Browsing by Author "Ay, Hilal"
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Publication Flavobacterium bernardetii sp. nov., a possible emerging pathogen of farmed rainbow trout (Oncorhynchus mykiss) in cold water(Elsevier, 2021-04-08) Satıcıoğlu, İzzet Burçin; Ay, Hilal; Altun, Soner; Şahin, Nevzat; Duman, Muhammed; ALTUN, SONER; DUMAN, MUHAMMED; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı; 0000-0001-7707-2705; 0000-0001-9096-875X; T-1697-2019; AAG-8518-2021Identification of novel Flavobacterium species from fish samples has growing importance due to their notorious effects on freshwater fish species. During the course of studying farmed rainbow trout (Oncorhynchus mykiss, Walbaum, 1792) samples exhibiting clinical signs in Rize, Turkey, two isolates were recovered, and their taxonomic positions were revealed based on a genome-based polyphasic taxonomy approach. Pairwise sequence analyses of the 16S rRNA genes confirmed that strains F-372T and F-408 belonged to the genus Flavobacterium. Strain F-372T exhibited the highest identity level of 98.37% with Flavobacterium terrigena DSM 17934T (=KCTC 12761T) while the 16S rRNA gene sequence identity between strain F-372T and F-408 was 99.8% A polyphasic taxonomy approach including phenotypic characterization as well as genomic and chemotaxonomic analyses was employed to confirm the novelty of the strains in the genus Flavobacterium. The major fatty acids were isoC15:0 and C15:1 omega 6c for both strains while their predominant menaquinone was MK-6. Both strains have genome size of 3.3 Mb. The genomic DNA G + C content of the strains was 30.89 mol%. In addition, strain F-372T was found to carry 68 high confidence (HC) functional genes encoding AMR and virulence factors implying a possible correlation between those factors and mortality in the rainbow trout. Phylogenomic analysis and whole genome nucleotide sequences confirmed that the isolates represent a new species for which the name Flavobacterium bernardetii sp. nov. is proposed, with F-372T as the type strain (=JCM 34204T = KCTC 82264 T).Publication Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout(Microbiology Soc, 2021-01-01) Duman, Muhammed; Ay, Hilal; Altun, Soner; Şahin, Nevzat; Satıcıoğlu, İzzet Burçin; DUMAN, MUHAMMED; ALTUN, SONER; Uludağ Üniversitesi/Veteriner Fakültesi/Su Ürünleri Hastalıkları Anabilim Dalı; 0000-0001-7707-2705; 0000-0001-9096-875X; AAG-8518-2021; T-1697-2019Two yellow-pigmented isolates, F-60(T) and F-392, were isolated from the internal organs of an apparently healthy rainbow trout (Oncorhynchus mykiss). The strains were identified as members of the genus Flavobacterium based on the results of 16S rRNA gene sequence analysis. Strains F-60(T) and F-392 had the highest 16S rRNA gene sequence identity level of 97.4% to the type strain of Flavobacterium crassostreae LPB0076(T). A polyphasic taxonomic approach including phenotypic, chemotaxonomic and genomic characterization was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity based on BLAST (ANIb) values for strains F-60(T) and F-392 were calculated as 100%. However, dDDH and ANI analyses between the strains and their close neighbours confirmed that both strains represent a novel species in the genus Flavobacterium. The strains shared the highest dDDH and ANIb levels of 23.3 and 77.9%, respectively, with the type strain of Flavobacterium frigidarium DSM 17623(T) while those values for F crassostreae LPB0076(T) were obtained as 21.4-21.5% and 76.3%. The DNA G+C content of the strains was 34.5 mol%. Chemotaxonomic and phylogenomic analyses of these isolates confirmed that both strains are representatives of a novel species for which the name Flavobacterium muglaense sp. nov. is proposed, with F-60(T) as the type strain (=JCM 34196(T) =KCIC 82256(T)).Publication Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey(Elsevier, 2021-02) Satıcıoğlu, İzzet Burçin; Ay, Hilal; Altun, Soner; Duman, Muhammed; Şahin, Nevzat; ALTUN, SONER; DUMAN, MUHAMMED; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Ürünleri Hastalıkları Anabilim Dalı; 0000-0001-9096-875X; 0000-0001-7707-2705; AAG-8518-2021; T-1697-2019During a study on culturable microorganisms from fish farms, four yellow-pigmented gram negative, rod shaped isolates, F-47(T), F-339(T), F-380 and F-400, were recovered from rainbow trout samples exhibiting clinical signs. Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Flavobacterium. Strains F-47(T) and F-380 shared the highest 16S rRNA gene sequence identity level of 97.6% with the type strain of Flavobacterium frigoris DSM 15719(T) while strains F-339(T) and F-400 shared the highest identity level of 97.6% with the type strain of F. caseinilyticum AT-3-2(T). A polyphasic taxonomic approach including phenotypic and genomic characterization as well as whole-cell MALDI-TOF mass spectrometry analyses was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains F-47(T), F-339(T) and their close neighbours F. frigoris DSM 15719(T) and F. caseinilyticum AT-3-2(T), respectively, confirmed that both strains represent novel species in the genus Flavobacterium. The DNA G+C contents of the strains F-47(T) and F-339(T) are 34.3% and 35.3%, respectively. It can be concluded on the basis of polyphasic characterization as well as pairwise genome comparisons that the strains F-47(T) and F-339(T) represent two novel species within the genus Flavobacterium, for which Flavobacterium kayseriense sp. nov. F-47(T) (=JCM 34195(T)=KCTC 82255(T)) and Flavobacterium turcicum sp. nov. F-339(T) (=JCM 34202(T)=KCTC 82262(T)) are proposed, respectively.