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- Sphingobium vermicomposti sp. nov., isolated from vermicompostPublication . Vaz-Moreira, Ivone; Faria, Cátia; Lopes, Ana R.; Svensson, Liselott; Falsen, Enevold; Moore, Edward R. B.; Ferreira, António C. Silva; Nunes, Olga C.; Manaia, Célia M.Strain VC-230T was isolated from homemade vermicompost produced from kitchen waste. The isolate was a Gram-negative-staining, catalase- and oxidase-positive, motile rod-shaped bacterium able to grow at 15–37 6C and pH 6–8. On the basis of 16S rRNA gene sequence analysis, strain VC-230T was determined to belong to the family Sphingomonadaceae by its clustering with type strains of the genus Sphingobium, with Sphingobium chlorophenolicum ATCC 33790T (97.7 %) and Sphingobium herbicidovorans DSM 11019T (97.4 %) as its closest neighbours. The polar lipid pattern, the presence of spermidine and ubiquinone 10, the predominance of the cellular fatty acids C18 : 1v7c/9t/12t, C16 : 1v7c and C16 : 0 and the G+C content of the genomic DNA supported the affiliation of this organism to the genus Sphingobium. The phylogenetic, chemotaxonomic, phenotypic and DNA–DNA hybridization analyses verify that strain VC-230T represents a novel species, for which the name Sphingobium vermicomposti sp. nov. is proposed. The type strain is VC-230T (5CCUG 55809T 5DSM 21299T).
- Diversity and antibiotic resistance of Acinetobacter spp. in water from the source to the tapPublication . Narciso-da-Rocha, Carlos; Vaz-Moreira, Ivone; Svensson-Stadler, Liselott; Moore, Edward R. B.; Manaia, Célia M.Acinetobacterspp. are ubiquitous bacteria in the environment.Acinetobacterspp. isolated from a municipal drinking water treatment plant and from connected tap waterwere identified to the species level on the basis ofrpoB genepartial sequence analysis. Intraspecies variation wasassessed based on the analysis of partial sequences of house-keeping genes (rpoB,gyrB, andrecA). Antibiotic resistancewas characterized using the disk diffusion method and iso-lates were classified as wild or non-wild type (non-WT),according to the observed phenotype. The strains ofAcinetobacterspp. were related to 11 different validly pub-lished species, although three groups of isolates, presentinglowrpoB sequence similarities with previously describedspecies, may represent new species. Most of the isolateswere related to the speciesA. johnsoniiandA. lwoffii.These two groups, as well as others related to the speciesA. parvusandA. tjernbergiae, were detected in the watertreatment plant and in tap water. Other strains, related to thespeciesA. pittiiandA. beijerinckii, were isolated only fromtap water. Most of the isolates (80 %) demonstrated wild type (WT) to all of the 12 antibiotics tested. Non-WT fortetracycline, meropenem, and ceftazidime, among others,were observed in water treatment plant or in tap watersamples. Although, in general, this study suggests a lowprevalence of acquired antibiotic resistance in waterAcinetobacterspp., the potential of some species to acquireand disseminate resistance via drinking water is suggested.
- Shinella fusca sp. nov., isolated from domestic waste compostPublication . Vaz-Moreira, Ivone; Faria, Cátia; Lopes, Ana R.; Svensson, Liselott A.; Moore, Edward R. B.; Nunes, Olga C.; Manaia, Célia M.A bacterium, designated strain DC-196T, isolated from kitchen refuse compost was analysed by using a polyphasic approach. Strain DC-196T was characterized as a Gram-negative short rod that was catalase- and oxidase-positive, and able to grow at 10–40 6C, pH 6–9 and in NaCl concentrations as high as 3%. Chemotaxonomically, C18 : 1 was observed to be the predominant cellular fatty acid and ubiquinone 10 (Q10) was the predominant respiratory quinone. The G+C content of the genomic DNA was determined to be 66 mol%. On the basis of the genotypic, phenotypic and chemotaxonomic characteristics, strain DC-196T was assigned to the genus Shinella, although with distinctive features. At the time of writing, 16S rRNA gene sequence similarities of 97.6–96.8% and the low DNA–DNA hybridization values of 38.2–32.2% with the type strains of the three recognized Shinella species confirmed that strain DC-196T represents a novel species of the genus, for which the name Shinella fusca sp. nov. is proposed (type strain DC-196T5CCUG 55808T5LMG 24714T).
- Bordetella bronchialis sp. nov., Bordetella flabilis sp. nov. and Bordetella sputigena sp. nov., isolated from human respiratory specimens, and reclassification of Achromobacter sediminum Zhang et al. 2014 as Verticia sediminum gen. nov., comb. nov.Publication . Vandamme, Peter A.; Peeters, Charlotte; Cnockaert, Margo; Ingana, Elisabeth; Falsen, Enevold; Moore, Edward R. B.; Nunes, Olga C.; Manaia, Célia M.; Spilker, Theodore; LiPuma, John J.The phenotypic and genotypic characteristics of four Bordetella hinzii-like strains from human respiratory specimens and representing nrdA gene sequence based genogroups 3, 14 and 15 were examined. In a 16S rRNA gene sequence based phylogenetic tree, the four strains consistently formed a single coherent lineage but their assignment to the genus Bordetella was equivocal. The respiratory quinone, polar lipid and fatty acid profiles generally conformed to those of species of the genus Bordetella and were characterized by the presence of ubiquinone 8, of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several aminolipids, and of high percentages of C16 : 0, cyclo-C17 : 0 and summed feature 2, as major chemotaxonomic marker molecules, respectively. The DNA G+C content was about 66 mol%, which corresponded with that of the high-percentage DNA G+C content genera of the family Alcaligenaceae including the genus Bordetella. DNA–DNA hybridization experiments revealed the presence of three distinct genomospecies and thus confirmed phenotypic differences as revealed by means of extensive biochemical characterization.We therefore propose to formally classify Bordetella genogroups 3, 14 and 15 as Bordetella bronchialis sp. nov. (type strain LMG 28640T5AU3182T5CCUG 56828T), Bordetella sputigena sp. nov. (type strain LMG 28641T5CCUG 56478T) and Bordetella flabilis sp. nov. (type strain LMG 28642T5AU10664T5CCUG 56827T). In addition, we propose to reclassify Achromobacter sediminum into the novel genus Verticia, as Verticia sediminum, gen. nov., comb. nov., on the basis of its unique phylogenetic position, its marine origin and its distinctive phenotypic, fatty acid and polar lipid profile
- Acinetobacter portensis sp. nov. and Acinetobacter guerrae sp. nov., isolated from raw meatPublication . Carvalheira, Ana; Gonzales Siles, Lucia; Salvà-Serra, Francisco; Lindgren, Åsa; Svensson-Stadler, Liselott; Thorell, Kaisa; Moore, Edward R. B.; Silva, Joana; Teixeira, PaulaThe taxonomic status of six strains of Acinetobacter obtained from meat samples, collected from supermarkets in Porto, Portugal, was investigated using polyphasic analysis. Partial rpoB sequence similarities lower than 95 % to other Acinetobacter species with validly published names led to the hypothesis that these strains represented novel species. This was confirmed based on comparative multilocus sequence analysis, which included the gyrB, recA and 16S rRNA genes, revealing that these strains represented two coherent lineages that were distinct from each other and from all known species. The names Acinetobacter portensis sp. nov. (comprising four strains) and Acinetobacter guerrae sp. nov. (comprising two strains) are proposed for these novel species. The species status of these two groups was confirmed by low (below 95 %) whole-genome sequence average nucleotide identity values and low (below 70 %) digital DNA–DNA hybridization similarities between the whole-genome sequences of the proposed type strains of each novel species and the representatives of the known Acinetobacter species. Phylogenomic treeing from core genome analysis supported these results. The coherence of each new species lineage was supported by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiation of the species at the protein level, by cellular fatty acid profiles, and by unique and differential combinations of metabolic and physiological properties shared by each novel species. The type strain of A. portensis sp. nov. is AC 877T (=CCUG 68672T=CCM 8789T) and the type strain of A. guerrae sp. nov. is AC 1271T (=CCUG 68674T=CCM 8791T).
- Diversity and antibiotic resistance of Acinetobacter spp. in water from the source to the tapPublication . Da Rocha, C. A. Narciso; Vaz-Moreira, Ivone; Svensson-Stadler, L.; Moore, E. R. B.; Manaia, C. M.
- Pseudomonas thermotolerans sp. nov., a thermotolerant species of the genus Pseudomonas sensu strictoPublication . Manaia, C. M.; Moore, Edward R. B.A bacterium, strain CM3T, which has an optimal growth temperature of approximately 47 °C and a maximal growth temperature of 55 SC, was isolated from a hexadecane enrichment culture, obtained from a sample of the industrial cooking water of a cork-processing plant. 16S rRNA gene sequence analysis demonstrated that this Gram-negative, aerobic, rod-shaped bacterium is related to species of the genus Pseudomonas. Phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of this isolate and the total fatty acid methyl ester profile revealed predominantly C16:1 and C18:1 at a growth temperature of 25 SC, whereas, at a growth temperature of 50 SC, C16:0 was the dominant fatty acid. This is the first report of a species of Pseudomonas sensu stricto that may be considered to be truly thermotolerant. Isolate CM3T (¯DSM 14292T¯LMG 21284T) represents the type strain of a novel species of the genus Pseudomonas, named Pseudomonas thermotolerans sp. nov.