Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

Abstract

Summary Atlantic cod (Gadus morhua) is an ecologically important species with a wide‐spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine‐scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway–located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, Photobacterium iliopiscarium and Photobacterium kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution.

Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes

“…Second, we observed no significant bacterial order-or species-level differences in the intestinal microbiome between different gadoid species, Atlantic cod (ecotype NCC), and Norway pout, which were sampled from different geographical locations (Lofoten and Oslo Fjord). We did not observe differentiation between the NCC sampled from Lofoten and the Oslo Fjord (although statistical certainly was low), which reflects an earlier observed lack of geographical structure for this ecotype (30). The similarity of the microbial compositions of the NCC and Norway pout is striking, as these are distinctly different genetic lineages with an evolutionary separation of at least 20 million years (24).…”

“…Studies that specifically integrate internal and external influences support a role for both factors driving the microbial community composition (13,29). Such studies, however, remain restricted in both the level of taxonomy of fishes (30) as well as taxonomical resolution of the microbial analyses (16S rRNA) (13,29,(31)(32)(33). Importantly, it often remains difficult to separate the correlated effects of distinct behavior (e.g., diet) and niche occupation with interspecific selection.…”

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity

“…However, such large-scale metagenome assembly-based approaches have not been as extensively applied to most non-human vertebrates. The low amount of metagenome reads classified in some recent studies of the rhinoceros, chicken, cod, and cow gut/rumen microbiome suggests that databases lack much of the genomic diversity in less-studied vertebrates [8][9][10][11] . Indeed, the limited number of studies incorporating metagenome assembly hint at the extensive amounts of as-of-yet novel microbial diversity across the >66,000 vertebrate species on our planet.…”

Reviews and syntheses: Bacterial bioluminescence – ecology and impact in the biological carbon pump

“…Le Doujet et al 2019demonstrated that Photobacterium genus represents 78 % of all present genera and identified the P. phosphoreum clade as the most abundant Photobacterium lineage. According to Riiser et al (2019), the luminous species P. kishitanii constitutes over 26 % of the Vibrionales community, which is the dominant clade, and the authors underlined the presence of the functional lux genes. Therefore, recent metagenomic studies seem to confirm the trend of a high occurrence of luminous bacteria in fish intestines.…”