Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax)

Rosado, Daniela; Xavier, Raquel; Severino, Ricardo; Tavares, Fernando; Cable, Joanne; Pérez‐Losada, Marcos

doi:10.1038/s41598-019-55314-4

Cited by 76 publications

(90 citation statements)

References 83 publications

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“…Furthermore, it was shown that while these communities stabilise during recovery, they do not appear to return to their original state in the short-term (~1 week). In some sh such as sea bass (Dicentrarchus labrax), it has also been shown that recovery over the longer term (~ 3 weeks following oral administration of oxytetracycline) may vary between the different mucosal surfaces, with the communities associated with the skin reported to be more resilient to those of the gills [71]. In support of this, we also observed here a greater disparity in the effects of antibiotic treatment on the gut rather than the skin bacterial communities.…”

Section: Discussionsupporting

confidence: 81%

Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota

Legrand

Catalano

Wos‐Oxley

et al. 2020

Preprint

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Background The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery and examination of these communities in fish of commercial importance is not well documented. Examining the impacts of antibiotics on farmed fish microbiota is fundamental for improving our understanding and management of healthy farmed fish. This work assessed yellowtail kingfish ( Seriola lalandi ) skin and gut bacterial communities after an oral antibiotic combination therapy in poor performing fish that displayed signs of enteritis over an 18-day period. In an attempt to promote improved bacterial re-establishment after antibiotic treatment, faecal microbiota transplantation (FMT) was also administered via gavage or in the surrounding seawater, and its affect was evaluated over 15 days post-delivery. Results Antibiotic treatment greatly perturbed the global gut bacterial communities of poor-performing fish – an effect that lasted for up to 18 days post treatment. This perturbation was marked by a significant decrease in species diversity and evenness, as well as a concomitant increase in particular taxa like an uncultured Mycoplasmataceae sp., which persisted and dominated antibiotic-treated fish for the entire 18-day period. The skin-associated bacterial communities were also perturbed by the antibiotic treatment, notably within the first 3 days; however, this was unlike the gut, as skin microbiota appeared to shift towards a more ‘normal’ (though disparate) state after 5 days post antibiotic treatment. FMT was only able to modulate the impacts of antibiotics in some individuals for a short time period, as the magnitude of change varied substantially between individuals. Some fish maintained certain transplanted gut taxa (i.e. present in the FMT inoculum; namely various Aliivibrio related ASVs) at Day 2 post FMT, although these were lost by Day 8 post FMT. Conclusion As we observed notable, prolonged perturbations induced by antibiotics on the gut bacterial assemblages, further work is required to better understand the processes/dynamics of their re-establishment following antibiotic exposure. In this regard, procedures like FMT represent a novel approach for promoting improved microbial recovery, although their efficacy and the factors that support their success requires further investigation.

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Section: Discussionsupporting

confidence: 81%

Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota

Legrand

Catalano

Wos‐Oxley

et al. 2020

Preprint

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“…Up to date, there are not studies on the effects of diet on skin mucus microbiota of farmed sh. However, since the feed catabolites are dispersed in the water, and the quality of water is one of the factors that can change the composition of sh microbiotas [28][29][30], it would be interesting to see the dynamics of both gut and skin microbiota in sh fed diets with insect meal.…”

Section: Introductionmentioning

confidence: 99%

Effects of Full Replacement of Dietary Fishmeal with Insect Meal from Tenebrio Molitor on Rainbow Trout Gut and Skin Microbiota.

Terova

Gini

Gasco

et al. 2020

Preprint

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Background: Aquaculture must continue to reduce dependence on fishmeal (FM) and oil in feeds to ensure sustainable sector growth. Therefore, the use of novel aquaculture feed ingredients is growing. In this regard, insects can represent a new world of sustainable and protein-rich ingredients for farmed fish feeds. Accordingly, we investigated the effects of full replacement of FM with Tenebrio molitor (TM) larvae meal in the diet of rainbow trout (Oncorhynchus mykiss) on fish growth performance and gut and skin microbiota. Methods: A feeding trial was conducted with trout of about 80 g mean initial weight that were fed for 22 weeks with two isonitrogenous, isolipidic, and isoenergetic extruded experimental diets. Partially defatted TM meal was included in the diets to replace 0% (TM 0) and 100% (TM 100) of FM. To analyse the microbial communities, the Illumina MiSeq platform for sequencing of 16S rRNA gene and Qiime pipeline were used to identify bacteria in the gut and skin mucosa, and in the diets. Results: The data showed no major effects of full FM substitution with TM meal on bacterial species richness and diversity in both, gut mucosa- and skin mucus-associated microbiome. Skin microbiome was dominated by phylum Proteobacteria and especially by Gammaproteobacteria class that constituted approximately half of the bacterial taxa found. The two dietary fish groups did not display distinctive features, except for a decrease in the relative abundance of Deefgea genus (family Neisseriaceae) in trout fed with insect meal. The metagenomic analysis of the gut mucosa indicated that Tenericutes was the most abundant phylum, regardless of the diet. Specifically, within this phylum, the Mollicutes, mainly represented by Mycoplasmataceae family, were the dominant class. However, we observed only a weak dietary modulation of intestinal bacterial communities. The only changes due to full FM replacement with TM meal were a decreased number of Proteobacteria and a reduced number of taxa assigned to Ruminococcaceae and Neisseriaceae families. Conclusions: the data demonstrated that TM larvae meal is a valid alternative animal protein to replace FM in the aquafeeds. Only slight gut and skin microbiota changes occurred in rainbow trout after total FM replacement with insect meal. The mapping of the trout skin microbiota represents a novel contribution of the present study. Indeed, in contrast to the increasing knowledge on gut microbiota, the skin microbiota of major farmed fish species remains largely unmapped but it deserves thorough consideration.

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“…7,8,36,61], including seabass and seabream [71], have shown remarkable differences in microbial composition and structure across host species and tissues. Additionally, a previous study by our group [72] showed that disease and antibiotic treatment in seabass leads to asymmetrical shifts in skin and gill microbial communities. Therefore, all our statistical analyses were carried out separately for each sh species and tissue.…”

Section: Data Processing and Statistical Analysismentioning

confidence: 84%

Characterization of the skin and gill microbiomes in farmed seabass and seabream across different age groups

Rosado

Pérez‐Losada

Pereira

et al. 2020

Preprint

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Background Important changes in microbiome 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 microbiomes 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 microbiome in shaping the fish skin and gill microbiomes.Results Microbiome diversity, composition and potential metabolic functions varied across fish maturity stages. Alpha-diversity in the seabass microbiome 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, although it was higher in the skin of juveniles. Microbiome structure varied significantly across age groups. Different bacterial metabolic pathways were predicted to be enriched in the microbiomes of both species. Finally, we found that the water microbiome is significantly distinct from all the fish microbiomes across the studied age groups, although a high percentage of ASVs is shared with the skin and gill microbiomes.Conclusions We report important microbial differences in composition and potential functionality across the 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 host coping mechanisms during stressful conditions. Our results provide new evidence suggesting that growth and sexual maturation have an important role in shaping the external mucosa microbiomes of fish and highlight the importance of considering different life stages in microbiome studies.

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Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax)

Cited by 76 publications

References 83 publications

Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota

Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota

Effects of Full Replacement of Dietary Fishmeal with Insect Meal from Tenebrio Molitor on Rainbow Trout Gut and Skin Microbiota.

Characterization of the skin and gill microbiomes in farmed seabass and seabream across different age groups

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