Ectotherms have peculiar relationships with microorganisms. For instance, bacteria are recovered from the blood and internal organs of healthy teleosts. However, the presence of microbial communities in the healthy teleost brain has not been proposed. Here, we report a living bacterial community in the brain of healthy salmonids with bacterial loads comparable to those of the spleen and 1000-fold lower than in the gut. Brain bacterial communities share >50% of their diversity with gut and blood bacterial communities. Using culturomics, we obtained 54 bacterial isolates from the brains of healthy trout. Comparative genomics suggests that brain bacteria may have adaptations for niche colonization and polyamine biosynthesis. In a natural system, Chinook salmon brain microbiomes shift from juveniles to reproductively mature adults. Our study redefines the physiological relationships between the brain and bacteria in teleosts. This symbiosis may endow salmonids with a direct mechanism to sense and respond to environmental microbes.

Center for Evolutionary and Theoretical Immunology Department of Biology University of New Mexico Albuquerque NM 87108 USA

Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis OR 97331 USA

Faculty of Fisheries and Protection of Waters South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses Institute of Aquaculture and Protection of Waters University of South Bohemia České Budějovice Czech Republic

Fish Health Division University of Veterinary Medicine Vienna Austria

Institute of Parasitology Biology Centre of the Czech Academy of Sciences České Budějovice Czech Republic

Norwegian Veterinary Institute Thormøhlens Gate 53C 5006 Bergen Norway

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