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It remains a challenge to obtain the desired phenotypic traits in aquacultural production of Atlantic salmon, and part of the challenge might come from the effect that host-associated microorganisms have on the fish phenotype. To manipulate the microbiota towards the desired host traits, it is critical to understand the factors that shape it. The bacterial gut microbiota composition can vary greatly among fish, even when reared in the same closed system. While such microbiota differences can be linked to diseases, the molecular effect of disease on host-microbiota interactions and the potential involvement of epigenetic factors remain largely unknown. The aim of this study was to investigate the DNA methylation differences associated with a tenacibaculosis outbreak and microbiota displacement in the gut of Atlantic salmon. Using Whole Genome Bisulfite Sequencing (WGBS) of distal gut tissue from 20 salmon, we compared the genome-wide DNA methylation levels between uninfected individuals and sick fish suffering from tenacibaculosis and microbiota displacement. We discovered >19,000 differentially methylated cytosine sites, often located in differentially methylated regions, and aggregated around genes. The 68 genes connected to the most significant regions had functions related to the ulcerous disease such as epor and slc48a1a but also included prkcda and LOC106590732 whose orthologs are linked to microbiota changes in other species. Although the expression level was not analysed, our epigenetic analysis suggests specific genes potentially involved in host-microbiota interactions and more broadly it highlights the value of considering epigenetic factors in efforts to manipulate the microbiota of farmed fish.

Large amounts of data from microbiome-related studies have been (and are currently being) deposited on international public databases. These datasets represent a valuable resource for the microbiome research community and could serve future researchers interested in integrating multiple datasets into powerful meta-analyses. However, this huge amount of data lacks harmonization and it is far from being completely exploited in its full potential to build a foundation that places microbiome research at the nexus of many subdisciplines within and beyond biology. Thus, it urges the need for data accessibility and reusability, according to findable, accessible, interoperable and reusable (FAIR) principles, as supported by National Microbiome Data Collaborative and FAIR Microbiome. To tackle the challenge of accelerating discovery and advances in skin microbiome research, we collected, integrated and organized existing microbiome data resources from human skin 16S rRNA amplicon-sequencing experiments. We generated a comprehensive collection of datasets, enriched in metadata, and organized this information into data frames ready to be integrated into microbiome research projects and advanced post-processing analyses, such as data science applications (e.g. machine learning). Furthermore, we have created a data retrieval and curation framework built on three different stages to maximize the retrieval of datasets and metadata associated with them. Lastly, we highlighted some caveats regarding metadata retrieval and suggested ways to improve future metadata submissions. Overall, our work resulted in a curated skin microbiome datasets collection accompanied by a state-of-the-art analysis of the last 10 years of the skin microbiome field. Database URL: https://github.com/giuliaago/SKIOMEMetadataRetrieval

BackgroundInfectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role in regulating the host immune system, health and physiology, altered gut microbiota compositions are often associated with a diseased status. However, few studies have examined the association between disease severity and degree of gut dysbiosis, especially when the gut is not the site of the primary infection. Moreover, there is a lack of knowledge on whether bath treatment with formalin, a disinfectant commonly used in aquaculture to treat external infections, might affect the gut microbiome as a consequence of formalin ingestion. Here we investigate, through 16S rRNA gene metabarcoding, changes in the distal gut microbiota composition of a captive-reared cohort of 80 Atlantic salmon (Salmo salarL.), in consequence of an external bacterial skin infection due to a natural outbreak and subsequent formalin treatment.ResultsWe identifiedTenacibaculum dicentrarchias the causative disease pathogen and we show that the distal gut of diseased salmon presented a different composition from that of healthy individuals. A new, yet undescribed,Mycoplasmagenus characterized the gut of healthy salmon, while in the sick fish we observed an increase in terms of relative abundance ofAliivibriosp., a strain regarded as opportunistic. We also noticed a positive correlation between fish weight andMycoplasmasp. relative abundance, potentially indicating a beneficial effect for its host. Moreover, we observed that the gut microbiota of fish treated with formalin was more similar to those of sick fish than healthy ones.ConclusionsWe conclude that externalTenacibaculuminfections have the potential of indirectly affecting the host gut microbiota. As such, treatment optimization procedures should account for that. Formalin treatment is not an optimal solution from a holistic perspective, since we observe an altered gut microbiota in the treated fish. We suggest its coupling with a probiotic treatment aimed at re-establishing a healthy community. Lastly, we have observed a positive correlation ofMycoplasmasp. with salmon health and weight, therefore we encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.

Background: Infectious diseases cause significant production losses in aquaculture every year. Given the pivotal role played by the gut microbiota in regulating the host immune system, health and physiology, interest has risen in the possibility of controlling the fish health status by modulating the gut microbiota. An altered gut microbiota is often associated with a disease status. However, few studies have examined the association between disease severity and degree of gut dysbiosis, especially when the gut is not the site of the primary infection. Moreover, there is a lack of knowledge on the impact of formalin, a commonly used disinfectant in aquaculture, on the gut microbiome. Here we investigate, through 16S rRNA gene metabarcoding, changes in the distal gut microbiota composition of a captive-reared cohort of Atlantic salmon (Salmo salar L.), in consequence of an external bacterial skin infection and the subsequent formalin treatment.Results: We show that the distal gut of diseased salmon presented a different composition from that of healthy individuals, with an increased relative abundance of strains regarded as opportunistic in sick fish. Conversely, healthy salmon were dominated by a new, yet undescribed, Mycoplasma genus. We also observed a positive correlation between fish weight and Mycoplasma sp. relative abundance, potentially indicating a beneficial effect for its host. Moreover, we observed that the treatment with formalin, while suited to resolve the external infection, was unable to recover the gut microbiota characteristic of healthy fish prior to treatment, potentially compromising the subsequent health status and growth performances of all treated fish.Conclusions: We conclude that infectious diseases have the potential of affecting the host gut microbiota at different body sites and that treatment optimization procedures should account for that. The formalin treatment is not an optimal solution from a holistic perspective, we suggest its coupling with a probiotic treatment aimed at re-establishing the original community. Lastly, we have observed a positive correlation of Mycoplasma sp. with salmon health and growth performances and, while inviting further research on this microorganism, we also encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.