Fishing for the Virome of Tropical Tuna

Abstract

While planktonic viruses have received much attention in recent decades, knowledge of the virome of marine organisms, especially fish, still remains rudimentary. This is notably the case with tuna, which are among the most consumed fish worldwide and represent considerable economic, social and nutritional value. Yet the composition of the tuna virome and its biological and environmental determinants remain unknown. To begin to address this gap, we investigated the taxonomic diversity of viral communities inhabiting the skin mucus, gut and liver of two major tropical tuna species (skipjack and yellowfin) in individuals fished in the Atlantic and Indian Oceans. While we found significant differences in the virome composition between the organs, this was totally independent of the tuna species or sex. The tuna virome was mainly dominated by eukaryotic viruses in the digestive organs (gut and liver), while bacteriophages were predominant in the mucus. We observed the presence of specific viral families in each organ, some previously identified as fish or human pathogens (e.g., Iridoviridae, Parvoviridae, Alloherpesviridae, Papillomaviridae). Interestingly, we also detected a ‘core virome’ that was shared by all the organs and was mainly composed of Caudovirales, Microviridae and Circoviridae. These results show that tuna host a mosaic of viral niches, whose establishment, role and circulation remain to be elucidated.

Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi

“…A limitation in the majority of microbiome studies, regardless of host species, is a focus on the bacterial community only with little or no attention given to the remaining microbial community members. This includes microeukaryotes, a taxonomic group that encompasses protists, microfungi, microalgae, and microbial metazoans (Bass and del Campo, 2020;del Campo et al, 2019), as well as viruses that infect an expansive host range including microeukaryotes, bacteria and the animal host (Gadoin et al, 2021). Microeukaryotic communities are well described in some settings, such as the contribution of microalgae to primary production in the ocean (Benoiston et al, 2017).…”

Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi

“…A limitation in the majority of microbiome studies, regardless of host species, is a focus on the bacterial community only with little or no attention given to the remaining microbial community members. This includes microeukaryotes, a taxonomic group that encompasses protists, microfungi, microalgae, and microbial metazoans (Bass and del Campo, 2020; del Campo et al, 2019), as well as viruses that infect an expansive host range including microeukaryotes, bacteria and the animal host (Gadoin et al, 2021). Microeukaryotic communities are well described in some settings, such as the contribution of microalgae to primary production in the ocean (Benoiston et al, 2017).…”

Five Species of Wild Freshwater Sport Fish in Wisconsin, USA, Reveal Highly Diverse Viromes

“…Our virome profiles surely underestimate the full diversity of viruses in the fish we examined. Among other considerations, we examined viruses in blood, and research on wild marine fish has documented significant differences in virome composition among organs [ 4 ]. Nevertheless, our results show that freshwater fish host distant relatives of pathogens impacting global fish and animal health, including several viruses of importance to human health, which is a notion previously supported by research on marine fish.…”

“…Much of our current understanding of viruses infecting fish is based on the study of pathogenic viruses in symptomatic hosts. However, the recent rise of metagenomic sequencing has led to the discovery that fish harbor a greater number of viruses than any other class of vertebrates [ 1 , 2 , 3 , 4 , 5 , 6 , 7 ]. Most families of RNA viruses once thought to infect mammals have been described in bony fishes [ 1 ].…”