Person: DUMAN, MUHAMMED
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MUHAMMED
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Publication Population genetic and evolution analysis of vibrio isolated from Turkish fish farms(Elsevier, 2022-08-27) Bujan, Noemi; Romalde, Jesus L.; DUMAN, MUHAMMED; Altun, Soner; ALTUN, SONER; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Keleş Meslek Yüksekokulu; 0000-0001-7707-2705; 0000-0003-4786-4773; 0000-0002-2721-3204; T-1697-2019; AAD-4156-2019The genus Vibrio includes important pathogenic species for human and aquatic organisms such as Vibrio cholera, V. parahaemolyticus, V. vulnificus, V. anguillarum or V. harveyi. At present, Vibrionaceae family consists of > 190 described species, classified into nine genera. Vibrio are widespread in shellfish, finfish and marine ecosystems and show resourceful ecologies, which recognized as one of the most diverse bacterial groups for illuminating the genome evolution. In the present study, to clarify the relationship among aquatic species in the genus, a multilocus sequence analysis (MLSA) and typing (MLST) approach was applied to characterize 51 Vibrio isolates from Turkish fish farms, 146 strains deposited in the PubMLST database and 59 type strains from GenBank. For all studied isolates (n = 256), diversity analysis, population structure, determination of recombination, demographic history and gene flow were performed based on the MLST scheme. Vibrio isolates, subjected to the study, showed a high diversity within the Vibrio population and also genetic interactions into the genus. We found 17 new described sequence types by MLST analysis that were isolated from rainbow trout, sea bream and sea bass in Turkish fish farms, which clearly indicate that the genes underwent recombination frequently. While predominant sequence types were found in the presented study, differences of genotypes need to be evaluated in a disease situation or preventing measurements. The findings about genetic recombination possibly helps to understand differences of Vibrio infections in fish. Furthermore, elucidating of genetic variability within species shed light on providing effective measurements in aquaculture by vaccine production and drug applications.Publication First occurrence and whole-genome comparison of Pseudomonas haemolytica isolated in farmed rainbow trout(Wiley, 2022-06-23) Burçin Satıcıoğlu, İzzet; Mulet, Magdalena; Duman, Muhammed; Altun, Soner; Gomila, Margarita; Lalucat, Jorge; Garcia-Valdes, Elena; DUMAN, MUHAMMED; ALTUN, SONER; Veteriner Fakültesi; Su Hayvanları Hastalıkları Ana Bilim Dalı; 0000-0001-7707-2705; AAG-8518-2021; T-1697-2019The isolation of Pseudomonas haemolytica from different habitats as well as its distribution over a wide geographical area, possible reservoir role for antibiotic resistance and zoonotic potential, all require the detailed characterization of P. haemolytica strains. In the present study, we describe 18 phenotypically similar strains isolated from the rainbow trout, Oncorhynchus mykiss (Walbaum, 1792). The strains were collected from seemingly healthy, symptomatic or moribund rainbow trout of all sizes, from fry to broodstock. The strains were morphologically, phenotypically (API20 NE and VITEK 2) and chemotaxonomically characterized by their methyl-fatty acid content (FAME), and mass spectrometry (MALDI-TOF) by their protein profiles. The 16S rRNA sequence similarity values grouped them into the Pseudomonas fluorescens phylogenetic group of species. The 18 strains were compared to 6 other previously described P. haemolytica strains, 2 of which were isolated from milk products and 4 from chicken products. A multilocus sequence analysis was performed for all strains. Strain P45 was selected to represent the 18 new isolates for genomic comparisons by ANIb, and GGDC was used to confirm the identification at species level. The presence of genes related to antimicrobial resistance, secretion systems and virulence was also assessed using comparative genomic analyses. This is the first comprehensive report on P. haemolytica strains isolated from fish.Publication Description of lens atrophy caused by Shewanella sp. strain S-1, a putative novel species isolated from cultured rainbow trout(Elsevier, 2021-04-13) Satıcıoğlu, İzzet Burçin; İsbilir, Fatma; Yavaş, Özkan; Avcı, Zehra; Özdemir, Burak; Süzer, Bayram; Altun, Soner; Duman, Muhammed; İŞBİLİR, FATMA; YAVAŞ, ÖZKAN; Avcı, Zehra; SÜZER, BAYRAM; ALTUN, SONER; DUMAN, MUHAMMED; Veteriner Fakültesi; Patoloji Ana Bilim Dalı; 0000-0002-2687-1221; 0000-0001-7707-2705; 0000-0001-9096-875X; HJI-5667-2023; KHD-4075-2024; X-2000-2019; GLV-3407-2022; T-1697-2019; EZZ-5951-2022; CCJ-5608-2022; AAG-8518-2021In the present study, we describe a pathogenic incidence of Shewanella sp. S-1 infection in cultured rainbow trout (Oncorhynchus mykiss, Walbaum, 1792), as evidenced by lens atrophy, inappetence, visual impairment, and growth retardation. Strain S-1 was identified using basic microbiological tests, the BD PhoenixTM rapid diagnostic kit, the MALDI-TOF MS system, and whole-genome analysis. This strain's pathogenicity was assessed based on the histopathological examination of the eyes, lens, muscle, brain, liver, kidney, spleen, and gills. The lens, brain, and eyes of the fish were also examined morphologically. According to genome-based delineation, strain S-1 was determined to belong to the genus Shewanella and was considered a putative novel Shewanella species. While we determined that the lens had atrophied at a level ranging from 30% to 40%, no severe lesion was detected in other organs. Fish that hatched in the same period were bred under uniform feeding and management conditions for a month. Monitoring data revealed that, at the end of this 1-month period, the growth rate and feed conversion rate of the diseased fish were significantly lower than those of the healthy group. Based on microbiological and pathological findings, we concluded that Shewanella sp. S-1 caused lens atrophy in the rainbow trout.Publication Pseudomonas piscium sp. nov., Pseudomonas pisciculturae sp. nov., Pseudomonas mucoides sp. nov. and Pseudomonas neuropathica sp. nov. isolated from rainbow trout(Microbiology Soc, 2021-01-01) Duman, Muhammed; Mulet, Magdalena; Altun, Soner; Satıcıoğlu, İzzet Burçin; Gomila, Margarita; Lalucat, Jorge; Garcia-Valdes, Elena; DUMAN, MUHAMMED; ALTUN, SONER; Veteriner Fakültesi; Su Hayvanları Hastalıkları Ana Bilim Dalı; 0000-0001-7707-2705; 0000-0001-9096-875X; T-1697-2019; AAG-8518-2021Six Gram negative, motile bacteria were isolated from rainbow trout (Oncorhynchus mykiss). The 16S rRNA sequence similarity values grouped them in the Pseudomonas mandelii (strains P49, P50(T), 154a(T) and P154b), Pseudomonas fluorescens (strain P115(T)) and Pseudomonas koreensis (strain P155(T)) phylogenetic subgroups in the genus Pseudomonas. The DNA G+C content ranged from 58.5 to 60mol%. The strains were characterized phenotypically using API 20NE and Biolog GENIII tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. Multi-locus sequence analysis with four housekeeping gene sequences (rpoD, rpoB, gyrB and 16S rRNA) together with genome comparisons by average nucleotide identity and genome-to-genome distance calculations were performed. Results showed that the similarity values of these strains to known species type strains were lower than the thresholds established for species in the genus Pseudomonas. Based on these data, we concluded that strains P49, P50(T), P115(T), P154a(T), P154b and P155(T) belonged to four novel species. The names proposed are: Pseudomonas piscium sp. nov. for strains P49 and P50(T) with P50(T) (=CECT 30175(T)=CCUG 74871(T)) as the type strain; Pseudomonas pisciculturae sp. nov. for strain P115(T) (CECT 30173(T)=CCUG 74873(T)); Pseudomonas mucoides sp. nov. for strains P154a(T) and P154b with P154a(T) (=CECT 30177(T)=CCUG 74874(T)) as the type strain; and Pseudomonas neuropathica sp. nov. for strain P155(T) (=CECT 30178(T)=CCUG 74875(T)).Publication Lyophilized extender supplemented with rainbow trout (oncorhynchus mykiss) seminal plasma improves cryopreservation of ram sperm(Kafkas Üniversitesi, 2022-03-13) Üstuner, Burcu; Alçay, Selim; Gökçe, Elif; Yılmaz, M. Melih; Aktar, Ahmet; Hüraydın, Oğuzhan; Duman, Muhammed; Önder, N. Tekin; Akal, Eser; Nur, Zekariya; ÜSTÜNER, BURCU; ALÇAY, SELİM; Yılmaz, M. Melih; Aktar, Ahmet; Hüraydın, Oğuzhan; DUMAN, MUHAMMED; NUR, ZEKARİYA; Veteriner Fakültesi; Su Hayvanları Hastalıkları Ana Bilim Dalı; 0000-0002-1438-221X ; 0000-0001-7707-2705 ; 0000-0002-4125-6841 ; AAG-7238-2021; CBC-7350-2022; GWC-2055-2022; CBC-1744-2022; AHB-0614-2022; T-1697-2019; AAH-2635-2021This study aimed to investigate the effect of the Rainbow trout seminal plasma (RTSP) supplemented (control, 10% or 15%) lyophilized extender on freezability of ram semen. Collected semen was pooled and split into two aliquots, and each of the ejaculates was diluted with fresh or lyophilized extenders with RTSP (0%, FC and LC; 10% F10 and L10or 15% F15 and L15) using two-step dilution method. Semen was frozen using the programmable freezing machine. Semen samples were examined for sperm motility, defective acrosomes, plasma membrane integrity and DNA fragmentation at native and post-thaw stage. The highest percentages of post-thaw motility and plasma integrity were observed in the F10, F15, and L15 (P 0.05). There was no significant difference in the rate of post-thaw defective acrosomes when the other extender groups were compared with the control (P 0.05). The highest percentage of post-thaw DNA fragmentation values were observed in the FC group, while the lowest DNA fragmentation was obtained in the F15 but only significant different from FC and LC groups. In conclusion, the findings of this study show that the lyophilized extender with 15% RTSP added can be used successfully for freezing ram semen.Publication A comprehensive perspective on a Vagococcus salmoninarum outbreak in rainbow trout broodstock(Elsevier, 2021-07-20) Satıcıoğlu, İzzet Burçin; Yardımcı, Banu; Altun, Soner; Duman, Muhammed; ALTUN, SONER; DUMAN, MUHAMMED; Veteriner Fakültesi; Su Hayvanları Hastalıkları Ana Bilim Dalı; 0000-0001-9096-875X ; 0000-0001-7707-2705; AAG-8518-2021 ; T-1697-2019Streptococcus species are of major concern for both warm-water and cold-water salmonid species, and have zoonotic importance. While Lactococcus garvieae, associated with warm-water streptococcosis, causes thousands of tons of mortalities, Vagococcus salmoninarum, the causative agent of cold-water streptococcosis, leads to chronic disease and devastating mortality in broodstock. In the present study, five bacterial samplings were performed from outbreaks that occurred between winter 2019 and summer 2020 in rainbow trout broodstock. The isolates were comprehensively characterized by phenotypic tests, using the API 20 Strept, Rapid ID 32 Strept and BIOLOG GENIII test kits. The antimicrobial susceptibilities of the strains were compared by the disk diffusion method, according to the guidelines of the Clinical & Laboratory Standards Institute (CLSI), additionally on commonly used media such as mueller-hinton agar and tryptic soy agar. Following a genomic approach, we analyzed the VS-1 strain by whole-genome sequencing. Virulence genes and correlation data were supported with the histopathological examination of the affected organs and tissues. The genome of the VS-1 strain included 69 virulence genes and 31 antimicrobial resistance genes. This study is one of the most comprehensive researches on V. salmoninarum, and elucidates the phenotypic, genotypic, antimicrobial resistance and virulence characteristics of this species.Publication Pseudomonas anatoliensis sp. nov and Pseudomonas iridis sp. nov. isolated from fish (vol 44, 126198, 2021)(Elsevier Gmbh, 2022-01-29) Mulet, Magdalena; Gomila, Margarita; Lalucat, Jorge; Garcia-Valdes, Elena; Satıcıoğlu, İzzet Burçin; Duman, Muhammed; DUMAN, MUHAMMED; Altun, Soner; Veteriner Fakültesi; 0000-0001-7707-2705; T-1697-2019Publication 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; Veteriner Fakültesi; 0000-0001-7707-2705; 0000-0002-2721-3204; T-1697-2019; AAG-8518-2021 ; AAD-4156-2019A 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)).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; Veteriner Fakültesi; Su Ürünleri Hastalıkları Ana Bilim 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 Pseudomonas arcuscaelestis sp. nov., isolated from rainbow trout and water(Microbiology Society, 2021-01-01) Mulet, Magdalena; Saticioglu, Izzet Burcin; Gomila, Margarita; Matthijs, Sandra; Lalucat, Jorge; Garcia-Valdes, Elena; Altun, Soner; ALTUN, SONER; Duman, Muhammed; DUMAN, MUHAMMED; Veteriner Fakültesi; 0000-0001-7707-2705; T-1697-2019Cells of strains P66(T), V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66(T) was isolated from rainbow trout (Oncorhynchus mykiss) cultivated at a fish farm in Turkey. Strain V1 was isolated from sand of an intertidal shore on the Galicia coast in Spain and strain W15Feb18 was isolated from water collected at the Woluwe River in Belgium. Based on 16S rRNA sequence similarity values, the strains were grouped under the genus Pseudomonas and the Pseudomonas putida phylogenetic group of species. The DNA G+C content ranged from 58.5 to 58.9 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. The absence of the hydrolysis of gelatin and the assimilation of arabinose. mannose and mannitol differentiated these strains from the closest species, Pseudomonas alkylphenolica. The major fatty acid components were C-16:0 (29.91-31.68%) and summed feature 3 (36.44-37.55%). Multilocus sequence analysis with four and 83 housekeeping gene sequences and a core proteome analysis showed that these strains formed a phylogenetic cluster in the P putida group of species. Genome comparisons by the average nucleotide identity based on BLAST and the Genome-to-Genome Distance Calculator demonstrated that the three strains belonged to the same genomic species and were distant from any known species, with similarity values lower than the thresholds established for species in the genus Pseudomonas. These data permitted us to conclude that strains P66(T), V1 and W15Feb18 belong to a novel species in the genus Pseudomonas, for which the name Pseudomonas arcuscaelestis sp. nov. is proposed. The type strain is P66(T) (=CECT 30176(T)=CCUG 74872(T)). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355).
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