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International Journal of Systematic... Oct 1990Pseudomonas facilis and Pseudomonas delafieldii are inappropriately assigned to the genus Pseudomonas. They belong to the acidovorans rRNA complex in rRNA superfamily...
Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov.
Pseudomonas facilis and Pseudomonas delafieldii are inappropriately assigned to the genus Pseudomonas. They belong to the acidovorans rRNA complex in rRNA superfamily III (i.e., the beta subclass of the Proteobacteria). The taxonomic relationships of both of these species, two groups of clinical isolates (E. Falsen [EF] group 13 and EF group 16), and several unidentified or presently misnamed strains were examined by using DNA:rRNA hybridization, numerical analyses of biochemical and auxanographic features and of fatty acid patterns, polyacrylamide gel electrophoresis of cellular proteins, and DNA:DNA hybridization. These organisms form a separate group within the acidovorans rRNA complex, and we propose to transfer them to a new genus, Acidovorax. We describe the following three species in this genus: the type species, Acidovorax facilis (formerly Pseudomonas facilis), with type strain LMG 2193 (= CCUG 2113 = ATCC 11228); Acidovorax delafieldii (for the former Pseudomonas delafieldii and most of the EF group 13 strains), with type strain LMG 5943 (= CCUG 1779 = ATCC 17505); and Acidovorax temperans (for several former Pseudomonas and Alcaligenes strains and most of the EF group 16 strains), with type strain CCUG 11779 (= LMG 7169).
Topics: Base Composition; Base Sequence; Chromatography, Gas; Cluster Analysis; DNA, Bacterial; Electrophoresis; Fatty Acids; Nucleic Acid Hybridization; Phenotype; Pseudomonas; Terminology as Topic
PubMed: 2275854
DOI: 10.1099/00207713-40-4-384 -
International Journal of Systematic and... May 2018A Gram-stain-negative, rod-shaped, aerobic, straw yellow, motile strain, designated KNDSW-TSA6, belonging to the genus Acidovorax, was isolated from a water sample of...
A Gram-stain-negative, rod-shaped, aerobic, straw yellow, motile strain, designated KNDSW-TSA6, belonging to the genus Acidovorax, was isolated from a water sample of the river Ganges, downstream of the city of Kanpur, Uttar Pradesh, India. Cells were aerobic, non-endospore-forming and motile with single polar flagella. It differed from its phylogenetically related strains by phenotypic characteristics such as hydrolysis of urea, gelatin, casein and DNA, and the catalase reaction. The major fatty acids were C16 : 1ω7c/C16 : 1ω6c, C16 : 0 and C18 : 1ω7c/C18 : 1ω6c. Phylogenetic analysis based on 16S rRNA and housekeeping genes (gyrb, recA and rpoB gene sequences), confirmed its placement within the genus Acidovorax as a novel species. Strain KNDSW-TSA6 showed highest 16S rRNA sequence similarity to Acidovorax soli BL21 (98.9 %), Acidovorax delafieldii ATCC 17505 (98.8 %), Acidovorax temperans CCUG 11779 (98.2 %), Acidovorax caeni R-24608 (97.9 %) and Acidovorax radicis N35 (97.6 %). The digital DNA-DNA hybridization and average nucleotide identity values calculated from whole genome sequences between strain KNDSW-TSA6 and the two most closely related strains A. soli BL21 and A. delafieldii ATCC 17505 were below the threshold values of 70 and 95 % respectively. Thus, the data from the polyphasic taxonomic analysis clearly indicates that strain KNDSW-TSA6 represents a novel species, for which the name Acidovorax kalamii sp. nov. is proposed. The type strain is Acidovorax kalamii (=MTCC 12652=KCTC 52819=VTCC-B-910010).
Topics: Bacterial Typing Techniques; Base Composition; Comamonadaceae; DNA, Bacterial; Fatty Acids; Genes, Bacterial; India; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Rivers; Sequence Analysis, DNA
PubMed: 29616893
DOI: 10.1099/ijsem.0.002736 -
Frontiers in Cellular and Infection... 2022Periodontitis and rheumatoid arthritis (RA) are two widespread chronic inflammatory diseases with a previously suggested association. The objective of the current study...
OBJECTIVES
Periodontitis and rheumatoid arthritis (RA) are two widespread chronic inflammatory diseases with a previously suggested association. The objective of the current study was to compare the oral microbial composition and host´s inflammatory mediator profile of saliva samples obtained from subjects with periodontitis, with and without RA, as well as to predict biomarkers, of bacterial pathogens and/or inflammatory mediators, for classification of samples associated with periodontitis and RA.
METHODS
Salivary samples were obtained from 53 patients with periodontitis and RA and 48 non-RA with chronic periodontitis. The microbial composition was identified using 16S rRNA gene sequencing and compared across periodontitis patients with and without RA. Levels of inflammatory mediators were determined using a multiplex bead assay, compared between the groups and correlated to the microbial profile. The achieved data was analysed using PCoA, DESeq2 and two machine learning algorithms, OPLS-DA and sPLS-DA.
RESULTS
Differential abundance DESeq2 analyses showed that the four most highly enriched (log2 FC >20) amplicon sequence variants (ASVs) in the non-RA periodontitis group included sp., sp., sp., and sp. whereas sp., sp., sp., and were the most highly enriched ASVs (log2 FC >20) in the RA group. OPLS-DA with log2 FC analyses demonstrated that the top ASVs with the highest importance included sp. having a positive correlation with non-RA group, and seven ASVs belonging to , sp., , , spp. and with a positive correlation with RA group. Among the detected inflammatory mediators in saliva samples, TWEAK/TNFSF12, IL-35, IFN-α2, pentraxin-3, gp130/sIL6Rb, sIL-6Ra, IL-19 and sTNF-R1 were found to be significantly increased in patients with periodontitis and RA compared to non-RA group with periodontitis. Moreover, correlations between ASVs and inflammatory mediators using sPLS-DA analysis revealed that TWEAK/TNFSF12, pentraxin-3 and IL-19 were positively correlated with the ASVs sp., , sp., and sp.
CONCLUSION
Our results suggest that the combination of microbes and host inflammatory mediators could be more efficient to be used as a predictable biomarker associated with periodontitis and RA, as compared to microbes and inflammatory mediators alone.
Topics: Arthritis, Rheumatoid; Chronic Periodontitis; Humans; Inflammation Mediators; Microbiota; RNA, Ribosomal, 16S
PubMed: 35360114
DOI: 10.3389/fcimb.2022.841139 -
Journal of Basic Microbiology 2005The regulation of de novo pyrimidine biosynthesis in the nutritionally versatile bacterium Acidovorax delafieldii ATCC 17505T was influenced by carbon source and...
The regulation of de novo pyrimidine biosynthesis in the nutritionally versatile bacterium Acidovorax delafieldii ATCC 17505T was influenced by carbon source and pyrimidine supplementation. Uracil supplementation of succinate-grown A. delafieldii ATCC 17505T cells produced a greater decrease in the de novo pyrimidine biosynthetic pathway enzyme activities than did orotic acid supplementation. The presence of orotic acid or uracil in the medium of the glucose-grown wild type cells generally increased the pyrimidine biosynthetic enzyme activities. After the pyrimidine limitation of an A. delafieldii orotate phosphoribosyltransferase mutant strain, the pyrimidine biosynthetic pathway enzyme activities in the glucose-grown mutant cells were more highly derepressed than in the succinate-grown mutant cells.
Topics: Comamonadaceae; Gene Expression Regulation, Bacterial; Glucose; Orotate Phosphoribosyltransferase; Orotic Acid; Pyrimidines; Succinic Acid
PubMed: 15812862
DOI: 10.1002/jobm.200410506 -
International Journal of Systematic and... Nov 2011Strain N35(T) was isolated from surface-sterilized wheat roots and is a Gram-negative, aerobic, motile straight rod. Strain N35(T) tested oxidase-positive and...
Strain N35(T) was isolated from surface-sterilized wheat roots and is a Gram-negative, aerobic, motile straight rod. Strain N35(T) tested oxidase-positive and catalase-negative and grew optimally at pH 7.0, 30 °C and in the absence of NaCl. 16S rRNA gene sequence analysis showed over 97 % sequence similarity to strains of the environmental species Acidovorax delafieldii, A. facilis, A. defluvii, A. temperans, A. caeni and A. soli, as well as Acidovorax valerianellae, A. anthurii and Simplicispira metamorpha. DNA-DNA hybridization between strain N35(T) and phylogenetically closely related type strains was 25.3-55.7 %, which clearly separates the strain from these closely related species. Additionally, phenotypic properties, such as substrate metabolism profiles as determined by a Biolog GN2 assay and cell-wall fatty acid profiles, particularly contents of the fatty acids C(16 : 0), C(16 : 1)ω7c/t, C(17 : 0), C(17 : 0) cyclo, C(18 : 0) cyclo and C(19 : 0) cyclo, facilitated the differentiation of the newly isolated strain N35(T) from its closest relatives. The isolate underwent phenotypic variation at high frequency in laboratory media. The DNA G+C content was 64.9 mol%. We propose that strain N35(T) is classified as a representative of a novel species within the genus Acidovorax, and suggest the name Acidovorax radicis sp. nov. The type strain is strain N35(T) ( = DSM 23535(T) = LMG 25767(T)).
Topics: Base Composition; Comamonadaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sodium Chloride; Soil Microbiology; Triticum
PubMed: 21131505
DOI: 10.1099/ijs.0.025296-0 -
European Journal of Biochemistry Feb 1993The functional properties of the major outer-membrane protein of Acidovorax delafieldii, the anion-selective porin Omp34, were investigated in artificial membranes....
The functional properties of the major outer-membrane protein of Acidovorax delafieldii, the anion-selective porin Omp34, were investigated in artificial membranes. Detergent-solubilized porin incorporates into the membrane in a undirectional orientation solely determined by protein features. This enabled us to characterize the vectorial properties of the porin channels. Omp34 is electrostatically asymmetric regarding both the ion conductivity of a single trimer and the macroscopic ion conductance of multiple porin molecules. Voltage-dependent closing occurred at negative potentials; 50% of the channels were already closed at -10 mV (switching voltage). Our experimental results suggest that protein charges situated on flexible parts inside the channel are involved in the gating mechanism. A simple model is proposed illustrating the mechanism of voltage-dependent opening and closing of the porin channels. This model explains the functional characteristics of Omp34 and the dependence of the switching voltage on the electrolyte concentration in particular. Further factors influencing voltage gating include the buffer concentration as well as the technique used for membrane formation. Altogether these factors may explain the relatively high voltages needed to obtain voltage gating with other porins.
Topics: Bacterial Outer Membrane Proteins; Hydrogen-Ion Concentration; Ion Channel Gating; Ion Channels; Lipid Bilayers; Porins; Pseudomonas
PubMed: 7680309
DOI: 10.1111/j.1432-1033.1993.tb17642.x -
Journal of Bioscience and Bioengineering 2002A gene encoding poly(tetramethylene succinate), PBS, depolymerase, pbsA, has been cloned from Acidovorax delafieldii strain BS-3 chromosomal DNA. The clone expressed in...
A gene encoding poly(tetramethylene succinate), PBS, depolymerase, pbsA, has been cloned from Acidovorax delafieldii strain BS-3 chromosomal DNA. The clone expressed in Escherichia coli showed the ability to degrade both PBS and poly[(tetramethylene succinate)-co-adipate] that are kinds of biodegradable plastics. PBS depolymerase was considered to be a kind of lipase, since it also degrades olive oil. It had no apparent hydrophobic-amino-acid-rich region which exists in other known plastic-degrading enzymes. From the result of amino acid homology search, PbsA was found to have some similarities with lipases of Streptomyces sp. and Mollaxella sp. In the motif surrounding the active site Ser residue (Gly-X1-Ser-X2-Gly), PbsA was revealed to have a Trp residue in the X1 position instead of His which is most likely found in other bacterial lipases.
PubMed: 16233195
DOI: 10.1263/jbb.93.245 -
Journal of Bacteriology Jul 1991The major outer membrane protein (Omp34) of Acidovorax delafieldii (formerly Pseudomonas delafieldii) was purified to homogeneity and was characterized biochemically and...
The major outer membrane protein (Omp34) of Acidovorax delafieldii (formerly Pseudomonas delafieldii) was purified to homogeneity and was characterized biochemically and functionally. The polypeptide has an apparent molecular weight (Mr) of 34,000, and it forms stable oligomers at pH 9.0 in the presence of 10% octylpolyoxyethylene or 2% lithium dodecyl sulfate below 70 degrees C. The intact protein has a characteristic secondary structure composition, as revealed by Fourier transforming infrared spectroscopy (about 60% beta sheet). These features and the amino acid composition are typical for porins. The purified Omp34 is associated with 1 to 2 mol of lipopolysaccharide per mol of the monomer. Pore-forming activity was demonstrated with lipid bilayer experiments. Single-channel and selectivity measurements showed that the protein forms highly anion-selective channels. The unusual dependence of the single-channel conductance on salt concentration suggests that the porin complexes bear positive surface charges, accumulating negatively charged counterions at the pore mouth.
Topics: Bacterial Outer Membrane Proteins; Ion Channels; Lipid Bilayers; Membrane Potentials; Molecular Weight; Porins; Protein Conformation; Pseudomonas; Salts
PubMed: 1712013
DOI: 10.1128/jb.173.13.4182-4187.1991 -
International Journal of Systematic and... Jan 2024A Gram-stain-negative strain, designated as D2M1 was isolated from xylene-degrading enrichment culture and characterized using a polyphasic approach to determine its...
A Gram-stain-negative strain, designated as D2M1 was isolated from xylene-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain D2M1 belongs to the genus , with the highest 16S rRNA gene similarity to DSM 64 (99.93 %), followed by DSM 23535 (98.77 %) and MTCC 12652 (98.76 %). The draft genome sequence of strain D2M1 is 5.49 Mb long, and the G+C content of the genome is 64.2 mol%. Orthologous average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain D2M1 and its closest relatives were below the threshold values for species demarcation confirming that strain D2M1 is distinctly separated from its closest relatives. The whole genome analysis of the strain revealed a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete -cleavage pathway including an I.2.C-type catechol 2,3-dioxygenase (C23O) gene. The strain was able to degrade benzene and ethylbenzene as sole sources of carbon and energy under aerobic and microaerobic conditions. Cells were facultatively aerobic rods and motile with a single polar flagellum. The predominant fatty acids (>10 % of the total) of strain D2M1 were summed feature 3 (C 7/C 6), C and summed feature 8 (C 7/C 6). The major ubiquinone of strain D2M1 was Q8, while the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on polyphasic data, it is concluded that strain D2M1 represents a novel species of the genus , for which the name of sp. nov. is proposed. The type strain of the species is strain D2M1 (=DSM 115238=NCAIM B.02679).
Topics: Xylenes; RNA, Ribosomal, 16S; Base Composition; Fatty Acids; Phylogeny; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Hydrocarbons, Aromatic; Bacteria
PubMed: 38180316
DOI: 10.1099/ijsem.0.006219 -
Systematic and Applied Microbiology Nov 2019During long-term extra-terrestrial missions, food is limited and waste is generated. By recycling valuable nutrients from this waste via regenerative life support...
During long-term extra-terrestrial missions, food is limited and waste is generated. By recycling valuable nutrients from this waste via regenerative life support systems, food can be produced in space. Astronauts' urine can, for instance, be nitrified by micro-organisms into a liquid nitrate fertilizer for plant growth in space. Due to stringent conditions in space, microbial communities need to be be defined (gnotobiotic); therefore, synthetic rather than mixed microbial communities are preferred. For urine nitrification, synthetic communities face challenges, such as from salinity, ureolysis, and organics. In this study, a synthetic microbial community containing an AOB (Nitrosomonas europaea), NOB (Nitrobacter winogradskyi), and three ureolytic heterotrophs (Pseudomonas fluorescens, Acidovorax delafieldii, and Delftia acidovorans) was compiled and evaluated for these challenges. In reactor 1, salt adaptation of the ammonium-fed AOB and NOB co-culture was possible up to 45mScm, which resembled undiluted nitrified urine, while maintaining a 44±10mgNH-NLd removal rate. In reactor 2, the nitrifiers and ureolytic heterotrophs were fed with urine and achieved a 15±6mg NO-NLd production rate for 1% and 10% synthetic and fresh real urine, respectively. Batch activity tests with this community using fresh real urine even reached 29±3mgNLd. Organics removal in the reactor (69±15%) should be optimized to generate a nitrate fertilizer for future space applications.
Topics: Ammonia; Bioreactors; Comamonadaceae; Delftia acidovorans; Microbiota; Nitrification; Nitrites; Nitrobacter; Nitrosomonas europaea; Pseudomonas fluorescens; Urea; Urine; Waste Disposal, Fluid
PubMed: 31623889
DOI: 10.1016/j.syapm.2019.126021