Person: DUMAN, MUHAMMED
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DUMAN
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MUHAMMED
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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; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Anatomi Anabilim Dalı.; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Patoloji Anabilim Dalı.; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim 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 anatoliensis sp. nov and Pseudomonas iridis sp. nov. isolated from fish(Elsevier Gmbh, 2021-03-09) Duman, Muhammed; Mulet, Magdalena; Altun, Soner; Satıcıoğlu, İzzet Burçin; Gomila, Margarita; Lalucat, Jorge; Garcia-Valdes, Elena; DUMAN, MUHAMMED; ALTUN, SONER; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-9096-875X ; 0000-0001-7707-2705; T-1697-2019; AAG-8518-2021In a study carried out between 2013 and 2018 in fish farms in Turkey, several putative novel species were isolated. The 16S rRNA nucleotide sequences of fourteen strains of Gram-negative rods, which were isolated from asymptomatic and symptomatic rainbow trouts (Onchorhynchus mykiss), placed them under the genus Pseudomonas. The similarity values of the concatenated nucleotide sequences of the rpoD, rpoB, gyrB and 16S rRNA genes clustered these isolates into the P. fluorescens phylogenetic group of species and into the Pseudomonas koreensis subgroup, close to Pseudomonas helmanticensis and Pseudomonas baetica. An isolate of a totally different origin, strain CCUG 67011, clustered with these isolates. Phenotypic characterization, together with the chemotaxonomic data, whole-cell MALDI-TOF MS and fatty acids methyl esters analyses were performed. The DNA G + C content was 58.7 mol% for isolate P9(T) and 58.8 mol% for isolate P42(T). The phylogenomic analysis and whole genome nucleotide sequences of four of these isolates confirmed that the isolates P9(T), P25 and P141, represent a novel species for which the name Pseudomonas anatoliensis sp. nov. is proposed, with P9(T) as the type strain (=CCUG 74755(T) = CECT 3172(T)). The isolates P1, P2, P10, P27, P30, P24a, P42(T), P117, P139, P152 and CCUG 67011 represent another novel secies, for which the name Pseudomonas iridis sp. nov. is proposed, with P42(T) as the type strain (=CCUG 74870(T) = CECT 3174(T)). (C) 2021 Elsevier GmbH. All rights reserved.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; Bursa Uludağ Üniversitesi/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).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 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; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim 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 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; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim 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 Molecular characterization and antimicrobial resistance profile of fecal contaminants and spoilage bacteria that emerge in rainbow trout ( oncorhynchus mykiss ) farms(Bmfh Press, 2019-01-01) Satıcıoğlu, İzzet Burçin; Duman, Muhammed; DUMAN, MUHAMMED; Altun, Soner; ALTUN, SONER; Bursa Uludağ Üniversitesi/Veteriner Fakültesi; 0000-0001-7707-2705; 0000-0002-2721-3204; AAG-8518-2021; T-1697-2019Fecal contaminants are a major public concern that directly affect human health in the fish production industry. In this study, we aimed to determine the fecal coliform, spoilage bacteria, and antimicrobial-resistant bacterial contamination in rainbow trout (Oncorhynchus mykiss) farms. Fish were sampled from rainbow trout farms that have a high production capacity and are established on spring water, stream water, and dammed lakes in six different regions of Turkey. A total of seven Enterobacter subspecies, two strains of Pseudomonas spp., and one isolate each of Morganella and Stenotrophomonas were characterized based on biochemical and molecular methods, including the 16S rRNA and gyrB housekeeping gene regions. The sequencing results obtained from the 16S rRNA and gyrB gene regions were deposited in the GenBank database and compared with isolates from different countries, which were registered in the database. Resistance to 10 different antimicrobial compounds was determined using the broth microdilution method, and molecular resistance genes against florfenicol, tetracycline, and sulfamethoxazole were identified by PCR. All detected resistance genes were confirmed by sequencing analyses. E. cloacae, E. asburiae, Pseudomonas spp., S. maltophilia, and M. psychrotolerans were identified using the gyrB housekeeping gene, while isolates showed different biochemical characteristics. All isolates were found to be phenotypically resistant to sulfamethoxazole, and some isolates were resistant to tetracycline, florfenicol, amoxicillin, and doxycycline; the resistance genes of these isolates included floR, tetC, tetD, and tetE. We showed that fecal coliforms, spoilage bacteria, and antimicrobial resistant bacteria were present in farmed rainbow trout, and they pose a threat for human health and must be controlled in the farming stage of fish production.Publication Genome analysis and antimicrobial resistance characteristics of Chryseobacterium aquaticum isolated from farmed salmonids(Elsevier, 2021-01-05) Satıcıoğlu, İzzet Burçin; Duman, Muhammed; Altun, Soner; DUMAN, MUHAMMED; ALTUN, SONER; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-9096-875X; 0000-0001-7707-2705; T-1697-2019; AAG-8518-2021Fish diseases caused by bacterial genera belonging to the family Flavobacteriaceae, especially Tenacibaculum, Flavobacterium, and Chryseobacterium, are responsible for losses in wild and farmed fish around the world. In the last decade, the genus Chryseobacterium has rapidly grown in parallel with numerous novel Chryseobacterium species described from systemic infections of fish. Members of the family Flavobacteriaceae, isolated from fish, the environment, and clinical samples, have been reported to show low susceptibility to a broad range of antimicrobials. In this study, seventy C. aquaticum strains were isolated from diseased salmonids in Turkey. The phylogenetic analysis of all C. aquaticum strains, together with the reference strains in GenBank, which were obtained from different sources, including fish, plants, soil, water, and other animals, was performed by 16S rRNA gene sequence analysis. The antimicrobial susceptibility of each C. aquaticum strain was determined by a minimum inhibitory concentration (MIC) test. The isolate with the highest level of antimicrobial resistance, strain C-174, underwent a more detailed whole-genome sequence analysis for virulence and antimicrobial resistance genes (AMR) genes, genome size, and guanine-cytosine (GC) content.Phylogenetically, the 70 strains isolated from Turkey were assigned to three genogroups. Strains previously recovered from the rainbow trout, brown trout, and Siberian sturgeon were genetically very close to our strains. Most of the strains isolated in this study grew even in the presence of high concentrations of the tested antimicrobials, excluding enrofloxacin. Strain C-174 carried 74 putative functional genes encoding AMR and virulence. The number of putative AMR genes detected in the genome of strain C-174 was 46. The regulatory mechanisms of these genes involve antibiotic efflux (13), antibiotic target alteration (17), antibiotic inactivation (7), antibiotic target replacement (3), and antibiotic target protection (6). AMR genes confer resistance to multiple antibiotic groups, including among others, macrolides, fluoroquinolones, beta-lactams, tetracyclines, phenicols, sulphonamides, and diaminopyrimidines. We concluded that antimicrobial resistance could be of intrinsic nature. Furthermore, we detected three putative virulence genes in the genome of strain C-174 that have not been reported for C. aquaticum before. The results of this study demonstrated a strong correlation between these genes in the genome of C-174 and mortality in the rainbow trout.Publication The diversity of Pseudomonas species isolated from fish farms in Turkey(Elsevier, 2021-01-07) Duman, Muhammed; Mulet, Magdalena; Altun, Soner; Satıcıoğlu, İzzet Burçin; Özdemir, Burak; Ajmi, Nihed; Lalucat, Jorge; Garcia-Valdes, Elena; DUMAN, MUHAMMED; ALTUN, SONER; Özdemir, Burak; Ajmi, Nihed; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; 0000-0001-9096-875X; 0000-0001-7714-9880; 0000-0002-5368-4819; T-1697-2019; AAG-8518-2021; HJI-5667-2023; ADL-2524-2022The prevalence of Pseudomonas species in freshwater fish and water from aquaculture farms in Turkey was determined on a monthly basis, in the period covering 2013-2017 and two seasons of 2018. The farms included in the study were located in six different regions of Turkey. A total of 90 Pseudomonas strains were isolated from water and diseased and healthy fish, and were classified under 20 species. The phenotypic characterization of the strains was based on oxidase and catalase activities, haemolysis, tolerance to temperature and sodium chloride, the production of fluorescent pigments and antibiotic resistance spectra. The phylogenetic identification of the 90 isolates was performed by a 4-gene multilocus sequence analysis, based on the partial sequencing of the 16S rRNA, gyrB, rpoB and rpoD genes. This is the first report on the isolation of several Pseudomonas species, namely, P. brenneri, P. defensor, P. haemolytica, P. lactis, P. lundensis, P. lurida, P. mandelii, P. meridiana, P. migulae, P. proteolytica, P. simiae, and P. weihenstephanensis, from freshwater salmonid fish. Two of these species, P. haemolytica and P. lactis have been isolated for the first time from fish farms, an environment quite different from their original isolation source, raw milk. Furthermore, seven putative new Pseudomonas species were isolated from water and farmed rainbow trout. During the 2013 to 2018 period, several Pseudomonas species were detected to have spread from the Aegean and Central Anatolia regions to the Eastern Anatolia and Black Sea regions.Publication Pseudomonas piscium sp. nov., Pseudomonas pisciculturae sp. nov., Pseudomonas mucoides sp. nov. and Pseudomonas neuropathica sp. nov. isolated from rainbow trout (vol 71, 004714, 2019)(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; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; 0000-0001-9096-875X; T-1697-2019; AAG-8518-2021
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