Characterization of the marine aquaculture microbiome: A seasonal survey in a seabass farm

Roquigny, Roxane; Mougin, Julia; Bris, Cédric Le; Bonnin-Jusserand, Maryse; Doyen, Périne; Grard, Thierry

doi:10.1016/j.aquaculture.2020.735987

Cited by 15 publications

(11 citation statements)

References 49 publications

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“…Furthermore, its success may require effective biocontrol techniques to reduce infections [ 97 , 98 ]. The rapid spread and the ubiquitous nature of fish pathogenic microorganisms mean that infection control and prevention can be difficult [ 99 , 100 ]. Preventing and controlling diseases in aquaculture becomes more challenging with: (1) severe fecal contamination in fish farm waters [ 101 , 102 ], because few medications are licensed for use in fisheries [ 2 , 25 ] and many chemotherapeutic agents are ineffective against endospores and zoospores, leading to treatment failure in the case of infection [ 103 , 104 ]; (2) irregular environmental conditions (e.g., elevated temperatures, salinity variations, decreased oxygen concentrations, high organic load) that may contribute to disease outbreaks, often weakened by the sensitive fish’s innate defense system [ 98 , 102 , 105 ]; (3) high fish densities (greater than the indicated for each species), common practice in farming systems, which reduces infection resistance [ 106 ]; (4) different stages of the fish life cycle, that affect the development of the immune system, increases the frequency of infections [ 106 , 107 ]; (5) the indiscriminate and prophylactic use of antibiotics that increases the resistance problem in common pathogenic bacteria and the concern with the antibiotic spread in the environment [ 25 , 28 , 108 ].…”

Section: Disease Control and Alternative Approachesmentioning

confidence: 99%

Bacteriophages in the Control of Aeromonas sp. in Aquaculture Systems: An Integrative View

et al. 2022

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Aeromonas species often cause disease in farmed fish and are responsible for causing significant economic losses worldwide. Although vaccination is the ideal method to prevent infectious diseases, there are still very few vaccines commercially available in the aquaculture field. Currently, aquaculture production relies heavily on antibiotics, contributing to the global issue of the emergence of antimicrobial-resistant bacteria and resistance genes. Therefore, it is essential to develop effective alternatives to antibiotics to reduce their use in aquaculture systems. Bacteriophage (or phage) therapy is a promising approach to control pathogenic bacteria in farmed fish that requires a heavy understanding of certain factors such as the selection of phages, the multiplicity of infection that produces the best bacterial inactivation, bacterial resistance, safety, the host’s immune response, administration route, phage stability and influence. This review focuses on the need to advance phage therapy research in aquaculture, its efficiency as an antimicrobial strategy and the critical aspects to successfully apply this therapy to control Aeromonas infection in fish.

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Section: Disease Control and Alternative Approachesmentioning

confidence: 99%

Bacteriophages in the Control of Aeromonas sp. in Aquaculture Systems: An Integrative View

et al. 2022

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“…Most of the research on European seabass microflora has focused on the gut microbiota that is exposed to conventional [10] and alternative diets [11], as well as on the effects of probiotics on the balance of the gut microbiota [12]. Several researchers focus on the seasonal survey of the marine aquaculture microbiome in a European seabass farm [13], the assessment of seawater microbial quality, and the health status of farmed European seabass [14], with more specific characterization of isolated Vibrio species [5]. The evaluation of the tissue-specific diversity of microbiomes within and between sea bass and sea bream [7], as well as the recent study of the effects of aging on the skin and gill microbiota of farmed European sea bass and sea bream, were done by Rosado et al [7,15].…”

Section: Introductionmentioning

confidence: 99%

Skin Culturable Microbiota in Farmed European Seabass (Dicentrarchuslabrax) in Two Aquacultures with and without Antibiotic Use

Ramljak

Smrzlić

Kapetanović

et al. 2022

JMSE

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This study examined culturable skin microbiota that was associated with farmed European seabass (Dicentrarchus labrax). Healthy European seabass were sampled during summer commercial harvest from one conventional fish farm where antibiotics are used, and from another practicing a certified antibiotic-free fish aquaculture. Physicochemical and microbiological analysis of seawater and sediment were performed, as well as determination of culturable bacteria, including Vibrio, from skin swabs of European seabass and seawater and sediment at both farms. Samples were processed for isolation of bacteria and their characterization by molecular and antibiotic susceptibility tests. In both fish farms, most of the bacteria that were identified in the skin belonged to the genera Pseudomonas and Vibrio. Some of the microbiota that were identified are known to be pathogenic to fish: V. alginolyticus, V. anguillarum, and V. harveyi. Vibrio strains showed higher resistance to certain antibiotics compared to previous studies. This study provides, for the first time, information on the culturable skin bacteria that is associated with healthy European seabass under culture conditions with and without the use of antibiotics. This information will be useful in assessing how changes in culturable microbiota may affect the health of farmed European seabass, indicating a potential problem for fish health management during disease outbreaks.

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“…In dry season, tiger groupers were highly dominated by Clostridiales, which is similar to the microbiome of bluegill (Lepomis macrochirus) during late summer and fall (Ray, 2016). The diversity of bacteria during wet season was also more diverse compared to the dry season, which was believed to be correlated with the decrease of pH and salinity (Roquigny et al, 2020). Unlike Asian seabass, the raising water temperature seemed to inhibit the proliferation of Vibrionales in tiger grouper.…”

Section: Discussionmentioning

confidence: 95%

Diversity, Relative Abundance, and Functional Genes of Intestinal Microbiota of Tiger Grouper (Epinephelus fuscoguttatus) and Asian Seabass (Lates calcarifer) Reared in A Semi-Closed Hatchery in Dry and Wet Seasons

Sutra¹,

Saadu²,

Hashim³

et al. 2021

JTAS

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Grouper and Asian seabass are among the economically important cultured marine fish in Malaysia. However, fry productions in large scale tend to introduce stress that changes the fish microbiota and increases susceptibility to diseases. Currently, high-throughput sequencing is used to study fish microbiota and their respective gene functions. In this study, we investigate the diversity, abundance and functional genes of intestinal microbiota of tiger grouper and Asian seabass that were reared in a semi-closed hatchery during dry and wet seasons. Intestinal samples were collected from tiger grouper and Asian seabass of different sizes before proceeded to DNA extraction. The extracted DNA were then subjected to 16S rRNA gene amplicon sequencing using the Illumina Miseq platform targeting V3 and V4 regions for determination of the bacterial diversity, abundance and functional genes in both seasons. The results revealed that intestinal microbiota of Asian seabass were dominated by the phylum Proteobacteria and order Vibrionales in both seasons. Meanwhile, intestinal microbiome of tiger groupers were shifted from domination of phylum Firmicutes and order Clostridiales in dry season to Proteobacteria and order Lactobacillales in wet season. PICRUSt analysis revealed that the functional genes that were dominantly present were the genes encoded for metabolism, genetic information processing, environmental information processing, cellular process and human diseases. Remarkably, SIMPER analysis showed several potential metagenomics biomarker genes in dry and wet seasons. This study revealed the importance of utilizing amplicon metagenomics approaches in microbiome studies for better identification of the microbial profiling in aquaculture systems.

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Characterization of the marine aquaculture microbiome: A seasonal survey in a seabass farm

Cited by 15 publications

References 49 publications

Bacteriophages in the Control of Aeromonas sp. in Aquaculture Systems: An Integrative View

Bacteriophages in the Control of Aeromonas sp. in Aquaculture Systems: An Integrative View

Skin Culturable Microbiota in Farmed European Seabass (Dicentrarchuslabrax) in Two Aquacultures with and without Antibiotic Use

Diversity, Relative Abundance, and Functional Genes of Intestinal Microbiota of Tiger Grouper (Epinephelus fuscoguttatus) and Asian Seabass (Lates calcarifer) Reared in A Semi-Closed Hatchery in Dry and Wet Seasons

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