An insight into gill microbiome of Eastern Mediterranean wild fish by applying next generation sequencing

Abstract

Bacterial diseases of marine fish inflict significant economic damage to fisheries and aquaculture and pose an increasing risk to public health. When addressing fish disease, an accumulating body of research suggests adding another factor to the classic epidemiological triangle of host-environment-pathogen: the microbiome. The gills, being a gateway into the fish body and bearing an important role in fish homeostasis, have been found to be a proxy of the gut microbiota as well as reflecting the microbial communities of surrounding water. In this study, 16S rRNA amplicons of bacterial DNA extracted from the gills of 89 asymptomatic specimens of three wild fish species (Pagrus caeruleostictus, Scomber colias and Saurida lessepsianus) were sequenced using Next Generation Sequencing methodology (NGS). Data analyses revealed the presence of 41 potentially pathogenic species, including several zoonotic agents. Five genera known to include widespread and potentially pathogenic species were chosen for further investigation: Photobacterium, Shewanella, Staphylococcus, Streptococcus and Vibrio. Of these, Photobacterium and Shewanella proved the most prevalent and abundant, making up 30.2% and 11.3% of the Bluespotted seabream (P. caeruleostictus) gill microbiome alone. Photobacterium damselae and Shewanella baltica were most common at the species level. The remaining genera - Vibrio, Staphylococcus and Streptococcus – were less prevalent, and at a species level were comprised of only 1−4% potentially pathogenic representatives. Gill microbiomes exhibited host species specificity, with strong correlations between certain bacterial taxonomic groups. No definite obligatory pathogenic bacteria were found in this study, and it was suggested that pathogenic species are present as either covert pathobionts or as opportunists of the fish found to host them.

Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander

“…Host-microbe and microbe-microbe interaction are gaining more and more attention due to their tremendous importance for sh health [30]. A few recent studies focused on the bacterial composition on gills in wild sh [31] assessing pathogen load from the presence of speci c genera and species [149], [157]. Here, we aimed to describe the holobiont incorporating bacterial abundance with tissue speci c gene expression patterns in the host.…”

“…Shewanella is recognized for its role in organic matter turnover under hypoxic conditions[166] and polyunsaturated fatty acids (PUFA) production [167]. Different strains were isolated from freshwater walleye gastrointestinal tracts[168] and gill mucus communities of different marine sh species [31], [157], with substantial numbers of ASVs resembling potentially pathogenic species [149]. The pathogenic role of Shewanella remains unclear [169] despite repeated recovery from diseased sh [170], [171].…”

Enhancing seafood traceability: tracking the origin of seabass and seabream from the tuscan coast area by the analysis of the gill bacterial communities

“…Therefore, the gills are receiving increasing attention, as they may be sampled without destroying or compromising the saleable parts of the fish (i.e. by swabbing or biopsy) [ 24 , 25 ]. In this context, we found several studies focused on the microbiota of molluscs [ 14 , 26 ], while those that analyzed fish concerned farmed specimens [ 16 ].…”

The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean

“…Acinetobacter has been reported as a possible contamination in lowbiomass samples (Salter et al 2014, Weyrich et al 2019) such as gills (François-Étienne et al 2023) but our blank extractions did not give any ampli able bacterial DNA and, in addition, Acinetobacter was found in low and variable abundances in the gut samples of the same shes (Varela, Papaspyrou, Kormas unpublished data).The second most likely core and obligate associate genus with the two investigated tissues is Staphylococcus and as for Acinetobacter, this is the rst time it is reported as an important bacterial community component of the gills and skin of the ve marine shes of the present study. It has been found as one of the major genera found in the gills of three Mediterranean species (Pagrus caeruleostictus, Scomber colias and Saurida lessepsianus)(Itay et al 2022) and the culturable bacterial fraction of farmed Thunnus thynnus gills and skin(Kapetanović et al 2017). It has been proposed that when Staphylococcus is detected in healthy specimens and since pathogenecity is also in uenced by abiotic and biotic factors, virulence of some bacterial taxa, such as Staphylococcus, is not obligatory and that potential pathogens do occur in healthy sh(Itay et al 2022).…”

“…It has been found as one of the major genera found in the gills of three Mediterranean species (Pagrus caeruleostictus, Scomber colias and Saurida lessepsianus)(Itay et al 2022) and the culturable bacterial fraction of farmed Thunnus thynnus gills and skin(Kapetanović et al 2017). It has been proposed that when Staphylococcus is detected in healthy specimens and since pathogenecity is also in uenced by abiotic and biotic factors, virulence of some bacterial taxa, such as Staphylococcus, is not obligatory and that potential pathogens do occur in healthy sh(Itay et al 2022). Our results, with the high dominance of Acinetobacter and Staphylococcus in healthy specimens enhance this concept.…”