Deciphering the microbial landscapes in the early life stages of a high-value marine fish, cobia (Rachycentron canadum, Rachycentridae) through high-resolution profiling by PacBio SMRT sequencing

Abstract

Microbial dynamics across multiple ontogenetic stages represent one confounding feature in teleost microbiome research. The present study recorded the dynamics in the whole microbiome of early life stages and the juvenile gut microbiome of a high-value mariculture species, cobia (Rachycentron canadum), during standard culturing practices. This is the first report on using the PacBio system targeting full-length 16S rRNA sequences, for deciphering fish microbiomes. The results highlighted a temporal shift in the whole microbiome compositions along the host's ontogenetic development. There was a significant decrease in Cyanobacteria and Firmicutes to Bacteroidetes ratio with a corresponding increase in Plactomycetacea and Bacteriodata in the whole microbiome profiles of the post-metamorphosis samples. The gut microbiome data suggested an adaptive mechanism toward establishing beneficial strains (Bacilli and Actinobacteria) alongside the ontogenetic progression. Nevertheless, a small, abundant core bacterial community occupied ∼50% and ∼ 64% of total abundance in the whole microbiome and gut microbiome, respectively. The results revealed high-dimensional microbial biomarkers for various ontogenetic stages of cobia during standard culturing practices. The composite dataset generated offers several possible sustainable means of microbiome manipulations to improve the low survival encountered in the early life stages of cobia.