| 1. |
- Gyllenberg, M, et al.
(författare)
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New methods for the analysis of binarized BIOLOG GN data of vibrio species : Minimization of stochastic complexity and cumulative classification
- 2002
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020 .- 1618-0984. ; 25:3, s. 403-415
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Tidskriftsartikel (refereegranskat)abstract
- We apply minimization of stochastic complexity and the closely related method of cumulative classification to analyse the extensively studied BIOLOG GN data of Vibrio spp. Minimization of stochastic complexity provides an objective tool of bacterial taxonomy as it produces classifications that are optimal from the point of view of information theory. We compare the outcome of our results with previously published classifications of the same data set. Our results both confirm earlier detected relationships between species and discover new ones.
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| 2. |
- Pettersson, B., et al.
(författare)
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Phylogenetic evidence for novel and genetically different intestinal spirochetes resembling Brachyspira aalborgi in the mucosa of the human colon as revealed by 165 rDNA analysis
- 2000
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Ingår i: Systematic and Applied Microbiology. - 0723-2020 .- 1618-0984. ; 23:3, s. 355-363
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Tidskriftsartikel (refereegranskat)abstract
- intestinal spirochetes (Brachyspira spp.) are causative agents of intestinal disorders in animals and humans. Phylogenetic analysis of cloned 16S rRNA genes from biopsies of the intestinal mucosa of the colon from two Swedish 60-years old adults without clinical symptoms revealed the presence of intestinal spirochetes. Seventeen clones from two individuals and 11 reference strains were analyzed and the intestinal spirochetes could be divided into two lineages, the Brachyspira aalborgi and the Brachyspira hyodysenteriae lineages. All of the clones grouped in the B. aalborgi lineage. Moreover, the B. aalborgi lineage could be divided into three distinct phylogenetic clusters as confirmed by bootstrap and signature nucleotide analysis. The first cluster comprised 6 clones and the type strain B. aalborgi NCTC 11492(T). The cluster 1 showed a 16S rRNA gene similarity of 99.4-99.9%. This cluster also harbored che only other strain of B. aalborgi isolated so far, namely strain W1, which was subjected to phylogenetic analysis in this work. The second cluster harbored 9 clones with a 98.7 to 99.5% range of 16S rDNA similarity ro the B. aalborgi cluster 1. Two clones branched distinct and early of the B. aalborgi, line forming the third cluster and was found to be 98.7% similar to cluster 1 and 98.3-99.1% to cluster 2. Interestingly, this shows that considerable variation of intestinal spirochetes can be found as constituents of the colonic microbiota in humans, genetically resembling B. aalborgi. The presented data aid significantly to the diagnostic and taxonomic work on these organisms.
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| 3. |
- Olsson, Crister, et al.
(författare)
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DNA based classification of food associated Enterobacteriaceae previously identified by biolog GN microplates
- 2004
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020 .- 1618-0984. ; 27:2, s. 219-228
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Tidskriftsartikel (refereegranskat)abstract
- Enterobacteriaceae are frequently isolated from food products and it is essential to have methods for correct identification for both food hygiene and epidemiology reasons. Phenotypic methods are not always sufficient and have to be supplemented by DNA based methods. In the present study, 70 strains of Enterobacteriaceae derived from milk, fish and meat that had previously been identified by Biolog GN Microplates were genomically classified together with 15 representative type strains of species of Enterobacteriaceae. The field strains were dominated by Hafnia alvei, Serratia liquefaciens and Rahnella aquatilis. All strains were subjected to temporal temperature gel electrophoresis (TTGE) analysis using amplicons encompassing the V3, V4 and V9 variable regions of the 16S rRNA gene. Selected strains were analysed by ribotyping and partial 16S rDNA sequencing. The type strains were differentiated into 10 different TTGE groups. Two of the groups contained two type strains. Enterobacter aerogenes and Klebsiella planticola were not distinguished due to their identical sequences and Yersinia ruckeri and Citrobacter freundii showed the same migration pattern. The 70 food strains could be differentiated into 14 TTGE groups where 33 strains (47.1%) could be assigned to TTGE groups including type or reference strains. Rabnella strains were dispersed into three TTGE groups of which one group corresponded to Rahnella genomospecies 1 and one to genomospecies 3. The grouping of Rabnella strains was supported by ribotyping and phylogenetic analysis. TTGE can be a useful additional tool for identification on the species level of food related Enterobacteriaceae.
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| 4. |
- Collins, Matthew D., et al.
(författare)
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Characterization of some Strains from Human Clinical Sources which resemble “Leptotrichia sanguinegens”: Description of Sneathia sanguinegens sp. nov., gen. nov.
- 2001
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 24:3, s. 358-361
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Tidskriftsartikel (refereegranskat)abstract
- Three strains of a Gram-negative, blood or serum requiring, rod-shaped bacterium recovered from human clinical specimens were characterised by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed the unknown rod-shaped strains are members of the same species as some fastidious isolates recovered from human blood specimens and previously designated “Leptotrichia sanguinegens”. Based on phylogenetic and phenotypic evidence, it is proposed that the isolates from human sources be classified in a new genus Sneathia, as Sneathia sanguinegens gen. nov., sp. nov. The type strain of Sneathia sanguinegens is CCUG 41628T.
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| 5. |
- Hoyles, Lesley, et al.
(författare)
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Transfer of members of the genus Falcivibrio to the genus Mobiluncus, and emended description of the genus Mobiluncus
- 2004
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Ingår i: SYSTEMATIC AND APPLIED MICROBIOLOGY. - : Elsevier BV. - 0723-2020. ; 27:1, s. 72-83
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Tidskriftsartikel (refereegranskat)abstract
- It has long been thought that the genera Mobiluncus and Falcivibrio contain the same organisms. Using a polyphasic approach, it was found that Mobiluncus curtisii and Mobiluncus mulieris were the same as Falcivibrio vaginalis and Falcivibrio grandis, respectively. As the genus name Mobiluncus takes precedence, it is proposed that F. vaginalis and F. grandis be transferred to the genus Mobiluncus. In agreement with previous studies, results from phenotypic tests did not support the separation of M. curtisii strains into its two subspecies, M. curtisii subsp. curtisii and M. curtisii subsp. holmesii. Phenotypic complexity within M. curtisii dictates that the species should be treated as a complex until more in-depth analyses of the species have been performed. Phylogenetic analyses, based on 16S rRNA gene sequences, demonstrated that the genus Mobiluncus was associated with Varibaculum cambriense and the two subspecies of Actinomyces neuii, and that A. neuii is only distantly related to Actinomyces sensu stricto. Key words: Mobiluncus; polyphasic taxonomy; PFGE; 16S rDNA; Actinomycetaceae; Falcivibrio
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| 6. |
- Lawson, Paul A, et al.
(författare)
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Dysgonomonas mossii sp. nov., from Human Sources
- 2002
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 25:2, s. 194-197
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Tidskriftsartikel (refereegranskat)abstract
- Phenotypic and phylogenetic studies were performed on seven unidentified Gram-negative, facultatively anaerobic, coccobacillus-shaped organisms isolated from human clinical specimens. Comparative 16S rRNA gene sequencing demonstrated that four of the strains corresponded to Dysgonomonas capnocytophagoides whereas the remaining three isolates represent a new sub-line within the genus Dysgonomonas, displaying greater than 5% sequence divergence with Dysgonomonas capnocytophagoides and Dysgonomonas gadei. The three novel isolates were readily distinguished from D.capnocytophagoides and D. gadei by biochemical tests. The DNA base composition of the novel species was consistent with its assignment to the genus Dysgonomonas. Based on phylogenetic and phenotypic evidence it is proposed that the unknown species, be classified as Dysgonomonas mossii sp. nov. The type strain of Dysgonomonas mossii is CCUG 43457T (= CIP 107079T).
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| 7. |
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| 8. |
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| 9. |
- Lee, N, et al.
(författare)
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Long-term population dynamics and in situ physiology in activated sludge systems with enhanced biological phosphorus removal operated with and without nitrogen removal
- 2003
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 26:2, s. 211-227
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Tidskriftsartikel (refereegranskat)abstract
- Quantitative fluorescence in situ hybridization (FISH) and the combination of FISH with microautoradiography (MAR) were used in order to study the long-term population dynamics (2.5 years) and the in situ physiology in two parallel activated sludge pilot systems with enhanced biological phosphorus removal (EBPR). The two systems received the same influent wastewater, but were differently operated (with and without nitrogen removal, respectively). Both systems showed a significant P removal that increased when different substrates (phosphorus (P), acetate and glucose, respectively) were added to the influent wastewater. Rhodocyclus-related bacteria were present in both systems in significant numbers (ranging from 4 to 28%) throughout the whole period. This supports the hypothesis that these bacteria occur in significant numbers in different types of well-operating EBPR activated sludge processes. However, we observed a lower correlation (<0.5) for the amount of Rhodocyclus-related bacteria to the P content in activated sludge than previous studies (>0.9). The Actinobacteria were the only additional group of bacteria which showed a similar degree of correlation to the P content in activated sludge as the Rhodocyclus-related bacteria - but only for the system without nitrogen removal. Significant amounts (less than or equal to12%) of glycogen-accumulating bacteria (GAOs) were detected in the system with nitrogen removal (but not in the other system), but had no, in contrast to previous observations, apparent negative effect on the overall EBPR performance. FISH-MAR indicated that a significant part of the Betaproteobacteria (part of them identified as Rhodocyclus-related bacteria) as well as the Actinobacteria were able to take up P-33(i), [H-3]-acetate and [H-3]-glucose under anaerobic-aerobic conditions. The contribution of anoxic P-33(i) uptake under alternating anaerobic-anoxic conditions was significantly lower. Interestingly, not all Rhodocyclus-related bacteria showed uptake of these three radioactive substrates. This may be due to differences in metabolic state, physiological potential or genotype, not detectable by the present probe set for Rhodocyclus-related bacteria. Comparison of the P-33(i), [H-3]-acetate and [H-3]-glucose uptake by activated sludge after different fixation and incubation procedures showed that a part of the observed P-33(i), uptake may have been caused by a combination of a biological and chemical or biologically induced chemical P adsorption.
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