ArticleMicrobiologyOpen2019
Full-length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis.
Article in MicrobiologyOpen, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Intestinal Microbial Profiles of Wild Zobaidy (Current issues in molecular biology · 2025Article
- Novel biomarker identification for oral squamous cell carcinoma development in nonsmoker, nondrinker, and nonchewer patients using third-generation sequencing of oral microbiome.Journal of oral microbiology · 2025Article
- Effect of the 16S rRNA Gene Hypervariable Region on the Microbiome Taxonomic Profile and Diversity in the Endangered FishMicroorganisms · 2024Article
- Comparison of the full-length sequence and sub-regions of 16S rRNA gene for skin microbiome profiling.mSystems · 2024Article
- The use of different 16S rRNA gene variable regions in biogeographical studies.Environmental microbiology reports · 2023Article
- Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems.Environmental microbiome · 2023Article
- AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.PloS one · 2023Article
- Comparison of rectum fecal bacterial community of finishing bulls fed high-concentrate diets with active dry yeast and yeast culture supplementation.Animal bioscience · 2023Article
- Heterogeneity of the Tissue-specific Mucosal Microbiome of Normal Grass Carp (Ctenopharyngodon idella).Marine biotechnology (New York, N.Y.) · 2022Article
- Alterations in the rumen bacterial communities and metabolites of finishing bulls fed high-concentrate diets supplemented with active dry yeast and yeast culture.Frontiers in microbiology · 2022Article
- 16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences.Frontiers in bioinformatics · 2022Article
- Tannic acid supplementation in the diet of Holstein bulls: Impacts on production performance, physiological and immunological characteristics, and ruminal microbiota.Frontiers in nutrition · 2022Article
- Comparative analysis of human facial skin microbiome between topical sites compared to entire face.Genes & genomics · 2021Article
- Molecular mechanisms of heavy metals resistance of Stenotrophomonas rhizophila JC1 by whole genome sequencing.Archives of microbiology · 2021Article
- Differences in the intestinal microbiota between insecticide-resistant and -sensitive Aedes albopictus based on full-length 16S rRNA sequencing.MicrobiologyOpen · 2021Article
- The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology.Scientific reports · 2021Article
- Fermented Soybean Meal Replacement in the Diet of Lactating Holstein Dairy Cows: Modulated Rumen Fermentation and Ruminal Microflora.Frontiers in microbiology · 2021Article
- Comparative analysis and gut bacterial community assemblages of grass carp and crucian carp in new lineages from the Dongting Lake area.MicrobiologyOpen · 2020Article
- Full-length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis.MicrobiologyOpen · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding fish-microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community associated with the rearing systems and fish surfaces. Accurate methods to generate and analyze these microbial communities would be an important tool to help improve understanding of microbial effects in the industry. In this study, we performed taxonomic classification and determination of operational taxonomic units on Atlantic salmon microbiota by taking advantage of full-length 16S rRNA gene sequences. Skin mucus was dominated by the genera Flavobacterium and Psychrobacter. Intestinal samples were dominated by the genera Carnobacterium, Aeromonas, Mycoplasma and by sequences assigned to the order Clostridiales. Applying Sanger sequencing on the full-length bacterial 16S rRNA gene from the pool of 46 isolates obtained in this study showed a clear assignment of the PacBio full-length bacterial 16S rRNA gene sequences down to the genus level. One of the bottlenecks in comparing microbial profiles is that different studies use different 16S rRNA gene regions. Comparisons of sequence assignments between full-length and in silico derived variable 16S rRNA gene regions showed different microbial profiles with variable effects between phylogenetic groups and taxonomic ranks.
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