The Microbiota of the Outer Gut Mucus Layer of the Migrating Northeast Arctic Cod (Gadus morhua) as Determined by Shotgun DNA Sequencing

Animals form functional units with their microbial communities, termed metaorganisms. While extensive research has been conducted on a few model animals, much remains unknown about the microbial diversity in most species. Here, we describe the taxonomic profile of the microbes from the outer gut mucus layer from the Northeast Arctic cod or also called the migrating Atlantic cod using a shotgun DNA sequencing approach. We provide metagenomes from six individuals. The results reveal three different taxonomic profile “types": Type I is dominated in numbers by Pseudomonaceae (44%) and Xanthomonadaceae (13%), Type II contains 65% Vibrionaceae and Type III contains 76% Enterobacteriaceae. This stands in sharp contrast to the bacterial diversity of the transient gut content (i.e., feces). Additionally, binning of assembled reads followed by phylogenomic analyses place a high-completeness bin of Type I within the Pseudomonas fluorescens group, one bin of Type II within the Photobacterium phosphoreum clade, and finally a bin of Type III within the Escherichia/Shigella group. In conclusion, we describe the adherent bacterial diversity in the Northeast Arctic cod's intestine using shotgun sequencing, revealing different taxonomic profiles compared to the more homogenous transient (fecal) microbiota. This suggests that the intestine contains two separate and distinct microbial populations.