It's in the Genes: Host Genetics and Microbiomes

The microbiomes of teleosts have been identified to play important roles in host disease immunity by excluding pathogens within mucus coatings and helping to develop immune responses. These microbiomes are developed early in a fish’s life and the communities often differ depending on diet, the external environment and the ability of microbes to outcompete others within the community. However, one somewhat understudied mechanism for the development of distinct microbiome communities in fish is the contribution of host genetics. Can genetics change the microbiome communities and increase resistance to disease?

Flavobacterium psychrophilum is a pathogenic bacteria and the causative agent of the Bacterial Cold Water Disease which wreaks havoc within Salmonid fish stocks. The disease causes caudal fin necrosis, skin lesions, and mortality and there is no commercially available vaccine to combat the infection. Therefore, it is imperative that we understand and characterize mechanisms, such as microbiome compositions and genetics, that increase resistance to this disease. The aims of the study presented here were to: investigate whether F. psychrophilum resistant and susceptible rainbow trout have bacterial assemblages associated with gut and gills, and, to investigate if host genetics and tank conditions also changed these assemblages.

Trout were selectively bred to produce F. psychrophilum resistant and susceptible lines and each line was placed into either high- or low-density holding tanks and left to grow. Disease resistance was tested on healthy fish from each line by injecting them with an F. psychrophilum strain and survival was recorded over 21 days. Community analysis was carried out by extracting genomic DNA from the gills and mid-guts of each line from the different holding densities. 16S rRNA was PCR amplified and sequenced on Illumina MiSeq high-throughput platform, microbiome community compositions and diversity indices were then calculated from these sequences.

Firstly, and rather unsurprisingly, the resistant trout line had much higher survival to infection (3% mortality) compared to the susceptible line (69% mortality), validating the resistance/susceptible phenotypes. Eight phyla were identified in the mid-guts from both lines with Tenericutes beginning the most abundant. The genus Mycoplasma made up almost all the Tenericutes but were found in lower abundance in susceptible fish. Perhaps a low Mycoplasma abundance is associated with disease susceptibility and that Mycoplasma could outcompete pathogens in the gut. At the gills, 9 phyla were found with Proteobacteria being the most abundant. Also, trace amounts of Flavobacteria sp. were detected at the gills. Flavobacteria infection may not be due to its abundance but its ability to displace other microbes within the community. Stock density and genetics did alter gut microbiome community structures, with high-density and low-density susceptible trout distinctly clustering from one another. Housing density had no effect on resistant fish gut community clustering, but the microbial diversities were much lower than susceptible fish. Resilience, therefore, may be associated with a less diverse microbiome.

This study does look to suggest that host genetics and the environment can have an influence over the mid-gut communities but not gill communities. Host genetics coupled with the external environment can select for distinct gut microbial communities and, in turn, determine an animal’s resilience to infection.

Paper reviewed:

Brown, R.M., Wiens, G.D., & Salinas, I. (2019). Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss). Fish and Shellfish Immunology, 86, 497-506.