Browsing by Author "Ay, Hilal"

Now showing 1 - 8 of 8

Description of a novel fish pathogen, plesiomonas shigelloides subsp. oncorhynchi , isolated from rainbow trout ( oncorhynchus mykiss ): First genome analysis and comparative genomics
(Mdpi, 2023-04-01) Valdes, Elena Garcia; Ay, Hilal; Altun, Soner; SATICIOĞLU, İZZET BURÇİN; DUMAN, MUHAMMED; Duman, Muhammed; Altun, Soner; ALTUN, SONER; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; 0000-0001-7707-2705; 0000-0002-2721-3204; AAD-4156-2019
Plesiomonas shigelloides is the only species in its genus, and has zoonotic importance due to the serious implications resulting from the consumption of contaminated seafood. This is the first report on the genomic features of the whole-genome sequence (WGS) of P. shigelloides strain V-78, recovered from diseased rainbow trout, Oncorhynchus mykiss. The genome of P. shigelloides V-78 consists of 4,478,098 base pairs (bp), which encode 3730 proteins, and has a G + C content of 51.1%. The bioinformatics analysis of WGS of V-78 confirmed the presence of 121 tRNA genes and 42 rRNA genes (15 genes for 5S rRNA, 13 genes for 16S rRNA, and 14 genes for 23S rRNA). Comprehensive genome analyses revealed that the strain encodes for secondary metabolites, antimicrobial resistance, and virulence genes. The strain V-78 has 31 known antibiotic resistance models, which encode many antimicrobial resistances. In addition, strain V-78 has 42 different virulence genes, such as adhesion, secretion system, and motility. The digital DNA-DNA hybridization value against P. shigelloides NCTC 10360 was 74.2%, while the average nucleotide identity value was 97.1%. Based on the scrutinized analysis of genomic data, strain V-78 should be considered a novel subspecies of P. shigelloides, for which Plesiomonas shigelloides subsp. oncorhynchi is proposed.
Description of the two novel species of the genus Helicobacter: Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., isolated from feces of urban wild birds
(Elsevier Gmbh, 2022-05-13) Aydın, Fuat; Ay, Hilal; Kayman, Tuba; Karakaya, Emre; Abay, Seçil; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu; AAD-4156-2019
A total of 26 Gram-negative, motile, gently curved, and rod-shaped isolates were recovered, during a study to determine the faeco-prevalence of Helicobacter spp. in urban wild birds. Pairwise comparisons of the 16S rRNA gene sequences indicated that these isolates belonged to the genus Helicobacter and phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolates were separated into two divergent groups. The first group consisted of 20 urease-positive isolates sharing the highest 16S rRNA gene sequence identity levels of 98.5-98.6% to H. mustelae ATCC 43772(T), while the second group contained six urease-negative isolates with the sequence identity level of 98.5% to the type strain of H. pametensis ATCC 51478(T). Five isolates were chosen and subjected to comparative whole-genome analysis. The phylogenetic analysis of the 16S rRNA, gyrA and atpA gene sequences showed that Helicobacter isolates formed two separate phylogenetic clades, differentiating the isolates from the other Helicobacter species. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains faydin-H8(T), faydin-H23(T) and their close neighbors H. anseris MIT 04-9362(T) and H. pametensis ATCC 51478(T), respectively, confirmed that both strains represent novel species in the genus Helicobacter. The DNA G+C contents of the strains faydin-H8(T) and faydin-H23(T) are 32.0% and 37.6%, respectively. The results obtained for the characterization of the wild bird isolates indicate that they represent two novel species, for which the names Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., are proposed, with faydin-H8(T)(=LMG 32237(T) = DSMZ 112312(T)) and faydin-H23(T)(=LMG 32236(T) = CECT 30508(T)) as respective type strains.
Description of the two novel species of the genus Helicobacter: Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., isolated from feces of urban wild birds (vol 45, 126326, 2022)
(Elsevier Gmbh, 2022-11-12) Aydın, Fuat; Ay, Hilal; Kayman, Tuba; Karakaya, Emre; Abay, Seçil; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu.; AAD-4156-2019
A total of 26 Gram-negative, motile, gently curved, and rod-shaped isolates were recovered, during a study to determine the faeco-prevalence of Helicobacter spp. in urban wild birds. Pairwise comparisons of the 16S rRNA gene sequences indicated that these isolates belonged to the genus Helicobacter and phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolates were separated into two divergent groups. The first group consisted of 20 urease-positive isolates sharing the highest 16S rRNA gene sequence identity levels of 98.5-98.6% to H. mustelae ATCC 43772(T), while the second group contained six urease-negative isolates with the sequence identity level of 98.5% to the type strain of H. pametensis ATCC 51478(T). Five isolates were chosen and subjected to comparative whole-genome analysis. The phylogenetic analysis of the 16S rRNA, gyrA and atpA gene sequences showed that Helicobacter isolates formed two separate phylogenetic clades, differentiating the isolates from the other Helicobacter species. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains faydin-H8T, faydin-H23(T) and their close neighbors H. anseris MIT 04-9362T and H. pametensis ATCC 51478(T), respectively, confirmed that both strains represent novel species in the genus Helicobacter. The DNA G + C contents of the strains faydin-H8(T) and faydin-H23T are 32.0% and 37.6%, respectively. The results obtained for the characterization of the wild bird isolates indicate that they represent two novel species, for which the names Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., are proposed, with faydin-H8T (=LMG 32237(T) = DSM 112312(T)) and faydin-H23(T) (=LMG 32236(T) = CECT 30508(T)) as respective type strains.
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-8518-2021
Identification 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).
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-1697-2019
Two 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)).
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-1697-2019
During 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.
Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey
(Elsevier Gmbh, 2022-11-18) Satıcıoğlu, İzzet Burçin; Ay, Hilal; Altun, Soner; Duman, Muhammed; SATICIOĞLU, İZZET BURÇİN; ALTUN, SONER; DUMAN, MUHAMMED; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; AAD-4156-2019; AAG-8518-2021; DYJ-5986-2022
Four strains, designated as C-2, C-17T, C-39T and Ch-15, were isolated from farmed rainbow trout samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089T while strains C-2, C-39T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic prove-nance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17T, C-39T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17T and C-39T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid qui -none and the presence of iso-C15:0 as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 - 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have antimicrobial resistance genes, prophages and horizontally acquired genes in addition to sec-ondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17T and C-39T are representatives of two novel species within the genus Chryseobacterium, for which the names Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. with the type strains C-17T (=JCM 34190T = KCTC 82250T) and C-39T (=JCM 34191T = KCTC 822251T), respectively, are proposed.
Shewanella oncorhynchi sp. nov., a novel member of the genus shewanella, isolated from rainbow trout (oncorhynchus mykiss)
(Microbiology Soc, 2022-01-01) Ay, Hilal; ALTUN, SONER; Duman, Muhammed; DUMAN, MUHAMMED; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu.; 0000-0001-7707-2705; 0000-0002-2721-3204; T-1697-2019; AAG-8518-2021 ; AAD-4156-2019
A strain, S-1(T) was isolated from rainbow trout (Oncorhynchus mykiss) exhibiting clinical symptoms of lens atrophy, inappetence, visual impairment and growth retardation. The strain was identified as representing a member of the genus Shewanella on the basis of the results of 16S rRNA gene sequence analysis. The neighbor-joining phylogenetic tree based on 16S rRNA gene sequences indicated that S-1(T) clustered with Shewanella putrefaciens JCM 20190(T), Shewanella profunda DSM 15900(T), and Shewanella hafniensis P010(T), sharing 99.3, 98.8 and 87.7% 16S rRNA gene similarities, respectively. A polyphasic taxonomic approach including phenotypic, chemotaxonomic, and genomic characterization was employed to ascertain the taxonomic position of S-1(T) within the genus Shewanella. The overall genome relatedness indices (OGRI) for S-1(T) compared with the most closely related type strains S. hafniensis ATCC BAA-1207(T), Shewanella baltica NCTC 10735(T), S. putrefaciens ATCC 8071(T) and S. profunda DSM 15900(T) were calculated as 40.8, 40.1, 28.5 and 27.3% for digital DNA-DNA hybridization (dDDH), and 91.6, 91.0, 86.3 and 85.1% for average nucleotide identity (ANI), respectively. OGRI values between S-1(T) and its close neighbours confirmed that the strain represents a novel species in the genus Shewanella. The DNA G+C content of the strain is 45.2%. Major fatty acids were C-17:1.8 omega 8c, C(15:0)iso, and summed feature 3 (C-16:1 omega 6c and/or C-16:1 omega 7c). The predominant polar lipids were phosphatidylethanolamine, phospholipid, amino-phospholipid and unidentified lipids. The major respiratory quinones were ubiquinone-8, ubiquinone-7 and menaquinone-7. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Shewanella oncorhynchi sp. nov. is proposed, with S-1(T) as the type strain (JCM 34183(T)= KCTC 82249(T)).