Host associated genotypes in the family Branchiomonaceae with proposal of Ca. Branchiomonas mykissicola n. sp. from rainbow trout (Oncorhynchus mykiss)

Candidatus Branchiomonas cysticola is the primary etiological agent of epitheliocystis and the most prevalent bacterium associated with gill disease (GD) in farmed Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) in Norway. Partial sequencing of seven of the bacterium's partial housekeeping (HK) genes (aceE, dnaK, lepA, gltA, rplB, rpoC, and typA) revealed few genetic differences, irrespective of geographic origin, reservoirs, and fish populations. Candidatus Branchiomonas cysticola sequenced from gill samples of wild and farmed salmon in Norway and United Kingdom likely represents a single clonal complex (CC). Highly divergent genotypes were, however, identified from gill samples of rainbow trout. Real-time reverse transcriptase PCR (real-time RT-PCR) and fluorescence in-situ hybridization (FISH) showed putative host-specific properties of the bacterial genotypes isolated from salmon and rainbow trout. Sequencing of the 16S and 23S rRNA ribosomal subunits from gills of these two hosts and from other fish species testing positive for Ca. B. cysticola revealed single nucleotide polymorphisms (SNPs). These results support the existence of host-associated bacteria and suggest a strong selection towards host-specific variants of Branchiomonas. A novel host-specific bacterial species from gill samples of rainbow trout, named Candidatus Branchiomonas mykissicola, has therefore been proposed.