Characterization of the intestinal microbiota of wild caught and farmed fine flounder (Paralichthys adspersus)

Salas‐Leiva, Joan; Opazo, Rafael; Remond, Camille; Uribe, Eduardo; Vélez, Antonio; Romero, Jaime

doi:10.3856/vol45-issue2-fulltext-12

Cited by 14 publications

(13 citation statements)

References 45 publications

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“…Among the isolates, Psychrobacter candidates were particularly interesting due to the fact that Psychrobacter species are commonly observed in the aquatic environment as well as commercially important freshwater [ 54 ] and marine teleost species, e.g., Atlantic cod Gadus morhua [ 55 ], mackerel Scomber scombus [ 56 ], fine flounder Paralichthys adspersus [ 57 ] or grouper Epinephelus coioides [ 35 , 58 ]. In our study, by far the most frequent genus was Psychrobacter accounting for 70 out of 195 (35.9%) isolates based on 16S rRNA information but unfortunately this does not allow species-specific distinction.…”

Section: Discussionmentioning

confidence: 99%

Isolation and characterization of native probiotics for fish farming

et al. 2018

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BackgroundInnovations in fish nutrition act as drivers for the sustainable development of the rapidly expanding aquaculture sector. Probiotic dietary supplements are able to improve health and nutrition of livestock, but respective bacteria have mainly been isolated from terrestrial, warm-blooded hosts, limiting an efficient application in fish. Native probiotics adapted to the gastrointestinal tract of the respective fish species will establish within the original host more efficiently.ResultsHere, 248 autochthonous isolates were cultured from the digestive system of three temperate flatfish species. Upon 16S rRNA gene sequencing of 195 isolates, 89.7% (n = 175) Gram-negatives belonging to the Alpha- (1.0%), Beta- (4.1%) and Gammaproteobacteria (84.6%) were identified. Candidate probiotics were further characterized using in vitro assays addressing 1) inhibition of pathogens, 2) degradation of plant derived anti-nutrient (saponin) and 3) the content of essential fatty acids (FA) and their precursors. Twelve isolates revealed an inhibition towards the common fish pathogen Tenacibaculum maritimum, seven were able to metabolize saponin as sole carbon and energy source and two isolates 012 Psychrobacter sp. and 047 Paracoccus sp. revealed remarkably high contents of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Furthermore, a rapid and cost-effective method to coat feed pellets revealed high viability of the supplemented probiotics over 54 d of storage at 4°C.ConclusionsHere, a strategy for the isolation and characterization of native probiotic candidates is presented that can easily be adapted to other farmed fish species. The simple coating procedure assures viability of probiotics and can thus be applied for the evaluation of probiotic candidates in the future.

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Section: Discussionmentioning

confidence: 99%

Isolation and characterization of native probiotics for fish farming

et al. 2018

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“…Plates were incubated at 25°C, 30°C, and 37°C for 48 h and at 15°C for 72 h, the aim of which being to assess the widest temperature range possible. TSA medium and incubation temperature have been commonly used to isolate bacteria from fish microbiota [ 31 – 33 ]. To prevent fungus and yeast growth, a 50 μg/mL concentration of cycloheximide was added as an antifungal agent.…”

Section: Methodsmentioning

confidence: 99%

Extended antibiotic treatment in salmon farms select multiresistant gut bacteria with a high prevalence of antibiotic resistance genes

et al. 2018

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The high use of antibiotics for the treatment of bacterial diseases is one of the main problems in the mass production of animal protein. Salmon farming in Chile is a clear example of the above statement, where more than 5,500 tonnes of antibiotics have been used over the last 10 years. This has caused a great impact both at the production level and on the environment; however, there are still few works in relation to it. In order to demonstrate the impact of the high use of antibiotics on fish gut microbiota, we have selected four salmon farms presenting a similar amount of fish of the Atlantic salmon species (Salmo salar), ranging from 4,500 to 6,000 tonnes. All of these farms used treatments with high doses of antibiotics. Thus, 15 healthy fish were selected and euthanised in order to isolate the bacteria resistant to the antibiotics oxytetracycline and florfenicol from the gut microbiota. In total, 47 bacterial isolates resistant to florfenicol and 44 resistant to oxytetracycline were isolated, among which isolates with Minimum Inhibitory Concentrations (MIC) exceeding 2048 μg/mL for florfenicol and 1024 μg/mL for oxytetracycline were found. In addition, another six different antibiotics were tested in order to demonstrate the multiresistance phenomenon. In this regard, six isolates of 91 showed elevated resistance values for the eight tested antibiotics, including florfenicol and oxytetracycline, were found. These bacteria were called “super-resistant” bacteria. This phenotypic resistance was verified at a genotypic level since most isolates showed antibiotic resistance genes (ARGs) to florfenicol and oxytetracycline. Specifically, 77% of antibiotic resistant bacteria showed at least one gene resistant to florfenicol and 89% showed at least one gene resistant to oxytetracycline. In the present study, it was demonstrated that the high use of the antibiotics florfenicol and oxytetracycline has, as a consequence, the selection of multiresistant bacteria in the gut microbiota of farmed fish of the Salmo salar species at the seawater stage. Also, the phenotypic resistance of these bacteria can be correlated with the presence of antibiotic resistance genes.

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“…Despite the importance of the gut microbiota in the fitness of wild and farmed animals, as seen for salmonids in Section 4, few studies have characterized the microbiota composition of farmed and wild fish and shellfish that are commonly consumed in Chile [107, [116][117][118][119][120][121]. Most of the best characterized microbiota corresponds to foreign species such as Atlantic salmon and rainbow trout, in agreement with their economic and social importance.…”

Section: Metagenomics In the Study Of Microbiota Of Wild And Farmed Fmentioning

confidence: 99%

“…In both cases, bacteria belonging to the phylum Proteobacteria were the most abundant group in wild specimens, while under aquaculture conditions, members of the phylum Firmicutes predominated. Under aquaculture conditions, the fine flounder shows a reduction of Actinobacteria, a group known to produce antimicrobial compounds [117,119]. Further, metagenomic characterization of the microbiota through the complete sequencing of all the microbial genomes is necessary to properly predict the function of the microorganisms that colonize wild or farmed fishes and so to have a better approach to the evolution of the host-microbiota relationship in Seriola lalandi and Paralichthys adspersus.…”

Section: Metagenomics In the Study Of Microbiota Of Wild And Farmed Fmentioning

confidence: 99%

Application of Metagenomics to Chilean Aquaculture

Tello¹,

Valdés²,

Vargas³

et al. 2020

Metagenomics - Basics, Methods and Applications

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Aquaculture is a rapidly expanding food production sector, facing the challenge of growth both increasing its efficiency and reducing its negative impact on the environment. Metagenomics is an emerging tool in aquaculture that helps to understand the complex host (fish-shellfish)-microbiota-pathogen-environment relationship underlying disease outbreaks, monitoring the dynamics of microbial diversity in farmed animals subject to different environmental conditions or perturbations. As Chile takes an important share of world aquaculture market, this chapter reviews the actual and potential applications of metagenomics to support a sustainable expansion and diversification of Chilean aquaculture. The focus is on (i) the role and function of the gut microbiota in the proper immunostimulation and disease control and (ii) the role of metagenomics in monitoring environmental microbial biodiversity and dynamics in relation to disease persistence and ecosystem stability. We conclude that despite the importance of the aquaculture sector in Chile, the application of metagenomics to deal with disease control and ecosystem preservation is still an emerging field of study. Understanding host (fish-shellfish)microbiota-pathogen-environment diversity of interactions in a more holistic view, i.e., the holobiome approach, could be key to develop rational strategies to improve productivity by increasing resistance to diseases and reducing the use of antibiotics and their negative environmental impact.

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Characterization of the intestinal microbiota of wild caught and farmed fine flounder (Paralichthys adspersus)

Cited by 14 publications

References 45 publications

Isolation and characterization of native probiotics for fish farming

Isolation and characterization of native probiotics for fish farming

Extended antibiotic treatment in salmon farms select multiresistant gut bacteria with a high prevalence of antibiotic resistance genes

Application of Metagenomics to Chilean Aquaculture

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