The biogeography of the atlantic salmon (<i>Salmo salar</i>) gut microbiome

Llewellyn, Martin S.; McGinnity, P.; Dionne, Mélanie; Létourneau, Justine; Thonier, Florian; Carvalho, Gary R.; Creer, Simon; Derôme, Nicolas

doi:10.1038/ismej.2015.189

Cited by 326 publications

(431 citation statements)

References 19 publications

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“…This observation has been confirmed by many researchers since then (Abid et al ; Green et al ; Zarkasi et al ; Lowrey et al ; Ozorio et al ; Llewellyn et al . ; Villasante et al ). The absence of this group of bacteria in the early studies could be explained by difficulties of their cultivation on artificial medias.…”

Section: Discussionmentioning

confidence: 97%

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish

Parshukov

Kashinskaya

Simonov

et al. 2019

J of Applied Microbiology

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Aims The aim of the present study was to investigate the composition of the intestinal microbiota during the acute stage of a bacterial infection to understand how dysbiosis of the gut may influence overall taxonomic hierarchy and diversity, and determine if there exists a bacterial taxon(s) that serve as markers for healthy or diseased rainbow trout (Oncorhynchus mykiss). Methods and Results From July to September 2015, 29 specimens of 3‐year‐old (an average weight from 240·9 ± 37·7 to 850·7 ± 70·1 g) rainbow trout O. mykiss were studied. Next‐generation high‐throughput sequencing of the 16S ribosomal RNA genes was applied to stomach and intestinal samples to compare the impact of infection status on the microbiota of rainbow trout O. mykiss (Walbaum) from the northwest part of Eurasia (Karelian region, Russia). The alpha diversity (Chao1, Simpson and Shannon index) of the microbial community of healthy rainbow trout was significantly higher than in unhealthy fish. The greatest contribution to the gut microbial composition of healthy fish was made by OTU's belonging to Bacillus, Serratia, Pseudomonas, Cetobacterium and Lactobacillus. Microbiota of unhealthy fish in most cases was represented by the genera Serratia, Bacillus and Pseudomonas. In microbiota of unhealthy fish there were also registered unique taxa such as bacteria from the family Mycoplasmataceae and Renibacterium. Analysis of similarities test revealed the significant dissimilarity between the microbiota of stomach and intestine (P ≤ 0·05). Conclusions A substantial finding was the absence of differences between microbial communities of the stomach and intestine in the unhealthy groups if compared with healthy fish. Significance and Impact of the Study These results demonstrated alterations of the gut microbiota of farmed rainbow trout, O. mykiss during co‐infections and can be useful for the development of new strategies for disease control programs.

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Section: Discussionmentioning

confidence: 97%

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish

Parshukov

Kashinskaya

Simonov

et al. 2019

J of Applied Microbiology

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“…Mycoplasma spp. are frequently dominant in the intestines of adult, but not juvenile or larval, salmon in the wild (Llewellyn et al, 2016), but they have only rarely been associated with disease in fish. A novel species of Mycoplasma, Mycoplasma mobile , was previously isolated from the gills of tench ( Tinca tinca ) fish with “red disease” and subsequently characterized (Kirchhoff et al, 1987; Kirchhoff & Rosengarten, 1984).…”

Section: Discussionmentioning

confidence: 99%

Transmission of a common intestinal neoplasm in zebrafish by cohabitation

Burns

Watral

Sichel

et al. 2017

Journal of Fish Diseases

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Intestinal neoplasms are common in zebrafish (Danio rerio) research facilities. These tumours are most often seen in older fish and are classified as small cell carcinomas or adenocarcinomas. Affected fish populations always contain subpopulations with preneoplastic lesions, characterized by epithelial hyperplasia or inflammation. Previous observations indicated that these tumours are unlikely caused by diet, water quality or genetic background, suggesting an infectious aetiology. We performed five transmission experiments by exposure of naïve fish to affected donor fish by cohabitation or exposure to tank effluent water. Intestinal lesions were observed in recipient fish in all exposure groups, including transmissions from previous recipient fish, and moribund fish exhibited a higher prevalence of neoplasms. We found a single 16S rRNA sequence, most similar to Mycoplasma penetrans, to be highly enriched in the donors and exposed recipients compared to unexposed control fish. We further tracked the presence of the Mycoplasma sp. using a targeted PCR test on individual dissected intestines or faeces or tank faeces. Original donor and exposed fish populations were positive for Mycoplasma, while corresponding unexposed control fish were negative. This study indicates an infectious aetiology for these transmissible tumours of zebrafish and suggests a possible candidate agent of a Mycoplasma species.

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“…Similarly, Llewellyn et al . () determined that the gut microbiome structure of Atlantic salmon ( S. salar ) was influenced by life cycle stage and not by geography. Despite migration between freshwater and marine habitats, adult salmon returning to rivers maintained many of the bacterial taxa associated with marine adults, and members of the Mycoplasmataceae were present throughout life stages.…”

Section: Factors Influencing Fish Gut Microbiome Structurementioning

confidence: 99%

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

et al. 2017

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Summary The gut microbiome of vertebrates plays an integral role in host health by stimulating development of the immune system, aiding in nutrient acquisition and outcompeting opportunistic pathogens. Development of next‐generation sequencing technologies allows researchers to survey complex communities of microorganisms within the microbiome at great depth with minimal costs, resulting in a surge of studies investigating bacterial diversity of fishes. Many of these studies have focused on the microbial structure of economically significant aquaculture species with the goal of manipulating the microbes to increase feed efficiency and decrease disease susceptibility. The unravelling of intricate host–microbe symbioses and identification of core microbiome functions is essential to our ability to use the benefits of a healthy microbiome to our advantage in fish culture, as well as gain deeper understanding of bacterial roles in vertebrate health. This review aims to summarize the available knowledge on fish gastrointestinal communities obtained from metagenomics, including biases from sample processing, factors influencing assemblage structure, intestinal microbiology of important aquaculture species and description of the teleostean core microbiome.

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The biogeography of the atlantic salmon (Salmo salar) gut microbiome

Cited by 326 publications

References 19 publications

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish

Transmission of a common intestinal neoplasm in zebrafish by cohabitation

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

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