Abstract
During a study aiming at isolation and genomic characterization of non-pathogenic fish symbionts, strain F-328T was isolated from skin mucus of healthy-seeming rainbow trout (Oncorhynchus mykiss) and subjected to polyphasic characterization, including a comprehensive genome analysis. Strain F-328T was Gram stain negative, none-gliding, strictly aerobic, and rod shaped. The 16S rRNA gene sequence of strain F-328T exhibited the highest level of identity (98.9%) with F. turcicum F-339T. The major fatty acids were iso-C15:0, C15:1 ω6c, and summed feature 3 (C16:1 ω7c, C16:1 ω6c). The polar lipid profile consisted mainly of phosphatidylethanolamine and aminolipids, while the predominant menaquinone was MK-6. The DNA G + C content and genome size of the strain were 35.3% and 3.4 Mb, respectively. Strain F-328T shows 93.8% average nucleotide identity and 53% digital DNA–DNA hybridization identity with the closest type strain F. turcicum F-339T. In addition, strain F-328T was found to carry antimicrobial resistance genes, which confer resistance to several antimicrobials, including aminoglycoside, macrolides, and streptogramin. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain F-328T should be classified as a novel species of the genus Flavobacterium for which the name Flavobacterium erciyesense sp. nov. is proposed, with F-328T as the type strain (= JCM 34201T = KCTC 82261T).
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Acknowledgements
This research was supported by The Research Fund of Erciyes University (Project Number: THD-2021-10873). The author also thanks Dr. Hilal Ay and Dr. Muhammed Duman for technical advice and support.
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There is no ethical issue associated with this manuscript because the presented data were obtained during routine diagnostics in the rainbow trout. Only the skin mucus layer was sampled without harming any fish. According to competent authorities, this kind of research does not require ethics approval or general approval with respect to Turkish law.
Nucleotide sequence accession numbers
The GenBank/EMBL/DDBJ Accession Numbers for the nucleotide sequences reported in this study are as follows: MW898288 (strain Flavobacterium erciyesense F-328T) for the 16S rRNA gene. The Accession Number for the draft whole-genome sequences of strain F. erciyesense F-328T is JAGPXB000000000. The version described in this paper is the first version.
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Supplementary Fig. S1 The morphological characters of strain F-328T observed on the R2A plate after incubation at 25°C for 72h. Colony (A), Gram staining (B), and Transmission Electron Microscopy (TEM) image (C) of the strain (PNG 732 KB)
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Supplementary Fig. S2 Polar lipid profile of strain F-328T identified on two-dimensional thin-layer chromatography; PE, phosphatidylethanolamine; AL, amino-lipid; L, unidentified lipid. Solvent 1: chloroform: methanol: distilled water (65:25:4); solvent 2: chloroform: glacial acetic acid: methanol: distilled water (80:12:15:4) (PNG 732 KB)
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Supplementary Fig. S3 Delineation of Flavobacterium erciyesense sp. nov. based on GBDP phylogenetic analyses retrieved from the TYGS website. Tree inferred with FastME 2.1.6.1 from GBDP distances calculated from genome sequences. Branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values >60% from 100 replications, with an average branch support of 91.6%. The tree was rooted at the midpoint. Legend to the squares is shown in the right-hand side columns. Species cluster: Strains of the same species cluster are indicated with the same color. Subspecies cluster: Strains of the same subspecies cluster are indicated with the same color. Delta statistics: δ values, overall tree likeness (PNG 732 KB)
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Supplementary Fig. S4 Genome alignment between strain F. erciyesense F-328T and F. turcicum F-339T. Each contiguously colored locally collinear block (LCB) represents regions of significant synteny between the strains. Colored lines between genomes indicate orthologous LCBs (PDF 103 KB)
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Saticioglu, I.B. Flavobacterium erciyesense sp. nov., a putative non-pathogenic fish symbiont. Arch Microbiol 203, 5783–5792 (2021). https://doi.org/10.1007/s00203-021-02566-2
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DOI: https://doi.org/10.1007/s00203-021-02566-2