| 1. |
- Vandamme, P. A., et al.
(author)
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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
- 2015
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In: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 65, s. 3674-3682
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Journal article (peer-reviewed)abstract
- 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 C-16 : 0, cyclo-C-17 : 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 hybridiiation 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 28640(T)=AU3182(T)=CCUG 56828(T)), Bordetella sputigena sp. nov. (type strain LMG 28641(T)=CCUG 56478(T)) and Bordetella flabilis sp. nov. (type strain LMG 28642(T)=AU10664(T)=CCUG 56827(T)). 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.
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| 2. |
- Vaz-Moreira, Ivone, et al.
(author)
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Sphingobium vermicomposti sp. nov., isolated from vermicompost.
- 2009
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In: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 59:12, s. 3145-3149
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Journal article (peer-reviewed)abstract
- Strain VC-230(T) 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 degrees C and pH 6-8. On the basis of 16S rRNA gene sequence analysis, strain VC-230(T) was determined to belong to the family Sphingomonadaceae by its clustering with type strains of the genus Sphingobium, with Sphingobium chlorophenolicum ATCC 33790(T) (97.7 %) and Sphingobium herbicidovorans DSM 11019(T) (97.4 %) as its closest neighbours. The polar lipid pattern, the presence of spermidine and ubiquinone 10, the predominance of the cellular fatty acids C(18 : 1)omega7c/9t/12t, C(16 : 1)omega7c and C(16 : 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-230(T) represents a novel species, for which the name Sphingobium vermicomposti sp. nov. is proposed. The type strain is VC-230(T) (=CCUG 55809(T) =DSM 21299(T)).
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| 3. |
- Alberdi-Saugstrup, M, et al.
(author)
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Non-HLA gene polymorphisms in juvenile idiopathic arthritis: associations with disease outcome.
- 2017
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In: Scandinavian journal of rheumatology. - : Informa UK Limited. - 1502-7732 .- 0300-9742. ; , s. 1-8
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Journal article (peer-reviewed)abstract
- To test the hypothesis that non-HLA single-nucleotide polymorphisms (SNPs) associated with the risk of juvenile idiopathic arthritis (JIA) are risk factors for an unfavourable disease outcome at long-term follow-up.The Nordic JIA cohort is a prospective multicentre study cohort of patients from the Nordic countries. In all, 193 patients met the inclusion criteria of having an 8year follow-up assessment and available DNA sample. Seventeen SNPs met the inclusion criteria of having significant associations with JIA in at least two previous independent study cohorts. Clinical endpoints were disease remission, actively inflamed joints and joints with limitation of motion (LOM), articular or extra-articular damage, and history of uveitis.Evidence of associations between genotypes and endpoints were found for STAT4, ADAD1-IL2-IL21, PTPN2, and VTCN1 (p=0.003-0.05). STAT4_rs7574865 TT was associated with the presence of actively inflamed joints [odds ratio (OR) 20.6, 95% confidence interval (CI) 2.2->100, p=0.003] and extra-articular damage (OR 7.9, 95% CI 1-56.6, p=0.057). ADAD1_rs17388568 AA was associated with a lower risk of having joints with LOM (OR 0.1, 95% CI 0-0.55, p=0.016). PTPN2_rs1893217 CC was associated with a lower risk of having joints with LOM (OR 0.2, 95% CI 0-0.99, p=0.026), while VTCN1_rs2358820 GA was associated with uveitis (OR 3.5, 95% CI 1-12.1, p=0.029).This exploratory study, using a prospectively followed JIA cohort, found significant associations between long-term outcome and SNPs, all previously associated with development of JIA and involved in immune regulation and signal transduction in immune cells.
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| 4. |
- Coenen, Marieke J H, et al.
(author)
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Genetic Variants in Toll-Like Receptors Are Not Associated with Rheumatoid Arthritis Susceptibility or Anti-Tumour Necrosis Factor Treatment Outcome
- 2010
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 5:12
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Journal article (peer-reviewed)abstract
- Background: Several studies point to a role of Toll-like receptors (TLRs) in the development of rheumatoid arthritis (RA). We investigated if genetic variants in TLR genes are associated with RA and response to tumour necrosis factor blocking (anti-TNF) medication. Methodology and Principal Findings: 22 single nucleotide polymorphisms (SNPs) in seven TLR genes were genotyped in a Dutch cohort consisting of 378 RA patients and 294 controls. Significantly associated variants were investigated in replication cohorts from The Netherlands, United Kingdom and Sweden (2877 RA patients and 2025 controls). 182 of the Dutch patients were treated with anti-TNF medication. Using these patients and a replication cohort (269 Swedish patients) we analysed if genetic variants in TLR genes were associated with anti-TNF outcome. In the discovery phase of the study we found a significant association of SNPs rs2072493 in TLR5 and rs3853839 in TLR7 with RA disease susceptibility. Meta-analysis of discovery and replication cohorts did not confirm these findings. SNP rs2072493 in TLR5 was associated with anti-TNF outcome in the Dutch but not in the Swedish population. Conclusion: We conclude that genetic variants in TLRs do not play a major role in susceptibility for developing RA nor in anti-TNF treatment outcome in a Caucasian population.
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| 5. |
- Huber, Birgit, et al.
(author)
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Ochrobactrum pituitosum sp. nov., isolated from an industrial environment.
- 2010
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In: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 60:Pt 2, s. 321-6
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Journal article (peer-reviewed)abstract
- Strain CCUG 50899, a Gram-negative, rod-shaped, non-spore-forming, motile bacterium isolated from industrial environment in Sweden and tentatively assigned to the species Ochrobactrum anthropi, was studied in order to clarify its taxonomic status. 16S rRNA gene sequence similarities placed the strain in the genus Ochrobactrum, sharing highest similarity with the type strains of Ochrobactrum rhizosphaerae (99.3 %), Ochrobactrum thiophenivorans (98.7 %), Ochrobactrum pseudogrignonense (98.6 %) and Ochrobactrum grignonense (98.5 %). The fatty acid profile of [O. anthropi] CCUG 50899 (major fatty acids C(18 : 1)omega7c and C(19 : 0) cyclo omega8c and presence of C(18 : 1) 2-OH), the polar lipid profile (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, two unknown aminolipids and an unknown phospholipid), the presence of the quinone system ubiquinone Q-10 and a polyamine pattern with the major compounds putrescine and spermidine and moderate amounts of sym-homospermidine supported its affiliation to the genus Ochrobactrum. DNA-DNA reassociation experiments with the type strains of its closest relatives O. rhizosphaerae, O. pseudogrignonense, O. thiophenivorans and O. grignonense demonstrated that [O. anthropi] CCUG 50899 should be placed in a novel species, which is distinguishable from related species by a set of biochemical traits. Based on these data, reclassification of [O. anthropi] CCUG 50899 as the type strain of a novel species appears to be justified. Hence, we describe a novel species to accommodate this strain, for which we propose the name Ochrobactrum pituitosum sp. nov. The type strain is CCUG 50899(T) (=DSM 22207(T)).
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| 6. |
- Lawson, PA, et al.
(author)
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Slackia faecicanis sp nov., isolated from canine faeces
- 2005
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In: INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 55, s. 1243-1246
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Journal article (peer-reviewed)abstract
- Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-positive, rod-shaped bacterium that was isolated from dog faeces. The bacterium grew under strictly anaerobic conditions, was asaccharolytic, and possessed a relatively high G+C content of 61 mol%. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium was a member of the family Coriobacteriaceae and represents a hitherto unknown subline within the genus Slackia. Based on the presented findings, a novel species, Slackia faecicanis sp. nov., is described. The type strain of Slackia faecicanis is 5WC12T (=CCUG 48399T=CIP 108281T).
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| 7. |
- Nikolaitchouk, Natalia, 1967, et al.
(author)
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Lactobacillus coleohominis sp. nov., isolated from human sources.
- 2001
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In: International journal of systematic and evolutionary microbiology. - 1466-5026. ; 51:Pt 6, s. 2081-5
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Journal article (peer-reviewed)abstract
- Four strains of a hitherto unrecognized gram-positive, catalase-negative, facultatively anaerobic, rod-shaped bacterium isolated from human sources were characterized using phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing demonstrated that the bacterium represents a new subline within the Lactobacillus casei/Pediococcus rRNA group of the genus Lactobacillus. The unknown bacterium was readily distinguished from all other described Lactobacillus species and related taxa by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Lactobacillus coleohominis sp. nov. The type strain of Lactobacillus coleohominis is CCUG 44007T (= CIP 106820T).
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| 8. |
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| 9. |
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| 10. |
- Tortoli, Enrico, et al.
(author)
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Mycobacterium europaeum sp. nov., a scotochromogenic species related to Mycobacterium simiae complex.
- 2011
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In: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 61:7, s. 1606-1611
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Journal article (peer-reviewed)abstract
- Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228T (=DSM 45397T =CCUG 58464T) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the ‘Mycobacterium simiae complex’ for this group.
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