The mucosal surfaces of fish harbour microbial communities that can act as the first-line of defense against pathogens. Infectious diseases are one of the main constraints to aquaculture growth leading to huge economic losses. Despite their negative impacts on microbial diversity and overall fish health, antibiotics are still the method of choice to treat many such diseases. Here, we use 16 rRNA V4 metataxonomics to study over a 6 week period the dynamics of the gill and skin microbiomes of farmed seabass before, during and after a natural disease outbreak and subsequent antibiotic treatment with oxytetracycline. Photobacterium damselae was identified as the most probable causative agent of disease. Both infection and antibiotic treatment caused significant, although asymmetrical, changes in the microbiome composition of the gills and skin. The most dramatic changes in microbial taxonomic abundance occurred between healthy and diseased fish. Disease led to a decrease in the bacterial core diversity in the skin, whereas in the gills there was both an increase and a shift in core diversity. Oxytetracycline caused a decrease in core diversity in the gill and an increase in the skin. Severe loss of core diversity in fish mucosae demonstrates the disruptive impact of disease and antibiotic treatment on the microbial communities of healthy fish.

There is substantial evidence showing that the microbiome of teleosts plays a key role in host health and wellbeing. Aquaculture practices increase the risk of dysbiosis (i.e. microbial imbalance), which is known to facilitate pathogen infections. The skin and gills are the primary defense organs against pathogens, thus, characterizing their microbiome composition in farmed fish is pivotal for detecting potential alterations that may lead to disease susceptibility.Here, we assessed the skin and gill microbiomes of two of the most important adult fish species farmed in southern Europe, the seabass and the seabream, during winter months. We coupled next-generation sequencing (MiSeq) of the 16S rRNA V4 region with the DADA2 bioinformatic pipeline to assess microbial composition and structure. Variation in microbial alpha-diversity (intra-sample) and taxa proportions were assessed using analysis of variance. Differences in beta-diversity (between-sample) were tested using permutational multivariate analysis of variance. Microbiomes of both tissues (n=30 per species) identified 19 bacteria phyla, dominated by the phyla Proteobacteria (44 -68%) andBacteroidetes (15 -37%); the families Flavobacteriaceae (11 -28%), Rhodobacteraeae (4 -8%) and Vibrionaceae (2 -17%); and the genera Rubritalea (4 -13%), Pseudomonas (4 -8%) and the NS3a marine group (4 -12%). Mean relative proportion of these taxa, some alpha-diversity indices and all beta-diversity distances varied significantly between tissues within and between species. ASVs belonging to the genera Polaribacter and Vibrio, which include several species that are pathogenic, were detected in the core microbiomes of seabass or seabream.

The microbiota of sh skin is the primary barrier against disease; however, it is highly dynamic being modulated by several factors. In sh aquaculture, disease outbreaks occur mainly during early-life stages with high associated losses. Antibiotic treatments sometimes remain as the best option to control bacterial diseases, despite many reported negative impacts of its use on sh and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of ngerlings are scarce. We used a 16S rRNA metataxonomic approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with umequine, on the skin microbiota of farmed seabass Dicentrarchus labrax ngerlings. Both disease and antibiotic treatment led to a signi cant increase in bacterial diversity and core microbial communities and impacted microbial structure. Dysbiosis was con rmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also signi cantly affected by umequine administration, suggesting a detriment to sh skin health. Our results add to an increasing body of literature, showing how sh microbiome response to disease and antibiotics is not easily predicted.

Fish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.

Background Important changes in microbial composition related to sexual maturation have been already reported in the gut of several vertebrates including mammals, amphibians and fish. Such changes in fish are linked to reproduction and growth during developmental stages, diet transitions and critical life events. We used amplicon (16S rRNA) high-throughput sequencing to characterize the skin and gill bacterial microbiota of farmed seabass and seabream belonging to three different developmental age groups: early and late juveniles and mature adults. We also assessed the impact of the surrounding estuarine water microbiota in shaping the fish skin and gill microbiota. Results Microbial diversity, composition and predicted metabolic functions varied across fish maturity stages. Alpha-diversity in the seabass microbiota varied significantly between age groups and was higher in older fish. Conversely, in the seabream, no significant differences were found in alpha-diversity between age groups. Microbial structure varied significantly across age groups; moreover, high structural variation was also observed within groups. Different bacterial metabolic pathways were predicted to be enriched in the microbiota of both species. Finally, we found that the water microbiota was significantly distinct from the fish microbiota across all the studied age groups, although a high percentage of ASVs was shared with the skin and gill microbiotas. Conclusions We report important microbial differences in composition and potential functionality across different ages of farmed seabass and seabream. These differences may be related to somatic growth and the onset of sexual maturation. Importantly, some of the inferred metabolic pathways could enhance the fish coping mechanisms during stressful conditions. Our results provide new evidence suggesting that growth and sexual maturation have an important role in shaping the microbiota of the fish external mucosae and highlight the importance of considering different life stages in microbiota studies.