Analysis of the Atlantic cod (Gadus morhua) intestinal microbiome based on high-throughput sequencing of the 16S rRNA gene.. Atlantic cod intestinal microbiome

Host-microbe interactions are particularly intriguing in Atlantic cod (Gadus morhua), as it lacks the MHC II complex involved in presentation of extracellular pathogens. Nonetheless, little is known about the diversity of its microbiome in natural populations. Here, we use 16S rRNA high-throughput sequencing to investigate the microbial community composition in gut content and mucosa of 22 adult individuals from two coastal populations in Norway, located 470 km apart.We obtain over 12 million reads and identify 139 OTUs (based on 97% sequence similarity) from 20 bacterial orders. The relative abundance of these OTUs differs several orders of magnitude, with the 10 most abundant OTUs comprising 89% of the reads in this dataset. While a significantly lower community diversity is found in mucosal samples compared to gut content samples, the composition of common OTUs did not differ significantly between the two populations. Even though detailed diversity analyses based on oligotyping reveal a slightly more complex community structure, we find that a single 16S rRNA oligotype (order Vibrionales, genus Photobacterium) comprises nearly 50% of the reads in both locations.Our results show that the intestinal bacterial community of two geographically separated coastal populations of Atlantic cod is dominated by a limited number of highly abundant 16S rRNA oligotypes shared by all specimens examined. The ubiquity of these oligotypes suggests that the northern coastal Atlantic cod gut microbiome is colonized by a limited number of species with excellent dispersal capabilities that are well suited to thrive in their host environment.