Browsing by Author "Gomila, Margarita"

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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-8518-2021
In 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.
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; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; 0000-0001-7707-2705; T-1697-2019
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-1697-2019
Cells 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).
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-8518-2021
Six 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)).
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
Pseudomonas sivasensis sp. nov. isolated from farm fisheries in Turkey
(Elsevier, 2020-06-12) Mulet, Magdalena; Satıcıoğlu, İzzet Burçin; Gomila, Margarita; Lalucat, Jorge; Garcia, Elena Valdes; Duman, Muhammed; Altun, Soner; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Ürünleri Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; 0000-0001-9096-875X; 55568071100; 56269221600
A study of 91 isolates from fish farms in Turkey showed that isolates P7(T), P11, P24b, P29, P72, P73 and P158 belonged to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. The analysis of the sequences of the RNA polymerase sigma factor gene (rpoD) located these strains in the Pseudomonas fluorescens lineage of species within the P. fluorescens subgroup, close to the cluster composed of the species Pseudomonas grimontii, Pseudomonas marginalia and Pseudomonas panacis. Based on similarities in the 16S rRNA and rpoD gene sequences of three previously isolated strains from other origins (CCUG 57209, CCUG 62357 and W5.2-93) linked them to the same cluster. A polyphasic taxonomic approach including phenotypic characterization, fatty acid composition, and multilocus sequence analysis, together with whole-cell MALDI-TOF data, corroborated this assumption. The genome G+C mol% contents were 59.48 and 59.71, respectively. The average nucleotide indices based on BLAST analysis and the genome-to-genome distance calculation for the P7T and CCUG 57209 strains with their closest relative, P. grimontii, were 88.16-88.29% and 38.10-38.20%, respectively. These data confirm that isolates P7(T), P11, P24b, P29, P72, P73, P158, CCUG 57209, CCUG 62357 and W5.2-93 represent a new species for which the name Pseudomonas sivasensis is proposed, with P7(T) as a type strain (=CCUG 74260(T)= and CECT30107(T)).