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"study-abstract": "Metagenomic raw reads, assemblies, and bins derived from HoloFood salmon gut samples from trial A and B. The samples in this project contributed to the salmon MAG catalogue (project: PRJEB55376 [ERP140265]).",
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"study-abstract": "Fish intestinal mycobiota are hitherto poorly characterized. Using next generation sequencing, we have profiled the intestinal mycobiota of wild caught, laboratory-reared and wild-caught-laboratory-kept zebrafish, which contained more than 15 fungal classes. In wild zebrafish, mycobiota comprised mainly Dothideomycetes, whereas saprotrophic Saccharomycetes were predominant in their laboratory-reared counterparts. This pioneer study shed light into differences in intestinal fungal communities of wild-caught and laboratory-reared zebrafish, thus enriching our knowledge on fish mycobiota.",
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"study-abstract": "Prebiotics are food/feed additives intended to sculpt gut microbial communities as they are selectively utilized by the microorganisms to exert beneficial health effects on hosts. Macroalga-derived oligosaccharides are potential prebiotics, and herein, we determined the effects of Laminaria sp.-derived alginate oligosaccharide (AlgOS) on the distal intestinal microbiota of Atlantic salmon (Salmo salar). Using a high-throughput 16S rRNA gene amplicon sequencing technique, we investigated the microbiota harboured in the intestinal content and mucus of Atlantic salmon offered feeds supplemented with 0.5 and 2.5% AlgOS. We found that AlgOS shifts the intestinal microbiota profile; alpha diversity was significantly reduced with 2.5% AlgOS while with 0.5% AlgOS the alteration occurred without impacting the bacterial diversity. Beta diversity showed a significant difference between control and AlgOS-fed groups. AlgOS supplementation facilitated the dominance of Proteobacteria and Spirochaetes, promoting the growth of presumed butyrate producers in the intestine. In addition, 0.5% AlgOS stimulated certain bacteria belonging to Proteobacteria, Spirochaetes and Actinobacteria. This indicates that the low inclusion of AlgOS can plausibly induce a prebiotic effect on the distal intestinal microbiota of Atlantic salmon. These results are expected to generate further interest in the potential of macroalgae-derived oligosaccharides as prebiotics for food and feed applications. ",
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"secondary-accession": "ERP107355",
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"study-abstract": "This study aimed to evaluate the potential beneficial effects of SCFAs, used as a feed additive, on intestinal microbiota composition. For this purpose, a specific combination of short and medium chain fatty acids was tested in juvenile gilthead sea bream (Sparus aurata) fed a plant-based diet. The Illumina MiSeq platform for high-throughput amplicon sequencing of 16S rRNA gene, and QIIME pipeline were used to analyse and characterize the whole microbiome associated to both, feeds and S.aurata intestine. In summary our findings clearly indicated that SCFAs positively modulated the fish intestinal microbiota by increasing the number of beneficial lactic acid bacteria, namely Lactobacillus, and reducing Gammaproteobacteria that include several potential pathogenic bacteria.",
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"study-abstract": "Intestinal microbiota is a complex ecosystem and plays an important role in host biology. More and more researches focus on the bacterial community of the host intestine. However, there is still limited information on a better understanding of fish intestinal microbiota. Due to the importance of grass carp in aquaculture of China, it is necessary to pay attention to its intestinal microbiota. In this study, the composition of bacterial communities in intestinal contents and mucosa of grass carp was analyzed by 454 pyrosequencing.",
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