Microbiome Profiling Reveals a Microbial Dysbiosis During a Natural Outbreak of Tenacibaculosis (Yellow Mouth) in Atlantic Salmon

Abstract

Tenacibaculosis remains a major health issue for a number of important aquaculture species globally. On the west coast of Canada, yellow mouth (YM) disease is responsible for significant economic loss to the Atlantic salmon industry. While Tenacibaculum maritimum is considered to be the primary agent of clinical YM, the impact of YM on the resident microbial community and their influence on the oral cavity is poorly understood. Using a 16s rRNA amplicon sequencing analysis, the present study demonstrates a significant dysbiosis and a reduction in diversity of the microbial community in the YM affected Atlantic salmon. The microbial community of YM affected fish was dominated by two amplicon sequence variants (ASVs) of T. maritimum, although other less abundant ASVs were also found. Interestingly clinically unaffected (healthy) and YM surviving fish also had a high relative abundance of T. maritimum, suggesting that the presence of T. maritimum is not solely responsible for YM. A statistically significant association was observed between the abundance of T. maritimum and increased abundance of Vibrio spp. within fish displaying clinical signs of YM. Findings from our study provide further evidence that YM is a complex multifactorial disease, characterized by a profound dysbiosis of the microbial community which is dominated by distinct ASVs of T. maritimum. Opportunistic taxa, including Vibrio spp., may also play a role in clinical disease progression.

Keywords: Tenacibaculum maritimum; aquaculture; dysbiosis; microbiome; yellow mouth.

FIGURE 1

Diversity ofthe microbial community within different disease states and water samples. Boxplots show species richness, Simpsons, Shannon’s, and Pielou’s diversity indices.

FIGURE 2

(A) Multivariate homogeneity of groups dispersions for Bray–Curtis distances between samples relative to the disease group centroid. (B) Beta diversity of microbial community derived from healthy, surviving, yellow mouth affected Atlantic salmon, and water. Non-metric dimensional scaling was performed using Bray–Curtis dissimilarity calculation (stress value = 0.20) and statistical significance testing was performed using the PERMANOVA test.

FIGURE 3

(A) Abundance of bacterial taxa at the “class” level from the 500 most abundant ASVs for individual animals derived from different disease states or water samples. (B) Abundance at the genus level for taxa classified with in the class Flavobacteria.

FIGURE 4

Log10 abundance for ASVs (with abundance > 1%) deemed significantly differentially abundant between the YM and healthy and/or survivor and healthy disease states. The genus level classification of each AVS is also provided.

FIGURE 5

Relative (log2) abundance of ASVs that were classified as T. maritimum for individual fish within different disease states. The genetic relationship between ASVs was explored using a neighbor joining tree analysis and is shown on the left. Asterisk denotes those ASVs that were deemed significantly more abundant in the YM samples compared to healthy fish.

FIGURE 6

Network of bacterial taxa based on co-occurrence on all fish clinically affected by YM. Each node represents a taxon (ASV) and connections between nodes (or edges) indicate a Spearman correlation coefficient > 0.3 and a correlation p-value corrected with Bonferroni (<0.05). The size of each node is proportional to the relative abundance of each taxon, and the color labels indicate different genera. Edge thickness is proportional to the Spearman correlation coefficient between each node.