoptena cervi has a wide geographical distribution and can be found from North America through Europe into East Asia. Deer keds occasionally bite humans and domestic animals and could act as vectors of disease. The microbiome associated with this species of biting insect has not been investigated. Methods Mass sequencing of both DNA and RNA extracted from L. cervi specimens collected from two locations in southern England was conducted to characterize the complete microbiome consisting of bacterial, viral and eukaryotic species. Three specimens were collected after landing on humans in Somerset and three specimens collected from European roe deer ( Capreolus capreolus ), in Oxfordshire. Bioinformatic analysis investigated the host and microbial composition of each specimen. Results Near complete mitochondrial genomes were assembled from all six specimens confirming morphological speciation as L. cervi . Bacterial endosymbionts were the most dominant organisms identified with Candidatus Arsenophonus lipoptenae being most abundant. In specimens that had fed on deer, the pathogen Bartonella schoenbuchensis was detected. A novel sigmavirus was also detected in five samples, four of which yielded near complete genomes. The closest relative of this virus was a sigmavirus found in the sheep ked ( Melophagus ovinus ) sampled in the Russian Federation. Conclusions The data from this study will allow for a better baseline understanding of the microbiome of L. cervi and provides evidence for their role as vectors of zoonotic pathogens.