| 1. |
- 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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| 2. |
- Inganäs, Elisabeth
(författare)
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Vad betyder CCUG – svaren
- 2010
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Ingår i: Mikrobiologiskt Vårmöte 2010, Göteborg, Sweden.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 3. |
- Jaén-Luchoro, Daniel, 1987, et al.
(författare)
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Corynebacterium sanguinis sp. nov., a clinical and environmental associated corynebacterium.
- 2020
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Ingår i: Systematic and applied microbiology. - : Elsevier BV. - 1618-0984 .- 0723-2020. ; 43:1
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Tidskriftsartikel (refereegranskat)abstract
- Clinical and environmental-associated strains (n=17), genotypically related to Corynebacterium spp., yet distinct from any species of the genus Corynebacterium with validly published names, have been isolated during the last 20 years and tentatively identified as Corynebacterium sanguinis, although the combination, "Corynebacterium sanguinis" was never validly published. The comprehensive genotypic and phenotypic characterisations and genomic analyses in this study support the proposal for recognizing the species within the genus Corynebacterium, for which the name, Corynebacterium sanguinis sp. nov., is reaffirmed and proposed. Strains of Corynebacterium sanguinis are Gram-positive, non-motile, non-spore-forming, short, pleomorphic and coryneform bacilli, growing aerobically, with CO2. They contain mycolic acids, major respiratory menaquinones, MK-8 (II-H2) and MK-9 (II-H2), and polar lipids, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphoglycolipid, glycolipids and a novel lipid that remains to be characterized and identified. Strains of Corynebacterium sanguinis are genotypically most similar to Corynebacterium lipophiliflavum, with 16S rRNA gene sequence similarities of 98.3% and rpoB sequence similarities of 94.9-95.2%. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis were able to clearly differentiate Corynebacterium sanguinis from the most closely related species. The genome size of Corynebacterium sanguinis is 2.28-2.37Mbp with 65.1-65.5mol% G+C content. A total of 2202-2318 ORFs were predicted, comprising 2141-2251 protein-encoding genes. The type strain is CCUG 58655T (=CCM 8873T=NCTC 14287T).
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| 4. |
- Jager, Edwin, 1973-, et al.
(författare)
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On-chip microelectrodes for electrochemistry with moveable PPy bilayer actuators as working electrodes
- 1999
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Ingår i: Sensors and actuators. B, Chemical. - 0925-4005 .- 1873-3077. ; 56:1-2, s. 73-78
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Tidskriftsartikel (refereegranskat)abstract
- We present electrochemical microactuators which have all the electrodes necessary for the actuation—the working, counter, and reference electrodes—on-chip. This is a first step towards an all-polymer system, i.e., a system that does not require a liquid electrolyte. The microactuators' performance was as good as when standard, off-chip counter and reference electrodes were used. Specifically, the speed of actuation was the same. In addition, we obtained a good cyclic voltammogram, although the oxidation and reduction peaks were shifted and some noise was present. Apart from application in an all-polymer system, we will also use these microactuators for studies on the effect of mechanical stimulation of living cells.
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| 5. |
- Jager, Edwin, 1973-, et al.
(författare)
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Polypyrrole micro actuators
- 1999
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Ingår i: Synthetic metals. - 0379-6779 .- 1879-3290. ; 102:1-3, s. 1309-1310
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Tidskriftsartikel (refereegranskat)abstract
- The doping and undoping of conjugated polymers is accompanied by a volume change. This volume change can be used to make micro-actuators. We have built polypyrrole (PPy) gold bilayer structures. The volume change of PPy induces a bending of the bilayer. We have made micro-actuators based on this principle, which have been examined with video-microscopy. Some applications for these microactuators are proposed, including opening and closing boxes for cell biology and nanoliter chemistry and micro-robotics.
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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. |
- Moore, Edward R.B. 1954, et al.
(författare)
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Considerations for Authenticating Bacterial Strains Coming Into and Going Out of Service Culture Collections
- 2008
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Ingår i: Proceedings of the XXVII ECCO Annual Meeting, June 10-11, Ghent, Belgium. ; , s. 22-24
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Konferensbidrag (refereegranskat)abstract
- Culture collections effectively provide important depositories of prokaryotic diversity, to be available for academic, biotechnological and commercial exploitation. Given the rationale for maintaining reference collections of bacterial strains, it is essential that the collections insure four important points: 1) the viability of strains; 2) the purity of strains; 3) the “authenticity” of strains, i.e., strains are what have been described and represented by the depositors; and 4) the accessibility of strains. Indeed, Rule 27(3) of the Code of Nomenclature of Prokaryotes states, “in the case of species or subspecies the culture collection numbers of at least two publicly accessible service collections in different countries where a subculture of the type strain has been deposited must be indicated”. Since 2002, proof of deposit and availability from culture collections has been required. Implicit in these requirements is the responsibility for the collection to provide proof of deposit to confirm the authenticity of the strain. However, culture collections should not consider themselves obligated to repeat the complete experimental procedures of depositors. The numbers of new taxonomic names included in categories covered by the rules of the Code of Nomenclature of Prokaryotes and validly published have risen an average of 14% each year for the last five years, to more than 900 in 2007 (www.bacterio.cict.fr/). The designated type strain for each of these new species and new combinations must be confirmed as available within culture collections. In principle, it is the responsibility of the respective culture collections to confirm the authenticity of these additions. In 2007, the CCUG issued 118 Certificates of Deposit (CoD) for type strains of newly proposed species. This represents 13% of the total number of new taxa described for that year and was an increase of 34% more than the number of CoD issued by the CCUG in 2006. In light of such increasing numbers of new taxa, culture collections must also respect the time, effort and expense required for “confirming” the authenticities of new deposits. The CCUG has assumed the responsibility for confirming authenticities of deposited strains, i.e., with respect to the protocols used to analyse the strains, and including the qualification: with a high degree of confidence. To this end, culture collections must consider carefully the methods they employ for analysing the authenticity of deposits. The methods to be used should necessarily be reproducible and elucidate the resolution adequate for recognising incorrect strains or contaminations. The CCUG employs phenotypic and cellular fatty acid (CFA) profiling as first- and second-phase analyses, with subsequent 16S rRNA gene sequencing as a tertiary-phase tool in cases wherein the phenotyping and CFA analyses prove to be inadequate. Phenotyping. CCUG “phenotyping” employs an initial screening of Gram-reaction, oxidase, catalase and cultivation on differential media. As has been pointed out before, if the results of simple, initial screening do not conform to the description of the organism, there is no need to carry on with more extensive analyses. Assuming that initial screening agrees with the description received from the depositor, phenotyping proceeds, employing taxon-specific customised and commercial (API, bioMérieux) tests (described in “CCUG Databases, Worksheets and Statistics”, www.ccug.se/default.cfm?navID=160). The resulting data are compared with the differential characteristics described by the depositors (i.e., the CCUG strongly recommends that depositors send the manuscript describing the strains, to be held in confidence). The CCUG carries out “phenotyping” analyses on most deposits. Thus, phenotypic authentications or identifications were performed on most of 1,715 strains deposited with the CCUG in 2007. Such analyses are reliable and useful for some taxa. Unfortunately, phenotyping also possesses well-known inherent problems. Firstly, the protocols require cultivation periods to allow the reactions to develop within the test panels. This generally takes 4 – 48 hours for most commercial systems, and some tests can require as long as six days. Secondly, reproducing phenotypic profiles in the culture collection lab that match those produced in the labs of depositors can be a challenge. Many reasons are responsible for inter-laboratory variability noted in phenotyping results. Additionally, it is recognised that some bacteria do not respond well to the substrates in commercial test panels (e.g., Stenotrophomonas spp., Sphingomonas spp.,), resulting in profiles of limited diversity. Deposits of such bacteria can not be reliably assessed, using phenotyping protocols. Furthermore, some bacteria do not present profiles that distinguish them from other species (e.g., Burkholderia cepacia complex spp., Streptococcus mitis complex spp., etc.). Thus, although bacteria belonging to closely related “species complexes” may be easily differentiated from organisms outside the respective species complex, the culture collection should be aware that inadvertent switches or contaminations with closely related species will most likely not be detected. For this reason, it is recommended that handling multiple samples of closely related and similar organisms on the bench should be done at different times. Chemotyping. CCUG “chemotyping”, may be applied, using cellular fatty acid (CFA) profiling and the protocols described in the MIDI Technical Note #101 (www.midi-inc.com). In 2007, the CCUG determined CFA profiles of 743 deposits (43%). In many cases, such analyses are able to confirm the authenticity of a deposited bacterial strain. Unfortunately, chemotyping faces some of the same limitations observed for phenotyping, in that some bacteria will produce CFA profiles of minimal diversity (e.g., Methylobacterium spp., etc.) or profiles that are not distinguishing (e.g., species of Enterobacteriaceae, etc.). The same risks associated with switching samples or contamination with closely related organisms must be acknowledged by culture collections. Furthermore, a minimal amount (100 mg) of biomass is necessary, which may be problematic to obtain from some fastidious organisms. Genotyping. It is clear that, just as phenotypic and chemotypic profiling may not be adequate for identifications of some bacteria, they also will prove less than perfect for reliable authentications of some bacteria. In such cases, 16S rRNA gene sequence determinations and comparative analyses may provide evidence supporting the authenticity of deposits. The CCUG employs partial 16S rRNA gene sequences for analysing the authenticities of deposited bacteria. The 16S rRNA genes are amplified by PCR, using universal primers. Amplification reactions are set up in duplicate, in order to minimise potential sequence mistakes caused by PCR error. The duplicate amplification products are combined prior to setting up sequence reactions. For purposes of authenticating deposited strains, the CCUG depends upon a single sequence reaction, resulting in determination of approximately 500 nucleotide positions (one third of the 16S rRNA gene) at the 5’-terminus of the 16S rRNA gene. Throughout the length of the 16S rRNA gene, five “hypervariable” regions have been observed to encompass the majority of nucleotide positions exhibiting variation. Three of the regions, comprising 71% of the variable positions in the five “hypervariable” regions, are located within the range of 500 nucleotide positions at the 5’-terminus of the gene. Thus, the probability is high that any deviation in sequence identity between sequences determined for deposited strains and the sequences determined for the strains by the depositors will be detected in this region. In order to provide a systematic assessment of deposited strains, using 16S rRNA gene sequence analysis, the exact region of sequence comparison must be specified, preferably with reference to the E. coli or other species 16S rRNA gene sequence. An extremely high, or perfect, correlation of sequence identities would be expected in order to confirm the deposited strains as being the same as described by the depositors. Of course, the limitations of using 16S rRNA gene sequence analysis as a tool for authenticating deposited strains can be the same as those faced by phenotyping and chemotyping, i.e., the problem of resolution between very closely related organisms. However, again, the question is whether the deposited strains can be considered to be the same organisms described by the depositors – with a high degree of confidence. In point of fact, the authentication process for strains coming into the CCUG is overly complex because information obtained from new organisms is, at the same time, incorporated into the CCUG identification databases. If the only issue were to confirm the authenticity of new strains deposited in the collection, a partial, single-reaction sequence of 16S rRNA genes could be recommended as adequate, in most cases. Such an approach would provide the necessary confidence in the authenticity of newly deposited strains and would help minimise the time, effort and expense of analyses. It is important to note that the 16S rRNA gene sequence is the only characteristic that is required in all cases of new bacterial species descriptions. Whereas phenotypic differential characteristics are required, the specific analyses are not defined. Chemotypic data may be recommended, but are not necessarily required. G+C% content and DNA-DNA similarities are required only in specific conditions. Thus, it is reasonable to assume that information certain to be included in the descriptions of new organisms would be used also by culture collections for authenticating new deposits. Although the methods described above may be considered to be “adequate” for authentication
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| 9. |
- Vandamme, P. A., et al.
(författare)
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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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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 65, s. 3674-3682
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Tidskriftsartikel (refereegranskat)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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| 10. |
- Vandamme, P. A., et al.
(författare)
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Taxonomic dissection of Achromobacter denitrificans Coenye et al. 2003 and proposal of Achromobacter agilis sp. nov., nom. rev., Achromobacter pestifer sp. nov., nom. rev., Achromobacter kerstersii sp. nov. and Achromobacter deleyi sp. nov
- 2016
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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 66:9, s. 3708-3717
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Tidskriftsartikel (refereegranskat)abstract
- The phenotypic and genotypic characteristics of a historical collection of strains identified as Achromobacter denitrificans were examined. Sequence analysis of a 765 bp nrdA gene fragment revealed that eight of these strains belonged to the recently described Achromobacter aegrifaciens, Achromobacter mucicolens, and Achromobacter insolitus, and that one strain belonged to Achromobacter xylosoxidans. The analysis also suggested the presence of four novel species of the genus Achromobacter among the remaining strains. The latter was confirmed by multilocus sequence analysis of concatenated nusA, eno, rpoB, gltB, lepA, nuoL and nrdA gene fragments and extensive genotypic and phenotypic characterization. We propose to name these novel species as Achromobacter agilis sp. nov., nom. rev. (type strain LMG 3411T=CCUG 62454T), Achromobacter pestifer sp. nov., nom. rev. (type strain LMG 3431T=CCUG 61959T), Achromobacter kerstersii sp. nov. (type strain LMG 3441T=CCUG 62449T) and Achromobacter deleyi sp. nov. (type strain LMG 3458T=CCUG 62433T). © 2016 IUMS.
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