| 1. |
- Bennasar-Figueras, Antoni, et al.
(författare)
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Complete Genome Sequence of Pseudomonas balearica DSM 6083T.
- 2016
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Ingår i: Genome Announcements. - 2169-8287. ; 4:2
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Tidskriftsartikel (refereegranskat)abstract
- The whole-genome sequence of ITALIC! Pseudomonas balearicaSP1402 (DSM 6083(T)) has been completed and annotated. It was isolated as a naphthalene degrader from water of a lagooning wastewater treatment plant. ITALIC! P.balearicastrains tolerate up to 8.5% NaCl and are considered true marine denitrifiers.
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| 2. |
- Bogas, Diana, et al.
(författare)
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Applications of optical DNA mapping in microbiology
- 2017
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Ingår i: BioTechniques. - : Future Science Ltd. - 0736-6205 .- 1940-9818. ; 62:6, s. 255-267
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Forskningsöversikt (refereegranskat)abstract
- Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.
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| 3. |
- Claverías, Fernanda, et al.
(författare)
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Corynebacterium alimapuense sp. nov., an obligate marine actinomycete isolated from sediment of Valparaíso bay, Chile.
- 2019
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 69:3, s. 783-790
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Tidskriftsartikel (refereegranskat)abstract
- A novel Gram-positive, non-motile, non-spore-forming and aerobic bacterium, designated strain VA37-3T, was isolated from a marine sediment sample collected at 19.2m water depth from Valparaíso bay, Chile. Strain VA37-3T exhibits 97.6% 16S rRNA gene sequence similarity to Corynebacterium marinum D7015T, 96.4% to Corynebacterium humireducens MFC-5T and 96% to Corynebacterium testudinoris M935/96/4T; and a rpoB gene sequence similarity of 85.1% to Corynebacterium pollutisoli VMS11T, both analyses suggesting that strain VA37-3T represents a novel species of Corynebacterium. Physiological testing indicated that strain VA37-3T requires artificial sea water or sodium-supplemented media for growth, representing the first obligate marine actinomycete of the genus Corynebacterium. The genome of the proposed new species, along with the type strains of its most closely related species were sequenced and characterized. In silico genome-based similarity analyses revealed an ANIb of 72.8% (C. marinum D7015T), ANIm of 85.0% (Corynebacterium mustelae DSM 45274T), tetra of 0.90 (Corynebacterium callunae DSM 20147T) and ggdc of 24.7% (Corynebacterium kutscheri DSM 20755T) when compared with the closest related strains. The genomic DNA G+Ccontent of strain VA37-3T was 57.0%. Chemotaxonomic assessment of strain VN6-2T showed the major fatty acids were C18:1ω9c and C16:0. Menaquinones predominantly consisted of MK-8(II-H2). Polar lipids consisted of diphosphatidylglycerol, glycolipids, phosphatidylglycerol, phosphoglycolipid and phosphatidylinositol. Mycolic acids also were present. Overall, the results from phylogenetic, phenotypic and genomic analyses confirmed that strain VA37-3T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium alimapuense sp. nov. is proposed, with VA37-3T as the type strain (=CCUG 69366T=NCIMB 15118T).
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| 4. |
- Cuadrado, Virginia, et al.
(författare)
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Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil
- 2010
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 60:11, s. 2606-2612
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Tidskriftsartikel (refereegranskat)abstract
- A bacterial consortium able to degrade the herbicide 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) was obtained from an agricultural soil of the Argentinean Humid Pampa region which has a history of long-term herbicide use. Four bacterial strains were isolated from the consortium and identified as members of the genera Cupriavidus, Labrys and Pseudomonas. A polyphasic systematic analysis was carried out on strain CPDB6(T), the member of the 2,4-DB-degrading consortium able to degrade 2,4-DB as a sole carbon and energy source. The Gram-negative, rod-shaped, motile, non-sporulating, non-fermenting bacterium was shown to belong to the genus Cupriavidus on the basis of 16S rRNA gene sequence analyses. Strain CPDB6(T) did not reduce nitrate, which differentiated it from the type species of the genus, Cupriavidus necator; it did not grow in 0.5-4.5% NaCl, although most species of Cupriavidus are able to grow at NaCl concentrations as high as 1.5%; and it was able to deamidate acetamide, which differentiated it from all other species of Cupriavidus. DNA-DNA hybridization data revealed low levels of genomic DNA similarity (less than 30%) between strain CPDB6(T) and the type strains of Cupriavidus species with validly published names. The major cellular fatty acids detected were cis-9-hexadecenoic (16:1ω7c) and hexadecanoic (16:0) acids. On the basis of phenotypic and genotypic characterizations, strain CPDB6(T) was recognized as a representative of a novel species within the genus Cupriavidus. The name Cupriavidus pampae sp. nov. is proposed, with strain CPDB6(T) (=CCUG 55948(T)=CCM-A-29:1289(T)) as the type strain.
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| 5. |
- Gomila, Margarita, et al.
(författare)
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Achromobacter marplatensis sp. nov., isolated from a pentachlorophenol contaminated soil.
- 2011
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 61:9, s. 2231-2237
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Tidskriftsartikel (refereegranskat)abstract
- A polyphasic taxonomic approach was applied for the study of a Gram negative bacterium (B2(T)) isolated from soil by selective enrichment with pentachlorophenol. The 16S rRNA gene sequence analysis of strain B2(T) showed that this strain belongs to the genus Achromobacter, within the Betaproteobacteria. The 16S rRNA gene sequence possessing more than 99% similarity to the sequences of the type strains of all species in Achromobacter, with the highest sequence similarities to those of A. spanius CCM 7183(T) and A. piechaudii CCM 2986(T) (99.8 %). On the basis of phylogenetic analysis, genomic DNA-DNA similarities and phenotypic characteristics, including chemotaxonomic (cell fatty acid profile) analysis, a novel species is proposed, Achromobacter marplatensis sp. nov., with the type strain B2(T) (= CCM 7608(T) = CCUG 56371(T) = CECT 7342(T)).
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| 6. |
- Gomila, Margarita, et al.
(författare)
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Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water.
- 2007
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 57:11, s. 2629-2635
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Tidskriftsartikel (refereegranskat)abstract
- Three Gram-negative, rod-shaped, non-spore-forming bacteria (strains CCUG 52769T, CCUG 52770 and CCUG 52771) isolated from haemodialysis water were characterized taxonomically, together with five strains isolated from industrial waters (CCUG 52428, CCUG 52507, CCUG 52575T, CCUG 52590 and CCUG 52631). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the class Betaproteobacteria and were related to the genus Pelomonas, with 16S rRNA gene sequence similarities higher than 99% with the only species of the genus, Pelomonas saccharophila and to Pseudomonas sp. DSM 2583. The type strains of Mitsuaria chitosanitabida and Roseateles depolymerans were their closest neighbours (97.9 and 97.3% 16S rRNA gene sequence similarity, respectively). Phylogenetic analysis was also performed for the internally transcribed spacer region and for three genes [hoxG (hydrogenase), cbbL/cbbM (Rubisco) and nifH (nitrogenase)] relevant for the metabolism of the genus Pelomonas. DNA-DNA hybridization, major fatty acid composition and phenotypical analyses were carried out, which included the type strain of Pelomonas saccharophila obtained from different culture collections (ATCC 15946T, CCUG 32988T, DSM 654T, IAM 14368T and LMG 2256T), as well as M. chitosanitabida IAM 14711T and R. depolymerans CCUG 52219T. Results of DNA-DNA hybridization, physiological and biochemical tests supported the conclusion that strains CCUG 52769, CCUG 52770 and CCUG 52771 represent a homogeneous phylogenetic and genomic group, including strain DSM 2583, clearly differentiated from the industrial water isolates and from the Pelomonas saccharophila type strain. On the basis of phenotypic and genotypic characteristics, these strains belong to two novel species within the genus Pelomonas, for which the names Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are proposed. The type strains of Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are CCUG 52769T (=CECT 7234T) and CCUG 52575T (=CECT 7233T), respectively.
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| 7. |
- Gomila, Margarita, et al.
(författare)
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Description of Roseateles aquatilis sp nov and Roseateles terrae sp nov., in the class Betaproteobacteria, and emended description of the genus Roseateles
- 2008
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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 58, s. 6-11
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Tidskriftsartikel (refereegranskat)abstract
- Three strains of aerobic Gram-negative bacilli, two isolated from industrial water and freshwater (strains CCUG 48205T and CCUG 52220) and the third from soil (strain CCUG 52222T), were analysed phenotypically and genotypically to clarify their taxonomic classification. 16S rRNA gene sequence analysis revealed that the three strains were located on the same phylogenetic branch, closely related to Roseateles depolymerans, the only recognized species in the genus. DNA–DNA hybridization studies, analyses of fatty acid contents, and physiological and biochemical tests supported the proposal of two novel species, Roseateles aquatilis sp. nov. (type strain, CCUG 48205T=CECT 7248T) and Roseateles terrae sp. nov. (type strain, CCUG 52222T=CECT 7247T).
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| 8. |
- Gomila, Margarita, et al.
(författare)
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Genotypic and phenotypic applications for the differentiation and species-level identification of achromobacter for clinical diagnoses.
- 2014
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Ingår i: PloS one. - : Public Library of Science (PLoS). - 1932-6203. ; 9:12
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Tidskriftsartikel (refereegranskat)abstract
- The Achromobacter is a genus in the family Alcaligenaceae, comprising fifteen species isolated from different sources, including clinical samples. The ability to detect and correctly identify Achromobacter species, particularly A. xylosoxidans, and differentiate them from other phenotypically similar and genotypically related Gram-negative, aerobic, non-fermenting species is important for patients with cystic fibrosis (CF), as well as for nosocomial and other opportunistic infections. Traditional phenotypic profile-based analyses have been demonstrated to be inadequate for reliable identifications of isolates of Achromobacter species and genotypic-based assays, relying upon comparative 16S rRNA gene sequence analyses are not able to insure definitive identifications of Achromobacter species, due to the inherently conserved nature of the gene. The uses of alternative methodologies to enable high-resolution differentiation between the species in the genus are needed. A comparative multi-locus sequence analysis (MLSA) of four selected 'house-keeping' genes (atpD, gyrB, recA, and rpoB) assessed the individual gene sequences for their potential in developing a reliable, rapid and cost-effective diagnostic protocol for Achromobacter species identifications. The analysis of the type strains of the species of the genus and 46 strains of Achromobacter species showed congruence between the cluster analyses derived from the individual genes. The MLSA gene sequences exhibited different levels of resolution in delineating the validly published Achromobacter species and elucidated strains that represent new genotypes and probable new species of the genus. Our results also suggested that the recently described A. spritinus is a later heterotypic synonym of A. marplatensis. Strains were analyzed, using whole-cell Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF MS), as an alternative phenotypic profile-based method with the potential to support the identifications determined by the genotypic DNA sequence-based MLSA. The MALDI-TOF MS data showed good accordance in strain groupings and identifications by the MLSA data.
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| 9. |
- Gomila, Margarita, et al.
(författare)
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Kinneretia asaccharophila gen. nov., sp. nov., isolated from a freshwater lake, a member of the Rubrivivax branch of the family Comamonadaceae.
- 2010
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 60:4, s. 809-814
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Tidskriftsartikel (refereegranskat)abstract
- A strictly aerobic, Gram-negative bacterium, strain KIN192(T), isolated from fresh water from Lake Kinneret, Israel, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA and gyrB genes and ITS1 revealed close relationships to species of the genera Pelomonas, Mitsuaria and Roseateles, in the Rubrivivax branch of the family Comamonadaceae of the Betaproteobacteria. Physiological and biochemical tests, cellular fatty acid analysis and DNA-DNA hybridizations indicated that this strain should be assigned to a new genus and species in the Rubrivivax phylogenetic branch, for which the name Kinneretia asaccharophila gen. nov., sp. nov., is proposed. The type strain of Kinneretia asaccharophila is strain KIN192(T) (=CCUG 53117(T) =CECT 7319(T)).
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| 10. |
- Gomila, Margarita, et al.
(författare)
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Molecular Techniques for the Identification of Clinical and Environmental Achromobacter strains
- 2009
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Ingår i: FEMS 2009 - 3rd Congress of European Microbiologists.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Background: The genus Achromobacter (βetaproteobacteria) comprises six species isolated from different sources, most from clinical samples. The ability to detect and correctly identify A. xylosoxidans and related Gram-negative, non-fermenting species is essential for patients with cystic fibrosis, as well as in nosocomial infections. Traditional phenotyping is not adequate for reliable, definitive identifications of Achromobacter species. Furthermore, sequence analyses of 16S rRNA gene sequences are also not able insure accurate identification of Achromobacter species, due to the limited resolution of the rRNA genes (greater than 98.5% to each other). Objectives: The objective of this study has been to establish a genotypic, multi-locus sequence analysis (MLSA), analysis for the reliable, definitive and cost-effective identification of Achromobacter species, and to apply the molecular tools for typing and identification of clinical isolates. Methods: 1) Selection of phenotypically well-described strains of Achromobacter species isolated from different sources (clinical and environmental). 2) Development of a MLSA strategy based on sequences of 16S rRNA, inter-genic spacer regions (IGS1), DNA gyrase subunit B (gyrB), and RNA polymerase subunit B (rpoB). 3) Comparison and correlation of MLSA data with other methodologies: DNA-DNA hybridisation; fingerprinting analysis; cellular fatty acids analysis; and MALDI-TOF mass spectrometry analyses. Results: Individual phylogenetic trees, as well as combined datasets were compared. The combined analysis of the MLSA data provided differentiation at the intra- and the interspecies levels and reliable identifications of isolates of Achromobacter spp. Conclusions: The MLSA methodology described allows for the rapid and reliable identification of the Achromobacter species, distinguished from related Gram-negative non-fermenting organisms, and is also useful for strain differentiation and typing in molecular epidemiological studies.
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