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At least 721 records · Page 40Linked to original sources
PubMed2001

The heterocyclic ring fission and dehydroxylation of catechins and related compounds by Eubacterium sp. strain SDG-2, a human intestinal bacterium.

A human intestinal bacterium, Eubacterium (E.) sp. strain SDG-2, was tested for its ability to metabolize various (3R)- and (3S)-flavan-3-ols and their 3-O-gallates. This bacterium cleaved the C-ring of (3R)- and (3S)-flavan-3-ols to give 1,3-diphenylpropan-2-ol derivatives, but not their 3-O-gallates. Furthermore, E. sp. strain SDG-2 had the ability of p-dehydroxylation in the B-ring of (3R)-flavan-3-ols, such as (-)-catechin, (-)-epicatechin, (-)-gallocatechin and (-)-epigallocatechin, but not of (3S)-flavan-3-ols, such as (+)-catechin and (+)-epicatechin.

Biotransformation↗
PubMed2006

Catechol siderophore excretion by magnetotactic bacterium Magnetospirillum magneticum AMB-1.

Siderophore activity was detected in the culture supernatant of the magnetotactic bacterium Magnetospirillum magneticum AMB-1. Here we report the first structural elucidation of a siderophore produced by a magnetotactic bacterium. The structure of the purified compound was 3,4-dihydroxybenzoic acid as determined by nuclear magnetic resonance (NMR) and electro-spray ionization mass spectroscopy (ESI-MS).

Catechols↗
PubMed2002

Effect of algal extract on H2 production by a photosynthetic bacterium Rhodobium marinum A-501: analysis of stimulating effect using a kinetic model.

We have established a system for hydrogen (H2) production from algal starch via lactic acid using a mixed culture of a lactic acid bacterium, Lactobacillus amylovorus, and a photosynthetic bacterium, Rhodobium marinum A-501. We found that the H2 production from lactate was stimulated in the presence of algal extract, which was obtained from algal biomass homogenate used as a substrate in the system by removing settleable solids including starch. To analyze the stimulating effect of algal extract on H2 production, we developed a kinetic model for H2 production by R. marinum A-501. The model revealed that approximately 20% of lactate was consumed for cell mass production, and the remaining portion was a source of reducing power to drive hydrogen production or other cellular processes. In the presence of algal extract, the model indicated that the conversion efficiency from lactate to the reducing power increased from 0.56 to 0.80 and nitrogenase activity increased up to twofold, resulting in the increase in yield of hydrogen from lactate from 29% to 48%. These results suggest that algal extract can attenuate the limitation process in lactate catabolism by which the supplementation of reducing power to drive H2 production was suppressed.

Journal Article↗
PubMed2000

Purification and characterization of a novel DNA repair enzyme from the extremely radioresistant bacterium Rubrobacter radiotolerans.

Rubrobacter radiotolerans is an extremely radioresistant bacterium. It exhibits higher resistance than the well-known radioresistant bacterium Deinococcus radiodurans, but the molecular mechanisms responsible for the radio-resistance of R. radiotolerans remain unknown. In the present study, we have demonstrated the presence of a novel DNA repair enzyme in R. radiotolerans cells that recognizes radiation-induced DNA damages such as thymine glycol, urea residues, and abasic sites. The enzyme was purified from the crude cell extract by a series of chromatography to an apparent physical homogeneity. The purified enzyme showed a single band with a molecular mass of approximately 40 kDa in SDS-polyacrylamide gel electrophoresis, and was designated as R-endonuclease. R-Endonuclease exhibited repair activity for thymine glycol, urea residues, and abasic sites present in plasmid DNA, but did not act on intact DNA, UV-irradiated DNA and DNA containing reduced abasic sites. The substrate specificity together with the salt and pH optima suggests that R-endonuclease is a functional homolog of endonuclease III of Escherichia coli.

Apurinic Acid↗
PubMed1994

Cloning and sequence of the L2 form of RubisCO from a marine obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110.

A form II ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) gene was isolated and sequenced from a marine hydrogen-oxidizing bacterium, Hydrogenovibrio marinus strain MH-110. To our knowledge, this is the first report for the sequence of a form II (L2-form) RubisCO gene derived from a chemolithoautotrophic bacterium. The form II RubisCO gene coded for 463 amino acid residues (1389 bp, M(r) = 50,655). The deduced amino acid sequence had high homology with those of the L2-form RubisCO of Rhodospirillum rubrum (63%) and the L4-form RubisCO from Rhodobacter sphaeroides (62%), but low similarity to other L8S8 form RubisCOs (under 40%).

Amino Acid Sequence↗
PubMed2006

Effect of cell appendages on the adhesion properties of a highly adhesive bacterium, Acinetobacter sp. Tol 5.

A toluene-degrading bacterium, Acinetobacter sp. Tol 5, shows noteworthy adhesiveness mediated by two types of cell appendages. In this study, we obtained a less-adhesive mutant, T1, which lost both types of appendages, and investigated how the cell appendages affect the adhesion properties of this useful bacterium for environmental technology. Wild-type cells attained irreversible adhesion to polyurethane carriers within 30 s, while adhesion of T1 cells was still reversible at that time. While T1 showed decreased adhesion with decreasing ionic strength and did not adhere at all at 0.015 mM, adhesion of the wild type was fully independent of ionic strength. Acinetobacter sp. Tol 5 was also found to be not motile. Our results suggest that through the long distant interaction mediated by the appendages between the cells and surfaces, Tol 5 cells can attain irreversible adhesion very quickly without approaching the vicinity of the substratum.

Acinetobacter↗
PubMed1998

Optimization for beta-mannanase production of a psychrophilic bacterium, Flavobacterium sp.

We found that a psychrophilic bacterium, Flavobacterium sp., characterized in this study, has a beta-mannanase (EC 3.2.1.78) activity in the culture medium. The mannanase activity was the highest in the culture medium, containing 1.0% (w/v) guar gum (as a carbon source), 0.3% (NH4)2SO4 (as a nitrogen source), and 0.06% (w/v) yeast extract, of five-days cultivation at 4 degrees C. No mannanase activity was found in the medium containing a monosaccharide or a disaccharide as a carbon source, although the psychrophile could use them. The enzyme activity was found only when the bacterium was cultured in the medium containing a polysaccharide. The enzyme preparation showed a single activity band on a washed gel of SDS-PAGE. The optimal temperature for the enzyme activity was 35 degrees C. When the reaction was done at 10 degrees C, the enzyme showed 25% of the optimal activity. The beta-mannanase preparation efficiently hydrolyzed guar gum, locust bean gum, and glucomannan as well as beta-mannan.

Bacterial Proteins↗
PubMed2001

A cryptic plasmid, pAO1, from a compost bacterium, Bacillus sp.

The complete nucleotide sequence of a new cryptic plasmid, pAO1 isolated from a compost bacterium Bacillus sp., has been analyzed. Analysis of the PCR-based 16S rRNA sequence showed the bacterium harboring pAO1 was closely related to Bacillus pallidus. The plasmid pAO1 was 3,325 bp in size. Two open reading frames, ORF1 and ORF2, encoding putative polypeptides of 248 and 290 amino acids, respectively, were identified within the sequence. The ORF1 has a limited sequence similarity to an integrase/recombinase, while the ORF2 has high similarity with the replication protein of pBC1 from Bacillus coagulans. A putative origin sequence for a plus-strand was located between ORFs. Southern blot analysis indicates this plasmid replicates via a rolling circle-type mechanism.

Bacillus↗
PubMed2001

Characterization of the gene encoding the beta-lactamase of the psychrophilic marine bacterium Moritella marina strain MP-1.

The beta-lactamase gene (mbla) of the psychrophilic marine bacterium Moritella marina strain MP-1 was identified in a previously isolated genomic DNA fragment and it was expressed in Escherichia coli cells. The mbla gene encoded a protein consisting of 287 amino acid residues. Its predicted amino acid sequence showed approximately 50% identity with that of a number of class A beta-lactamases, especially with that of CARB/PSE type of beta-lactamases (carbenicillinases). E. coli transformed with the plasmid containing mbla grew on an ampicillin-containing plate at 37 degrees C but not at 42 degrees C, suggesting that the beta-lactamase of this bacterium is heat-labile.

Amino Acid Sequence↗
PubMed2001

Piezoresponse of the cyo-operon coding for quinol oxidase subunits in a deep-sea piezophilic bacterium, Shewanella violacea.

We have isolated the genes for quinol oxidase from a deep-sea piezophilic bacterium, Shewanella violacea. Analysis of the deduced amino acid sequences of the cyo subunits showed that this oxidase has high similarity to Escherichia coli bo-type quinol oxidase. Northern blot analysis showed that these genes are expressed at a high level when the bacterium is grown at elevated pressure. Upstream in the cyo-operon, a sigma54-binding motif and an octamer sequence unit were found, suggesting that these elements may play a role in regulation of expression of the cyo-operon in response to changes in pressure.

Base Sequence↗
PubMed2001

A novel cryoprotective protein (CRP) with high activity from the ice-nucleating bacterium, Pantoea agglomerans IFO12686.

The ice-nucleating bacterium, Pantoea agglomerans IFO12686, induces the cryoprotective protein (CRP) by cold acclimation at 12 degrees C. The CRP was purified to apparent homogeneity by various chromatographies. We found that the purified CRP was a monomer of approximately 29,000 according to gel filtration chromatography and SDS-PAGE, and was a heat-stable protein. The CRP could protect freeze-labile enzymes, lactate dehydrogenase (LDH), alcohol dehydrogenase (ADH) and isocitrate dehydrogenase (iCDH), against freezing-thawing denaturation. The activity of the CRP was about 3.5 x 10(4) times more effective than bovine serum albumin (BSA) and 2 x 10(6) times than COR26 from the ice-nucleating bacterium Pseudomonas fluorescens KUIN-1. We confirmed that the CRP was a novel protein, as judged by the a different molecule mass from the already-known cryoprotectants, and has an extremely high cryoprotective activity.

Ammonium Sulfate↗
PubMed2004

Rare bacterium of new genus isolated with prolonged enrichment culture.

Dynamic change in microbial flora was monitored with an oxygen electrode. The 1st phase microorganisms, which first grew well in LB medium, were followed by the 2nd phase microorganisms, which supposedly assimilated microbial cells of the 1st phase and their metabolites. In a similar way, a change in microbial flora was observed from the 1st phase to the 4th phase in 84 hr. Based on this observation, prolonged enrichment culture was done for as long as two months to increase the ratio of existence of rare microorganisms. From these culture liquids, four slow-growing bacteria (provisionally named Shinshu-ah1, -ah2, -ah3, and -ah4), which formed scarcely visible small colonies, were isolated. Sequence analysis of their 16S rDNA showed that Shinshu-ah1 had 97% homology with Bradyrhizobium japonicum and uncultured alpha proteobacterium clone blaii 16, Shinshu-ah2 91% with Rasbo bacterium, Alpha proteobacterium 34619, Bradyrhizobium genosp. P, Afipia felis and an unidentified bacterium, Shinshu-ah3 99% with Methylobacterium mesophilicum, and Shinshu-ah4 95% with Agromyces ramosus DSM 43045. Phylogenetic study indicated that Shinshu-ah2 had a possibility to form a new family, Shinshu-ah1 a new genus, and Shinshu-ah4 a new species.

Afipia↗
PubMed2001

Isolation of a bacterium from mangrove soil for degradation of sea sludge.

Sea sludge, which is sediment of fish excrement and sewage on the sea bottom, continues to be a serious environmental problem. It has the potential to cause eutrophication and red tide, resulting in the death of shellfish and leading to an offensive odor. Soil taken from a mangrove swamp was added to sea sludge, which promoted an initial fermentation of the sludge components. This article reports on the isolation of a bacterium from mangrove soil that is involved in that fermentation. Three bacteria were isolated on a marine agar plate after incubating for 12 h at 60 degrees C. One of these bacteria fermented sea sludge. 16S rDNA of this bacterium was sequenced, and it had a high homology with that of Bacillus fumarioli LMG17489 (AJ250056).

Bacteria↗
PubMedDate not supplied

Up-regulation of pathogenesis-related proteins in the apoplast of Malus domestica after application of a non-pathogenic bacterium.

The intercellular washing fluid (IWF) of Malus domestica cv. Holsteiner Cox before and after application of the non-pathogenic bacterium Pseudomonas fluorescens Bk3 to the leaves was investigated in a comparative manner. SDS-PAGE in combination with ESI Q-ToF mass spectrometry, and homology search in relevant data bases revealed the highly up-regulated expression of several pathogenesis-related plant proteins in the apoplast of the leaves treated with P. fluorescens. These proteins were beta3-1,3-glucanase, chitinase, thaumatin-like protein, ribonuclease-like protein, and a hevein-like protein. Moreover, a 9 kDa non-specific lipid transfer protein was significantly reduced after the application of P. fluorescens. The possible relevance of a pre-treatment of apple cultivars with the non-pathogenic bacterium P. fluorescens Bk3, as an alternative method to the treatment with fungicides, for increasing the resistance of susceptible apple cultivars against an infection with the fungus Venturia inaequalis is discussed.

Amino Acid Sequence↗
PubMed2005

Pathogenicity of bacterium, Xenorhabdus nematophila isolated from entomopathogenic nematode (Steinernema carpocapsae) and its secretion against Galleria mellonella larvae.

The entomopathogenic bacterium, Xenorhabdus nematophila was isolated from the hemolymph of Galleria mellonella infected with Steinernema carpocapsae. The bacterial cells and its metabolic secretions have been found lethal to the Galleria larvae. Toxic secretion in broth caused 95% mortality within 4 d of application whereas the bacterial cells caused 93% mortality after 6 d. When filter and sand substrates were compared, the later one was observed as appropriate. Similarly, bacterial cells and secretion in broth were more effective at 14% moisture and 25 degrees C temperature treatments. Maximum insect mortality (100%) was observed when bacterial concentration of 4x10(6) cells/ml was used. Similarly, maximum bacterial cells in broth (95%) were penetrated into the insect body within 2 h of their application. However, when stored bacterial toxic secretion was applied to the insects its efficacy declined. On the other hand, when the same toxic secretion was dried and then dissolved either in broth or water was proved to be effective. The present study showed that the bacterium, X. nematophila or its toxic secretion can be used as an important component of integrated pest management against Galleria.

Animals↗
PubMedDate not supplied

Isolation of an unidentified, nonfermentative, gram-negative bacterium from turkeys and chickens: 38 cases (1995-2001).

Thirty-eight cases were identified in which a nonfermentative, gram-negative, rod-shaped bacterium was isolated from the respiratory system of turkeys and chickens. Cases were submitted from various parts of the country. Preliminary assessment of phenotypic characteristics indicated this bacterium was different from common pathogenic or opportunistic bacteria isolated from the avian respiratory tract. Most cases reported a history of respiratory distress and/or increased flock mortality. Lesions seen in infected birds included tracheitis and pneumonia, which correlate with the sites of isolation. Sixty-one percent of the isolations were made from the trachea and 25% from the lung. Age of infected birds ranged from 35 to 315 days in turkeys and 53 days to 3 yr in chickens. In most instances (90%), other bacteria were also isolated from affected sites. The significance of this organism in respiratory disease in birds is unknown.

Animals↗
PubMed2005

Recovery of microbially mediated processes in soil augmented with a pentachlorophenol-mineralizing bacterium.

Specific physiological groups can be used to evaluate the recovery of soil microbial communities following disturbance. In this study, soil was contaminated with pentachlorophenol (PCP) to assess the resiliency of microorganisms responsible for carbon and nitrogen cycling. Methane fluxes were monitored in soil microcosms to evaluate the effects of contamination and augmentation on microbial populations involved in carbon cycling. The addition of a PCP-mineralizing bacterium, Sphingomonas chlorophenolica strain RA2, enhanced the recovery of methane-oxidizing capacity relative to uninoculated treatments when soil was contaminated with low concentrations of PCP (10 and 50 microg/g soil, ppm). At the highest level of PCP contamination tested (300 ppm), there was no recovery of methane-oxidizing capacity whether or not the PCP-mineralizing bacterium was added to soil. The nitrogen-cycling capacity of contaminated and augmented soil was tested by measuring nitrification potentials. The addition of PCP resulted in a concentration-dependent reduction in nitrification rates. After three months of incubation, all augmented soils had nitrification rates equivalent to the uncontaminated control, and the uninoculated soils contaminated with 100 and 300 ppm PCP still were impaired in their nitrification potentials. These results indicate that biological removal of a contaminant has the potential to restore microbially mediated processes to levels observed prior to contamination.

Ammonia↗
PubMed2006

Evaluation of nitrate removal by continuous culturing of an aerobic denitrifying bacterium, Paracoccus pantotrophus.

Nitrate removal under aerobic conditions was investigated using pure cultures of Paracoccus pantotrophus, which is a well-known aerobic-denitrifying (AD) bacterium. When a high concentration of cultures with a high carbon/nitrogen (C/N) ratio was preserved at the beginning of batch experiments, subsequently added nitrate was completely removed. When continuous culturing was perpetuated, a high nitrate removal rate (66.5%) was observed on day 4 post-culture, although gradual decreases in AD ability with time were observed. The attenuation in AD ability was probably caused by carbon limitation, because when carbon concentration of inflow water was doubled, nitrate removal efficiency improved from 18.1% to 59.6%. Bacterial community analysis using the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method showed that P. pantotrophus disappeared in the suspended medium on day 8 post-culture, whereas other bacterial communities dominated by Acidovorax sp. appeared. Interestingly, this replaced bacterial community also showed AD ability. As P. pantotrophus was detected as attached colonies around the membrane and bottom of the reactor, this bacterium can therefore be introduced in a fixed form for treatment of wastewater containing nitrate with a high C/N ratio.

Aerobiosis↗