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Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings

  • Host Microbe Interactions
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Abstract

The microbiota of fish skin, the primary barrier against disease, is highly dynamic and modulated by several factors. In fish aquaculture, disease outbreaks occur mainly during early-life stages, with associated high economic losses. Antibiotic treatments sometimes remain the best option to control bacterial diseases, despite many reported negative impacts of its use on fish and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of fingerlings are scarce. We sequenced the bacterial 16S rRNA V4 gene region using a metabarcoding approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with flumequine, on the skin microbiota of farmed seabass (Dicentrarchus labrax) fingerlings. Both infection and antibiotic treatment led to a significant increase in bacterial diversity and core microbial communities and impacted microbiome structure. Dysbiosis was confirmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also significantly affected by flumequine administration, suggesting a detriment to fish skin health. Our results add to an increasing body of literature, showing how fish microbiome response to infection and antibiotics cannot be easily predicted.

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Data Availability

The raw sequences are available at NCBI Sequence Read Archive (SRA) database within the BioProject ID PRJNA741392.

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Funding

This work was funded by the European Regional Development Fund (ERDF) through the COMPETE program and by National Funds through FCT—Foundation for Science and Technology (project PTDC/BIA-MIC/27995/2017 POCI-01–0145-FEDER-027995); DR, MP-L, and RX were supported by FCT under the Programa Operacional Potencial Humano – Quadro de Referência Estratégico Nacional funds from the European Social Fund and Portuguese Ministério da Educação e Ciência (DR doctoral grant SFRH/BD/117943/2016; MP-L: IF/00764/2013; RX: IF/00359/2015; and 2020.00854.CEECIND).

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Authors and Affiliations

  1. CIBIO-InBIO, Investigation Centre for Biodiversity, Genetics and Evolution, Porto University, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal

    Daniela Rosado, Marcos Pérez-Losada & Raquel Xavier

  2. Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052-0066, USA

    Marcos Pérez-Losada

  3. Piscicultura Vale da Lama, Sapal Do Vale da Lama, Odiáxere, 8600-258, Lagos, Portugal

    Ricardo Severino

Authors
  1. Daniela Rosado
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  2. Marcos Pérez-Losada
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  3. Ricardo Severino
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  4. Raquel Xavier
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Contributions

DR, RX, and RS designed the research. RS collected the samples. DR performed laboratory work and analyzed the results. MP-L contributed to the statistical analysis. RX and MP-L supervised and provided intellectual content. All authors reviewed the manuscript. The author(s) read and approved the final manuscript.

Corresponding authors

Correspondence to Daniela Rosado or Raquel Xavier.

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Ethics Approval

Animals in this study were reared in a commercial fish farm located in the estuarine environment of the Alvor Estuary (Portimão), southern Portugal. Fish were handled by the fish farm employees and samples were taken non-invasively. According to the Portuguese legislation DL Nº 113/2013, our work does not involve animal experimentation and therefore is exempted from the need of ethical approval.

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Rosado, D., Pérez-Losada, M., Severino, R. et al. Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings. Microb Ecol 83, 789–797 (2022). https://doi.org/10.1007/s00248-021-01795-8

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