Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
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| high-resolution x-ray structure of the dna-binding protein hu from the hyper-thermophilic thermotoga maritima and the determinants of its thermostability. | the histone-like dna-binding proteins (hu) are a convenient model for studying factors affecting thermostability because of their relatively simple, easily comparable structures, their common function, and their presence in organisms of widely differing thermostability. we report the determination of the high-resolution structure (1.53 a) at 273 k and 100 k of the hu protein from the hyper-thermophilic eubacterium thermotoga maritima(hu tmar, t(m)=80.5 degrees c). the structural data presented c ... | 2003 | 12664263 |
| contribution of acetate to butyrate formation by human faecal bacteria. | acetate is normally regarded as an endproduct of anaerobic fermentation, but butyrate-producing bacteria found in the human colon can be net utilisers of acetate. the butyrate formed provides a fuel for epithelial cells of the large intestine and influences colonic health. [1-(13)c]acetate was used to investigate the contribution of exogenous acetate to butyrate formation. faecalibacterium prausnitzii and roseburia spp. grown in the presence of 60 mm-acetate and 10 mm-glucose derived 85-90 % but ... | 2004 | 15182395 |
| metabolic properties of eubacterium pyruvativorans, a ruminal 'hyper-ammonia-producing' anaerobe with metabolic properties analogous to those of clostridium kluyveri. | eubacterium pyruvativorans i-6(t) is a non-saccharolytic, amino-acid-fermenting anaerobe from the rumen, isolated by its ability to grow on pancreatic casein hydrolysate (pch) as sole c source. this study investigated its metabolic properties and its likely ecological niche. additional growth was supported by pyruvate, vinyl acetate, and, to a lesser extent, lactate and crotonate, and also by a mixture of amino acids (alanine, glycine, serine and threonine) predicted to be catabolized to pyruvat ... | 2004 | 15347751 |
| comparison of type 1 and type 2 cytokine production by mononuclear cells cultured with streptococcus mutans and selected other caries bacteria. | a feature of pulpal immune responses is the predominance of type 1 cytokine mrna under shallow caries and a mixed (type 1/type 2) profile under deep caries. these results prompted an examination of the cytokine profiles induced by bacteria in shallow caries (streptococcus mutans and actinomyces viscosus) and deep caries (lactobacillus casei, pseudoramibacter alactolyticus, and prevotella intermedia). all isolates induced interferon-gamma and interleukin-10, whereas interleukin-4 and interleukin- ... | 2004 | 15107645 |
| the crystal structure of an est2 mutant unveils structural insights on the h group of the carboxylesterase/lipase family. | esterase 2 (est2) from the thermophilic eubacterium alicyclobacillus acidocaldarius is a thermostable serine hydrolase belonging to the h group of the esterase/lipase family. this enzyme hydrolyzes monoacylesters of different acyl-chain length and various compounds with industrial interest. est2 displays an optimal temperature at 70 degrees c and maximal activity with pnp-esters having acyl-chain bearing from six to eight carbon atoms. est2 mutants with different substrate specificity were also ... | 2004 | 15381425 |
| ribosomal antibiotics: structural basis for resistance, synergism and selectivity. | various antibiotics bind to ribosomes at functionally relevant locations such as the peptidyl-transferase center (ptc) and the exit tunnel for nascent proteins. high-resolution structures of antibiotics bound to ribosomal particles from a eubacterium that is similar to pathogens and an archaeon that shares properties with eukaryotes are deciphering subtle differences in these highly conserved locations that lead to drug selectivity and thereby facilitate clinical usage. these structures also sho ... | 2004 | 15491801 |
| characterization of a 5'-polynucleotide kinase/3'-phosphatase from bacteriophage rm378. | a polynucleotide kinase from the thermophilic bacteriophage rm378 that infects the thermophilic eubacterium rhodothermus marinus was identified, expressed, and purified. this polynucleotide kinase was demonstrated to have a 5'-kinase domain as well as a 3'-phosphohydrolase domain. the rm378 polynucleotide kinase had limited sequence similarity to the 5'-kinase domain of the t4 bacteriophage polynucleotide kinase, but apparent homology was not evident within the 3'-phosphohydrolase domain. the do ... | 2004 | 15579472 |
| effects of deoxynivalenol on general performance and electrophysiological properties of intestinal mucosa of broiler chickens. | a feeding trial was conducted to evaluate the effects of diets contaminated with deoxynivalenol (don on the performance of broilers and on the electro-physiological parameters of the gut. the control group was fed the starter and finisher diets without addition of don. another group of broilers was fed the starter and finisher diets with 10 mg/kg don, whereas another group was fed the don-contaminated diets supplemented with a microbial feed additive (eubacterium sp.). the diets were provided ad ... | 2004 | 15615008 |
| protein-based biosensors for diabetic patients. | in this article we show the recent progress in the field of glucose sensing based on the utilization of enzymes and proteins as probes for stable and non-consuming fluorescence biosensors. we developed a new methodology for glucose sensing using inactive forms of enzymes such as the glucose oxidase from aspergillus niger, the glucose dehydrogenase from the thermophilic microorganism thermoplasma acidophilum, and the glucokinase from the thermophilic eubacterium bacillus stearothermophilus. gluco ... | 2004 | 15617257 |
| enhanced biohydrogen production from sewage sludge with alkaline pretreatment. | batch tests were carried out to analyze influences of the alkaline pretreatment and initial ph value on biohydrogen production from sewage sludge. experimental results of the impact of different initial ph on biohydrogen production showed that both the maximal hydrogen yield occurred and that no methane was detected in the tests of at the initial ph of 11.0. the final ph decreased at the initial ph of 7.0-12.5 but increased atthe initial ph of 3.0-6.0, probably due to the combination of solubili ... | 2004 | 15224755 |
| a new real time pcr (taqman pcr) system for detection of the16s rdna gene associated with fecal bacteria. | a recent pcr detection technique (taqman) based on a 3'-minor groove binder (mgb) probe was applied to the detection of fecal-dominant bacteria to assess fecal contamination in environmental samples. primers and probes used bacterial 16s ribosomal dna (16s rdna) as a gene marker and accurately defined with specificity a cluster of phylotypes within the gram-positive low gc division. this cluster of phylotypes, called fec1, corresponds to around 5% of human fecal microflora. fec1 clustered 16s rd ... | 2004 | 15325749 |
| bacillus odysseyi sp. nov., a round-spore-forming bacillus isolated from the mars odyssey spacecraft. | a round-spore-forming bacillus species that produces an exosporium was isolated from the surface of the mars odyssey spacecraft. this novel species has been characterized on the basis of phenotypic traits, 16s rdna sequence analysis and dna-dna hybridization. according to the results of these analyses, this strain belongs to the genus bacillus and is a gram-positive, aerobic, rod-shaped, endospore-forming eubacterium. ultrathin sections of the spores showed the presence of an exosporium, spore c ... | 2004 | 14742480 |
| reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. | the intestinal bacterial microflora plays an important role in the aetiology of inflammatory bowel disease (ibd). as most of the colonic bacteria cannot be identified by culture techniques, genomic technology can be used for analysis of the composition of the microflora. | 2004 | 15082587 |
| first bacterial chalcone isomerase isolated from eubacterium ramulus. | the human fecal anaerobe eubacterium ramulus is capable of degrading various flavonoids, including the flavone naringenin. the first step in the proposed degradation pathway is the isomerization of naringenin to the corresponding chalcone. cell-free extracts of e. ramulus displayed chalcone isomerase activity. the enzyme from e. ramulus was purified to homogeneity. its apparent molecular mass was estimated to be 136 and 129 kda according to gel filtration and native polyacrylamide gel electropho ... | 2004 | 15127184 |
| investigation of zinc-containing peptide deformylase from leptospira interrogans by x-ray absorption near-edge spectroscopy. | peptide deformylase (pdf, ec 3.5.1.27) is essential for the normal growth of eubacterium but not for mammalians. recently, pdf has been studied as a target for new antibiotics. its activity is strongly dependent on the bound metal ion. the crystallographic studies did not show any significant structural difference upon various bound metal ions. in this paper, x-ray absorption spectroscopy was employed to determine the local structure around the zinc ion of pdf from leptospira interrogans in dry ... | 2004 | 15616374 |
| tungsten-containing aldehyde oxidoreductase of eubacterium acidaminophilum. | aldehyde oxidoreductase of eubacterium acidaminophilum was purified to homogeneity under strict anaerobic conditions using a four-step procedure. the purified enzyme was present as a monomer with an apparent molecular mass of 67 kda and contained 6.0 +/- 0.1 iron, 1.1 +/- 0.2 tungsten, about 0.6 mol pterin cofactor and zinc, but no molybdenum. the enzyme activity was induced if a molar excess of electron donors, such as serine and/or formate, were supplied in the growth medium compared to readil ... | 2004 | 14686934 |
| a cross-genomic approach for systematic mapping of phenotypic traits to genes. | we present a computational method for de novo identification of gene function using only cross-organismal distribution of phenotypic traits. our approach assumes that proteins necessary for a set of phenotypic traits are preferentially conserved among organisms that share those traits. this method combines organism-to-phenotype associations,along with phylogenetic profiles,to identify proteins that have high propensities for the query phenotype; it does not require the use of any functional anno ... | 2004 | 14707173 |
| stereochemical course of the generation of 3-mercaptohexanal and 3-mercaptohexanol by beta-lyase-catalyzed cleavage of cysteine conjugates. | the product resulting from the reaction between e-2-hexenal and l-cysteine was shown to be a diastereoisomeric mixture of 2-(2-s-l-cysteinylpentyl)-1,3-thiazolidine-4-carboxylic acid 1. treatment of the conjugate with two sources of cysteine-s-conjugate beta-lyase (tryptophanase from e. coli and a crude enzyme extract prepared from eubacterium limosum) resulted in the formation of 3-mercaptohexanal. the reaction proceeded with a slight preference for the (s)-configured product, however, with low ... | 2004 | 14709022 |
| genomic investigation of the system for selenocysteine incorporation in the bacterial domain. | the elucidation of nearly 100 bacterial genomes has made it possible to categorize them into two groups, according to the presence or absence of a selenocysteine (sec) trna. in the group with the trna, a sec incorporation system like that of escherichia coli would be expected. however, for the other group, the following question has been left unsolved. is it reasonable to assume that bacteria without the trna lack the entire sec system, and do such bacteria exist commonly? to explore it experime ... | 2004 | 14732487 |
| the role of colonic microbiota in lactose intolerance. | in a previous study we observed a clear difference in lactose intolerance symptoms after a 25-g lactose load in two groups of persons with lactase nonpersistence and similar small intestinal lactase activity. from this observation we hypothesized a colon resistance factor. to identify this factor, the microbial composition of fecal samples of the two lactose intolerant groups (one with mild symptoms, n = 16, and one with diarrhea-predominant symptoms, n = 11) was compared using the fluorescent i ... | 2004 | 14992439 |
| malic enzymes of trichomonas vaginalis: two enzyme families, two distinct origins. | the cytosolic malic enzyme of the amitochondriate protist trichomonas vaginalis was purified to homogeneity and characterized. the corresponding gene was sequenced and compared with its hydrogenosomal homologue from the same organism. the enzymes were found to differ in coenzyme specificity, molecular mass and physiological role. the cytosolic malic enzyme is a dimer consisting of two 42-kda subunits with strict specificity for nicotinamide adenine dinucleotide phosphate (nadp(+)), and has a pre ... | 2004 | 15033531 |
| functional analysis of the small subunit of the putative homoaconitase from pyrococcus horikoshii in the thermus lysine biosynthetic pathway. | an in vivo disruption-integration vector system for thermus thermophilus was developed and used for the functional analysis of an evolutionary-related archaeal protein for lysine biosynthesis. in contrast to fungal one, the putative homoaconitase of t. thermophilus consists of two subunits and catalyzes the second and third steps of lysine biosynthesis. orfs from hyperthermophilic archaeon pyrococcus horikoshii, ph1726 and ph1724, share a high degree of amino acid identity with the t. thermophil ... | 2004 | 15063502 |
| thermodynamic analysis of the unfolding and stability of the dimeric dna-binding protein hu from the hyperthermophilic eubacterium thermotoga maritima and its e34d mutant. | we have studied the stability of the histone-like, dna-binding protein hu from the hyperthermophilic eubacterium thermotoga maritima and its e34d mutant by differential scanning microcalorimetry and cd under acidic conditions at various concentrations within the range of 2-225 micro m of monomer. the thermal unfolding of both proteins is highly reversible and clearly follows a two-state dissociation/unfolding model from the folded, dimeric state to the unfolded, monomeric one. the unfolding enth ... | 2004 | 15066175 |
| crystal structure of the phosphoenolpyruvate-binding enzyme i-domain from the thermoanaerobacter tengcongensis pep: sugar phosphotransferase system (pts). | enzyme i (ei), the first component of the phosphoenolpyruvate (pep):sugar phosphotransferase system (pts), consists of an n-terminal protein-binding domain (ein) and a c-terminal pep-binding domain (eic). ei transfers phosphate from pep by double displacement via a histidine residue on ein to the general phosphoryl carrier protein hpr. here, we report the 1.82a crystal structure of the homodimeric eic domain from thermoanaerobacter tengcongensis, a saccharolytic eubacterium that grows optimally ... | 2004 | 15670601 |
| [screening of natural compounds with hypolipidemic activity]. | in the screening programme for natural hypolipidemic compounds 702 strains of soil microorganisms were tested and 25 of them were selected because of their ability to produce compounds inhibiting sterol synthesis in hep g2 hepatoma cells. the compounds were estimated in the microbiological model with tolypocladium inflatum 106 as the test microbe. the 2nd stage of the screening resulted in isolation of 13 strains producing compounds with high hypolipidemic activity, analogous to or higher than t ... | 2004 | 15727139 |
| characterisation of the microbial diversity in a pig manure storage pit using small subunit rdna sequence analysis. | the microbial community structure of pig manure slurry (pms) was determined with comparative analysis of 202 bacterial, 44 archaeal and 33 eukaryotic small subunit (ssu) rdna partial sequences. based on a criterion of 97% of sequence similarity, the phylogenetic analyses revealed a total of 108, eight and five phylotypes for the bacteria, archaea and eukarya lineages, respectively. only 36% of the bacterial phylotypes were closely related (>or=97% similarity) to any previously known sequence in ... | 2004 | 16329909 |
| detection of cellulolytic bacteria from the human colon. | the main representatives of bacteria in the human colon were investigated by specific pcr and denaturing gradient gel electrophoresis (dgge). prevalent in both cases were species of bifidobacterium, clostridium, bacteroides, faecalibacterium and eubacterium. simultaneously, cellulolytic bacteria were isolated from the human feces. the largest proportion was represented by ruminococcus-like isolates. their presence was confirmed both by pcr and dgge methods; the latter one was able to give more c ... | 2004 | 15227792 |
| lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. | the microbial community of the human colon contains many bacteria that produce lactic acid, but lactate is normally detected only at low concentrations (<5 mm) in feces from healthy individuals. it is not clear, however, which bacteria are mainly responsible for lactate utilization in the human colon. here, bacteria able to utilize lactate and produce butyrate were identified among isolates obtained from 10(-8) dilutions of fecal samples from five different subjects. out of nine such strains ide ... | 2004 | 15466518 |
| bacteremia following surgical dental extraction with an emphasis on anaerobic strains. | our aim was to investigate bacteremia caused by surgical extraction of partly erupted mandibular third molars. from 16 young adults, bacterial samples were taken from the third-molar pericoronal pocket and post-operatively from the extraction socket, and blood samples were drawn from the ante-cubital vein up to 30 min after surgery. of the subjects, 88% had detectable bacteremia-50% 1 min after the incision, 44% immediately after extraction. the respective percentages at 10, 15, and 30 min were ... | 2004 | 14742658 |
| polymerase chain reaction-based analysis of microorganisms associated with failed endodontic treatment. | in this study, we aimed to investigate the occurrence of several microbial species in cases of failed endodontic therapy by means of the polymerase chain reaction (pcr). study design root canal samples were taken from 22 root-filled teeth with persistent periradicular lesions selected for re-treatment. dna was extracted from the samples and analyzed for the presence of 19 microbial taxa by using the polymerase chain reaction. | 2004 | 14716262 |
| identification and characterization of the cytoplasmic tungstate/molybdate-binding protein (mop) from eubacterium acidaminophilum. | the mop gene, encoding the molybdate-binding protein from eubacterium acidaminophilum, was cloned using clostridium pasteurianum mopi as a probe for heterologous hybridization. mop encodes a 69-amino-acid protein ( m(r) 7,328) with high sequence similarities to members of the molbindin protein family, which have been implicated in molybdenum storage and homeostasis. northern blot analysis showed three mrna transcripts (1.0, 1.6, and 2.6 kb) for mop. this result was obtained independent of the av ... | 2004 | 14624334 |
| in vitro activities of the new semisynthetic glycopeptide telavancin (td-6424), vancomycin, daptomycin, linezolid, and four comparator agents against anaerobic gram-positive species and corynebacterium spp. | telavancin is a new semisynthetic glycopeptide anti-infective with multiple mechanisms of action, including inhibition of bacterial membrane phospholipid synthesis and inhibition of bacterial cell wall synthesis. we determined the in vitro activities of telavancin, vancomycin, daptomycin, linezolid, quinupristin-dalfopristin, imipenem, piperacillin-tazobactam, and ampicillin against 268 clinical isolates of anaerobic gram-positive organisms and 31 corynebacterium strains using agar dilution meth ... | 2004 | 15155214 |
| identification of bacterial populations in dairy wastewaters by use of 16s rrna gene sequences and other genetic markers. | hydraulic flush waste removal systems coupled to solid/liquid separators and circulated treatment lagoons are commonly utilized to manage the large amounts of animal waste produced on high-intensity dairy farms. although these systems are common, little is known about the microbial populations that inhabit them or how they change as they traverse the system. using culture-based and non-culture-based methods, we characterized the microbial community structure of manure, water from the separator p ... | 2004 | 15240310 |
| dna microarray analysis of predominant human intestinal bacteria in fecal samples. | a microarray method was developed for the detection of 40 bacterial species reported in the literature to be predominant in the human gastrointestinal tract. the 40 species include seven species each of bacteroides and clostridium, six species of ruminococcus, five species of bifidobacterium, four species of eubacterium, two species each of fusobacterium, lactobacillus and enterococcus, and single species each of collinsella, eggerthella, escherichia, faecalibacterium and finegoldia. three 40-me ... | 2004 | 15271382 |
| microbiological examination of infected dental root canals. | the aim of this study was to investigate the root canal microbiota of primary and secondary root-infected canals and the association of constituent species with specific endodontic signs and symptoms. | 2004 | 14871344 |
| characterization of a thermostable l-arabinose (d-galactose) isomerase from the hyperthermophilic eubacterium thermotoga maritima. | the araa gene encoding l-arabinose isomerase (ai) from the hyperthermophilic bacterium thermotoga maritima was cloned and overexpressed in escherichia coli as a fusion protein containing a c-terminal hexahistidine sequence. this gene encodes a 497-amino-acid protein with a calculated molecular weight of 56,658. the recombinant enzyme was purified to homogeneity by heat precipitation followed by ni(2+) affinity chromatography. the native enzyme was estimated by gel filtration chromatography to be ... | 2004 | 15006759 |
| [the prevalence of actinobaculum suis in boars of breeding herds in the omsk region (russian federation) by indirect immunofluorescence technique]. | actinobaculum suis (corynebacterium suis, eubacterium suis, actinomyces suis) was detected in the preputial diverticulum of 64,8% of 162 boars investigated in 8 districts of the region omsk (russian federation) by indirect immunofluorescent technique. until yet no informations were available about the prevalence of actinobaculum (a.) suis in swine herds of the russian federation. the study shows that a. suis, as a main aetiological factor of cystitis and pyelonephritis in sows, is widely spread ... | 2004 | 15032264 |
| molecular analysis of the xylfgh operon, coding for xylose abc transport, in thermoanaerobacter ethanolicus. | a xylose abc (atp-binding cassette) transport operon, xylfgh, was cloned from thermoanaerobacter ethanolicus, a thermophilic ethanol-producing eubacterium. the cistrons code for a periplasmic d-xylose-binding protein (xylf, partial sequence of 250 amino acids), atp-binding protein (xylg, 505 amino acids), and integral membrane protein (xylh, 388 amino acids). these results, together with previous work, indicate that duplicate copies of both xylf and xylh are present in the t. ethanolicus chromos ... | 2004 | 15057456 |
| anaerobic, non-sporulating, gram-positive bacilli bacteraemia characterized by 16s rrna gene sequencing. | owing to the difficulties in identifying anaerobic, non-sporulating, gram-positive bacilli in clinical microbiology laboratories, the epidemiology and clinical spectrum of disease of many of these bacteria have been poorly understood. the application of 16s rrna gene sequencing in characterizing bacteraemia due to anaerobic, non-sporulating gram-positive bacilli during a 4-year period is described. the first case of olsenella uli bacteraemia, in a patient with acute cholangitis, is also reported ... | 2004 | 15585505 |
| elongation factor ts from the antarctic eubacterium pseudoalteromonas haloplanktis tac 125: biochemical characterization and cloning of the encoding gene. | the elongation factor ts was isolated from the psychrophilic antarctic eubacterium pseudoalteromonas haloplanktis tac 125 strain (phef-ts), and its functional properties were studied. at 0 degrees c phef-ts enhanced the [(3)h]gdp/gdp exchange rate on the preformed phef-tu.[(3)h]gdp complex by 2 orders of magnitude even at very low tu:ts ratio, by lowering the energy of activation of the exchange reaction. phef-ts is a monomeric protein, and in solution it forms a stable dimeric complex with phef ... | 2004 | 15544346 |
| trigger factor from thermus thermophilus is a zn2+-dependent chaperone. | the ribosome-associated chaperone trigger factor (tf) of escherichia coli interacts with a variety of newly synthesized polypeptides to assist their correct folding. here, we report that the tf of thermophilic eubacterium, thermus thermophilus, arrested spontaneous folding of green fluorescent protein by forming a 1:1 binary complex. the complex was isolable by gel-filtration but was shown to be dynamic because green fluorescent protein was released by alpha-casein in large excess. unexpectedly, ... | 2004 | 14602709 |
| cloning and expression of a phloretin hydrolase gene from eubacterium ramulus and characterization of the recombinant enzyme. | phloretin hydrolase catalyzes the hydrolytic c-c cleavage of phloretin to phloroglucinol and 3-(4-hydroxyphenyl)propionic acid during flavonoid degradation in eubacterium ramulus. the gene encoding the enzyme was cloned by screening a gene library for hydrolase activity. the insert of a clone conferring phloretin hydrolase activity was sequenced. sequence analysis revealed an open reading frame of 822 bp (phy), a putative promoter region, and a terminating stem-loop structure. the deduced amino ... | 2004 | 15466559 |
| detection frequency of periodontitis-associated bacteria by polymerase chain reaction in subgingival and supragingival plaque of periodontitis and healthy subjects. | the aim of this study was to compare the detection frequencies of 25 bacterial species in subgingival and supragingival plaque of 18 untreated periodontitis subjects and 12 periodontally healthy subjects. genomic dna was extracted from subgingival and supragingival plaque samples, and bacterial detection was performed by polymerase chain reaction of the 16s rrna genes. fourteen bacteria showed no relationship with periodontitis, and 11 of these 14 species were frequently detected (> or =50%) in ... | 2004 | 15491463 |
| gram-positive rods prevailing in teeth with apical periodontitis undergoing root canal treatment. | to identify gram-positive rods from root canals of teeth with apical periodontitis and to examine their associations with other species. | 2004 | 15317560 |
| conservation of functional domain structure in bicarbonate-regulated "soluble" adenylyl cyclases in bacteria and eukaryotes. | soluble adenylyl cyclase (sac) is an evolutionarily conserved bicarbonate sensor. in mammals, it is responsible for bicarbonate-induced, camp-dependent processes in sperm required for fertilization and postulated to be involved in other bicarbonate- and carbon dioxide-dependent functions throughout the body. among eukaryotes, sac-like cyclases have been detected in mammals and in the fungi dictyostelium; these enzymes display extensive similarity extending through two cyclase catalytic domains a ... | 2004 | 15322879 |
| initial antimicrobial effect of controlled-release doxycycline in subgingival sites. | to determine the ability of a 10% doxycycline hyclate controlled-release polymer (atridox) to suppress periodontopathic bacteria when placed subgingivally following scaling and root planing (sc/rp). | 2004 | 15324352 |
| crystallization and preliminary x-ray analysis of carboxypeptidase 1 from thermus thermophilus. | carboxypeptidase 1 from the thermophilic eubacterium thermus thermophilus (tthcp1, 58 kda), a member of the m32 family of metallocarboxypeptidases, was crystallized by the sitting-drop vapour-diffusion method using peg 8000 as the precipitant. the crystals diffracted x-rays to beyond 2.6 a resolution using a synchrotron-radiation source. the crystals belonged to the orthorhombic space group c222(1), with unit-cell parameters a = 171.0, b = 231.6, c = 124.9 a. the crystal contains three molecules ... | 2004 | 15272172 |
| dna-dna relatedness and phylogenetic positions of slackia exigua, slackia heliotrinireducens, eggerthella lenta, and other related bacteria. | recently, two asaccharolytic eubacterium species, eubacterium exiguum and eubacterium lentum, and peptostreptococcus heliotrinreducens have been reclassified as slackia exigua, eggerthella lenta and slackia heliotrinireducens in the novel genera on the basis of 16s rdna sequence analysis. but dna-dna relatedness among these species and other related bacteria have not been reported yet. dna-dna relatedness is the standard arbiter and the recommended method for the designation and evaluation of ne ... | 2004 | 15327650 |
| clinical and microbiological changes associated with the use of combined antimicrobial therapies to treat "refractory" periodontitis. | the present investigation examined clinical and microbial changes after a combined aggressive antimicrobial therapy in subjects identified as "refractory" to conventional periodontal therapy. | 2004 | 15367191 |
| validation of fluorescent in situ hybridization combined with flow cytometry for assessing interindividual variation in the composition of human fecal microflora during long-term storage of samples. | this work was conducted to assess the accuracy of in situ hybridization to show differences in human microflora composition between volunteers and to optimize the storage of fecal samples to allow delayed analysis of gut microflora composition in humans. fecal samples from 25 healthy subjects (14 women, 11 men aged 24-51) were collected. the samples were fixed in 4% paraformaldehyde (pfa) solution at 4 degrees c overnight and stored at -70 degrees c. twenty samples were analysed to quantify the ... | 2004 | 15369862 |
| pcr detection and 16s rrna sequence-based phylogeny of a novel propionibacterium acidipropionici applicable for enhanced fermentation of high moisture corn. | the aims of this study were to develop a sensitive and more rapid detection of propionibacterium acidipropionici dh42 in silage and rumen fluid samples, and to explore its 16s rrna sequence-based phylogeny. | 2004 | 15186440 |
| gram-positive anaerobic bacilli in human periodontal disease. | the uncertain taxonomy of oral anaerobic gram-positive bacilli and their generally slow growing nature has limited the understanding of their role in periodontal disease. the current objective was to design and use species-specific oligonucleotide probes to investigate the relationship of selected gram-positive anaerobic bacilli to periodontal disease. | 2004 | 15206913 |
| anaerofustis stercorihominis gen. nov., sp. nov., from human feces. | phenotypic and phylogenetic studies were performed on an unidentified gram-positive, strictly anaerobic, non-spore-forming, rod-shaped bacterium isolated from human feces. the organism was catalase-negative, resistant to 20% bile, produced acetic and butyric acids as end products of glucose metabolism, and possessed a g+c content of approximately 70 mol%. comparative 16s rrna gene sequencing demonstrated that the unidentified bacterium was a member of the clostridium sub-phylum of the gram-posit ... | 2004 | 16701499 |
| atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit. | phenotypic and molecular genetic studies were performed on an unknown facultative anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from a pig manure storage pit. the unknown bacterium was nutritionally fastidious with growth enhanced by the addition of rumen fluid and was phenotypically initially identified as an eubacterium species. comparative 16s rrna gene sequencing studies, however, revealed that the unknown bacterium was phylogenetically distant from eubacteri ... | 2004 | 16701518 |
| allobaculum stercoricanis gen. nov., sp. nov., isolated from canine feces. | morphological, biochemical, and molecular genetic studies were performed on an unknown anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from dog feces. the unknown bacterium was tentatively identified as a eubacterium species, based on cellular morphological and biochemical tests. 16s rrna gene sequencing studies, however, revealed that it was phylogenetically distant from eubacterium limosum, the type species of the genus eubacterium. phylogenetically, the unknown ... | 2004 | 16701531 |
| rotation, structure, and classification of prokaryotic v-atpase. | the prokaryotic v-type atpase/synthases (prokaryotic v-atpases) have simpler subunit compositions than eukaryotic v-atpases, and thus are useful subjects for studying chemical, physical and structural properties of v-atpase. in this review, we focus on the results of recent studies on the structure/function relationships in the v-atpase from the eubacterium thermus thermophilus. first, we describe single-molecule analyses of t. thermophilus v-atpase. using the single-molecule technique, it was e ... | 2005 | 16691473 |
| in vitro determination of prebiotic properties of oligosaccharides derived from an orange juice manufacturing by-product stream. | fermentation properties of oligosaccharides derived from orange peel pectin were assessed in mixed fecal bacterial culture. the orange peel oligosaccharide fraction contained glucose in addition to rhamnogalacturonan and xylogalacturonan pectic oligosaccharides. twenty-four-hour, temperature- and ph-controlled, stirred anaerobic fecal batch cultures were used to determine the effects that oligosaccharides derived from orange products had on the composition of the fecal microbiota. the effects we ... | 2005 | 16332825 |
| functional identification of an 8-oxoguanine specific endonuclease from thermotoga maritima. | to date, no 8-oxoguanine-specific endonuclease-coding gene has been identified in thermotoga maritima of the order thermotogales, although its entire genome has been deciphered. however, the hypothetical protein tm1821 from t. maritima, has a helix-hairpin-helix motif that is considered to be important for dna binding and catalytic activity. here, tm1821 was overexpressed in escherichia coli and purified using ni-nta affinity chromatography, protease digestion, and gel filtration. tm1821 protein ... | 2005 | 16336782 |
| structural and functional reconstruction in situ of the [cusmoo2] active site of carbon monoxide dehydrogenase from the carbon monoxide oxidizing eubacterium oligotropha carboxidovorans. | carbon monoxide dehydrogenase from the bacterium oligotropha carboxidovorans catalyzes the oxidation of co to co(2) at a unique [cusmoo(2)] cluster. in the bacteria the cluster is assembled post-translational. the integration of s, and particularly of cu, is rate limiting in vivo, which leads to co dehydrogenase preparations containing the mature and fully functional enzyme along with forms of the enzyme deficient in one or both of these elements. the active sites of mature and immature forms of ... | 2005 | 16091936 |
| substrate specificity and transglycosylation catalyzed by a thermostable beta-glucosidase from marine hyperthermophile thermotoga neapolitana. | the gene encoding beta-glucosidase of the marine hyperthermophilic eubacterium thermotoga neapolitana (bgla) was subcloned and expressed in escherichia coli. the recombinant bgla (rbgla) was efficiently purified by heat treatment at 75 degrees c, and a ni-nta affinity chromatography and its molecular mass were determined to be 56.2 kda by mass spectrometry (ms). at 100 degrees c, the enzyme showed more than 94% of its optimal activity. the half-life of the enzyme was 3.6 h and 12 min at 100 and ... | 2005 | 16082555 |
| genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16s rrna gene analysis. | a novel approach combining a flow cytometric in situ viability assay with 16s rrna gene analysis was used to study the relationship between diversity and activity of the fecal microbiota. simultaneous staining with propidium iodide (pi) and syto bc provided clear discrimination between intact cells (49%), injured or damaged cells (19%), and dead cells (32%). the three subpopulations were sorted and characterized by denaturing gradient gel electrophoresis (dgge) of 16s rrna gene amplicons obtaine ... | 2005 | 16085863 |
| toxicity of methoprene as assessed by the use of a model microorganism. | methoprene is an insect juvenile growth hormone mimic, commonly used as a pesticide. although widely used for the control of several pests, toxic effects on organisms of different phyla have been reported. these events triggered studies to clarify the mechanisms of toxicity of this insecticide putatively involved in ecological issues. here we show the effect of methoprene on the normal cell growth and viability of a strain of the thermophilic eubacterium bacillus stearothermophilus, previously u ... | 2005 | 16081242 |
| [anaerobic bacteria isolated from patients with suspected anaerobic infections]. | the study involved 394 clinical samples sent to the clinical microbiology laboratory of hacettepe university adult hospital between january 1997 and may 2004 for anaerobic cultivation. since multiple cultures from the same clinical samples of the same patient were excluded, the study was carried on 367 samples. the anaerobic cultures were performed in anaerobic jar using anaerogen kits (oxoid, basingstoke, u.k.) or genbox (biomérieux, lyon, france). the isolates were identified by both classical ... | 2005 | 16544546 |
| structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action. | trigger factor (tf), the first chaperone in eubacteria to encounter the emerging nascent chain, binds to the large ribosomal subunit in the vicinity of the protein exit tunnel opening and forms a sheltered folding space. here, we present the 3.5-a crystal structure of the physiological complex of the large ribosomal subunit from the eubacterium deinococcus radiodurans with the n-terminal domain of tf (tfa) from the same organism. for anchoring, tfa exploits a small ribosomal surface area in the ... | 2005 | 16091460 |
| analysis of the antibacterial activity and plaque control benefit of colgate total dentifrice via clinical evaluation and real-time polymerase chain reaction. | this study analyzed, from a combined clinical and molecular biologic perspective, the antibacterial and antiplaque efficacy of colgate total dentifrice (ctd). | 2005 | 16583596 |
| phylogenetic analysis of tce-dechlorinating consortia enriched on a variety of electron donors. | two rapidly fermented electron donors, lactate and methanol, and two slowly fermented electron donors, propionate and butyrate, were selected for enrichment studies to evaluate the characteristics of anaerobic microbial consortia that reductively dechlorinate tce to ethene. each electron donor enrichment subculture demonstrated the ability to dechlorinate tce to ethene through several serial transfers. microbial community analyses based upon 16s rdna, including terminal restriction fragment leng ... | 2005 | 16294874 |
| isoflavones and functional foods alter the dominant intestinal microbiota in postmenopausal women. | dietary phytoestrogens, such as isoflavones, are used as food additives to prevent menopause-related disorders. in addition to other factors, their bioavailability strongly depends on the activity of intestinal bacteria but the underlying interactions remain poorly understood. a randomized, double-blind, placebo-controlled study was undertaken with 39 postmenopausal women to characterize changes in the dominant microbial communities of the intestinal tract after 2 mo of isoflavone supplementatio ... | 2005 | 16317121 |
| domain reorientation and induced fit upon rna binding: solution structure and dynamics of ribosomal protein l11 from thermotoga maritima. | l11, a protein of the large ribosomal subunit, binds to a highly conserved domain of 23s rrna and mediates ribosomal gtpase activity. its c-terminal domain is the main determinant for rrna binding, whereas its n-terminal domain plays only a limited role in rna binding. the n-terminal domain is thought to be involved in interactions with elongation and release factors as well as with the antibiotics thiostrepton and micrococcin. this report presents the nmr solution structure of the full-length l ... | 2005 | 16094695 |
| xanthorhodopsin: a proton pump with a light-harvesting carotenoid antenna. | energy transfer from light-harvesting carotenoids to chlorophyll is common in photosynthesis, but such antenna pigments have not been observed in retinal-based ion pumps and photoreceptors. here we describe xanthorhodopsin, a proton-pumping retinal protein/carotenoid complex in the eubacterium salinibacter ruber. the wavelength dependence of the rate of pumping and difference absorption spectra measured under a variety of conditions indicate that this protein contains two chromophores, retinal a ... | 2005 | 16179480 |
| cloning, nucleotide sequence and module structure of the gene encoding the cellulose-binding protein b (cbpb) of eubacterium cellulosolvens 5. | the nucleotide sequence of the gene encoding the cellulose-binding protein b (cbpb) of eubacterium cellulosolvens 5 was determined. the gene consists of an open reading frame of 3,429 nucleotides. the deduced amino acid sequence of cbpb contained one module highly similar to a catalytic module of glycosyl hydrolase family 9 (ghf9), one module partially similar to a family 3 carbohydrate-binding module (cbm3), two linkers, one module similar to a cbm of cellulose-binding protein a (cbpa) from e. ... | 2005 | 16205028 |
| aquifex aeolicus trm1[trna (m2(2)g26) methyltransferase] has a novel recognition mechanism of the substrate rna. | aquifex aeolicus is a hyper-thermophilic eubacterium, which probably diverged at the earliest period from the other bacteria on the evolution of life. therefore, analyses of rna modification enzymes of this bacterium may supply important information in relation to the establishment of the early protein synthesis. in the previous meeting, we have reported that aquifex aeolicus trm1 gene product possesses a trna (m2(2)g26) methyltransferase activity. this enzyme catalyzes the methyl-transfer from ... | 2005 | 17150754 |
| activation of proestrogens from hops (humulus lupulus l.) by intestinal microbiota; conversion of isoxanthohumol into 8-prenylnaringenin. | hop, an essential ingredient in most beers, contains a number of prenylflavonoids, among which 8-prenylnaringenin (8-pn) would be the most potent phytoestrogen currently known. although a number of health effects are attributed to these compounds, only a few reports are available about the bioavailability of prenylflavonoids and the transformation potency of the intestinal microbial community. to test these transformations, four fecal samples were incubated with xanthohumol, isoxanthohumol (ix), ... | 2005 | 16076107 |
| cutaneous abscess due to eubacterium lentum in injection drug user: a case report and review of the literature. | we described the first case, to the best of our knowledge, of cutaneous abscess due to eubacterium lentum in a parenteral drug user, after complete fracture of the right femor. the case underlines the importance of carefully performed microbiological tests, due to the peculiar cultural needs of the micro-organism. | 2005 | 16038756 |
| cloning, sequencing, and expression of a eubacterium cellulosolvens 5 gene encoding an endoglucanase (cel5a) with novel carbohydrate-binding modules, and properties of cel5a. | a novel eubacterium cellulosolvens 5 gene encoding an endoglucanase (cel5a) was cloned and expressed in escherichia coli, and its enzymatic properties were characterized. the cel5a gene consists of a 3,444-bp open reading frame and encodes a 1,148-amino-acid protein with a molecular mass of 127,047 da. cel5a is a modular enzyme consisting of an n-terminal signal peptide, two glycosyl hydrolase family 5 catalytic modules, two novel carbohydrate-binding modules (cbms), two linker sequences, and a ... | 2005 | 16204489 |
| differences in the subgingival microbiota of swedish and usa subjects who were periodontally healthy or exhibited minimal periodontal disease. | previous studies have shown differences in the mean proportions of subgingival species in samples from periodontitis subjects in different countries, which may relate to differences in diet, genetics, disease susceptibility and manifestation. the purpose of the present investigation was to determine whether there were differences in the subgingival microbiotas of swedish and american subjects who exhibited periodontal health or minimal periodontal disease. | 2005 | 15642056 |
| [soft tissue infections in oral, maxillofacial, and plastic surgery. bacterial spectra and antibiotics]. | soft tissue infections in the maxillofacial region are mainly caused by staphylococcus aureus, pseudomonas aeruginosa, and escherichia coli but also by members of the genera enterococcus, klebsiella, and enterobacter, respectively. | 2005 | 16228187 |
| effects of macromolecular impurities and of crystallization method on the quality of eubacterial aspartyl-trna synthetase crystals. | although macromolecular purity is thought to be essential for the growth of flawless protein crystals, only a few studies have investigated how contaminants alter the crystallization process and crystal quality. likewise, the outcome of a crystallization process may vary with the crystallization method. here, it is reported how these two variables affect the crystallogenesis of aspartyl-trna synthetase from the eubacterium thermus thermophilus. this homodimeric enzyme (mr=130,000) possesses a mu ... | 2005 | 15930641 |
| [the structure-function relationship of thermostable beta-glycosidase from the thermophilic eubacterium thermus nonproteolyticus hg102]. | beta-glycosidase (tngly) from the thermophilic eubacterium thermus nonproteolyticus hg102, which is a thermostable monomeric protein and adopts the (beta/alpha)8 barrel fold, is an excellent model system to be investigated for the thermostable mechanism, activity and substrate specificity. here, based on the analysis of structural basis for thermostability of tngly (wang et al, 2003) and comparison of other proteins structure of homofamily, glu164 and glu338 may act as proton donor and nucleophi ... | 2005 | 15859334 |
| a four-subunit cytochrome bc(1) complex complements the respiratory chain of thermus thermophilus. | several components of the respiratory chain of the eubacterium thermus thermophilus have previously been characterized to various extent, while no conclusive evidence for a cytochrome bc(1) complex has been obtained. here, we show that four consecutive genes encoding cytochrome bc(1) subunits are organized in an operon-like structure termed fbccxfb. the four gene products are identified as genuine subunits of a cytochrome bc(1) complex isolated from membranes of t. thermophilus. while both the c ... | 2005 | 15869739 |
| modulation of the fecal microbiota by the intake of a lactobacillus johnsonii la1-containing product in human volunteers. | lactobacillus johnsonii la1 (la1) is a probiotic strain capable of stimulating the immune system of the host and interfering with gastrointestinal pathogens. this study evaluates how the ingestion of different amounts of la1 influences the main bacterial populations of the fecal microbiota. eight asymptomatic volunteers participated in the study. after a basal period, they ingested daily 100 ml of a product containing 10(8) cfu ml(-1) of la1 during the first week, 200 ml during the second week a ... | 2005 | 15970400 |
| the role of 16s rrna gene sequencing in identification of microorganisms misidentified by conventional methods. | traditional methods for microbial identification require the recognition of differences in morphology, growth, enzymatic activity, and metabolism to define genera and species. full and partial 16s rrna gene sequencing methods have emerged as useful tools for identifying phenotypically aberrant microorganisms. we report on three bacterial blood isolates from three different college of american pathologists-certified laboratories that were referred to arup laboratories for definitive identificatio ... | 2005 | 16333109 |
| searching for intermediates in the carbon skeleton rearrangement of 2-methyleneglutarate to (r)-3-methylitaconate catalyzed by coenzyme b12-dependent 2-methyleneglutarate mutase from eubacterium barkeri. | coenzyme b(12)-dependent 2-methyleneglutarate mutase from the strict anaerobe eubacterium barkeri catalyzes the equilibration of 2-methyleneglutarate with (r)-3-methylitaconate. proteins with mutations in the highly conserved coenzyme binding-motif dxh(x)(2)g(x)(41)gg (d483n and h485q) exhibited decreased substrate turnover by 2000-fold and >4000-fold, respectively. these findings are consistent with the notion of h485 hydrogen-bonded to d483 being the lower axial ligand of adenosylcobalamin in ... | 2005 | 16060663 |
| degradation of neohesperidin dihydrochalcone by human intestinal bacteria. | the degradation of neohesperidin dihydrochalcone by human intestinal microbiota was studied in vitro. human fecal slurries converted neohesperidin dihydrochalcone anoxically to 3-(3-hydroxy-4-methoxyphenyl)propionic acid or 3-(3,4-dihydroxyphenyl)propionic acid. two transient intermediates were identified as hesperetin dihydrochalcone 4'-beta-d-glucoside and hesperetin dihydrochalcone. these metabolites suggest that neohesperidin dihydrochalcone is first deglycosylated to hesperetin dihydrochalc ... | 2005 | 15740074 |
| differential dna binding and protection by dimeric and dodecameric forms of the ferritin homolog dps from deinococcus radiodurans. | bacterial iron storage proteins such as ferritin serve as intracellular iron reserves. members of the dna protection during starvation (dps) family of proteins are structurally related to ferritins, and their function is to protect the genome from iron-induced free radical damage. some members of the dps family bind dna and are thought to do so only as fully assembled dodecamers. we present the cloning and characterization of a dps homolog encoded by the radiation-resistant eubacterium deinococc ... | 2005 | 15755446 |
| guggenheimella bovis gen. nov., sp. nov., isolated from lesions of bovine dermatitis digitalis. | dermatitis digitalis is an economically important ulcerative disease of undetermined aetiology affecting the hooves of cattle. material was examined from two independent cases of this disease in switzerland. cultures from the advancing front of both lesions yielded large numbers of closely related short, mesophilic, non-motile, non-spore-forming, anaerobic, proteolytic, gram-positive rods. the 16s rrna gene sequences of strains omz 913(t) and omz 915 were identical and indicate tindallia magadie ... | 2005 | 15774641 |
| [bacterial spectra and antibiotics in odontogenic infections. renaissance of the penicillins?]. | the role played by odontogenic infection in dental, oral, and maxillofacial surgery is not to be underestimated even at the present time. an extensive, standardized, prospective study was performed with the intention of verifying the bacterial spectrum of odontogenic infections to evaluate antibiotic sensitivity. | 2005 | 16261393 |
| mitochondrial genetics of aging: intergenomic conflict resolution. | mitochondria are the organelles of aerobic respiration. they consume the oxygen we breathe to stay alive and generate energy for cells to function. but oxygen can be dangerous. indeed, mitochondria generate the majority of reactive oxygen species that are prime suspects among the causes of aging. mitochondria have been influential elements of evolving eukaryotic cells for perhaps 2 billion years, since a eubacterium fused with an archaebacterium. the picture that has emerged from this long histo ... | 2005 | 16282285 |
| oxalate degrading bacteria: new treatment option for patients with primary and secondary hyperoxaluria? | current treatment options in patients with primary and secondary hyperoxaluria are limited and do not always lead to sufficient reduction in urinary oxalate excretion. intestinal oxalate degrading bacteria are capable of degrading oxalate to co(2) and formate, the latter being further metabolized and excreted via the feces. it is speculated, that both endogenously produced, as well as dietary oxalate can be significantly removed via the intestinal tract. oxalobacter formigenes, an obligate anaer ... | 2005 | 16284877 |
| mucosa-associated bacteria in ulcerative colitis before and after antibiotic combination therapy. | we proposed that fusobacterium varium is one of the causative agents in ulcerative colitis. | 2005 | 15813838 |
| the effect of haart on salivary microbiota in the women's interagency hiv study (wihs). | study the prevalence of potentially pathogenic microorganisms in saliva of hiv-positive women in the women's interagency hiv study. | 2005 | 16301151 |
| decoding the genomic tree of life. | genomes hold within them the record of the evolution of life on earth. but genome fusions and horizontal gene transfer (hgt) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. hgt among prokaryotes is not random, however. some genes (informational genes) are more difficult to transfer than others (operational genes). furthermore, environmental, metabolic, and genetic differences among organisms restrict hgt, so that ... | 2005 | 15851667 |
| the beneficial effects of microflora, especially obligate anaerobes, and their products on the colonic environment in inflammatory bowel disease. | because intestinal microflora play a pivotal role in the development of inflammatory bowel disease (ibd), there is currently some interest in alternating the composition of the microflora toward a potentially more remedial community. this paper summarizes the clinical and experimental efficacy of the manipulation of microflora by the use of antibiotics, probiotics, and prebiotics in ibd. germinated barley foodstuff (gbf) is a prebiotic whose unique characteristics make it highly suitable for app ... | 2005 | 15777254 |
| isolation and characterization of a thermostable rna ligase 1 from a thermus scotoductus bacteriophage ts2126 with good single-stranded dna ligation properties. | we have recently sequenced the genome of a novel thermophilic bacteriophage designated as ts2126 that infects the thermophilic eubacterium thermus scotoductus. one of the annotated open reading frames (orfs) shows homology to t4 rna ligase 1, an enzyme of great importance in molecular biology, owing to its ability to ligate single-stranded nucleic acids. the orf was cloned, and recombinant protein was expressed, purified and characterized. the recombinant enzyme ligates single-stranded nucleic a ... | 2005 | 15642699 |
| molecular analysis of microbial diversity in advanced caries. | real-time pcr analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. this suggests that an unresolved complexity exists in bacteria associated with advanced caries. in this report, the profile of the microflora of carious dentine was explored by using dna extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of prevotella spp. using universal primers for t ... | 2005 | 15695690 |
| microarrays complement culture methods for identification of bacteria in endodontic infections. | the aim of this study was to investigate the microbial composition of necrotic root canals using culture methods and microarray technology. twenty uniradicular teeth with radiographic evidence of periapical bone loss and with no previous endodontic treatment were selected for this study. for molecular diagnosis a dna chip with 20 different species-specific, 16s-rdna-directed catcher probes was used. the microorganisms most frequently detected by the dna chip were: micromonas micros, fusobacteriu ... | 2005 | 15943771 |
| characterization of aquifex aeolicus rnase e/g. | the rnase e/g homologue from the thermophilic eubacterium aquifex aeolicus has been overexpressed in escherichia coli, purified, and characterized in vitro. we show that a. aeolicus rnase e/g has a temperature-dependent, endoribonucleolytic activity. the enzyme site-specifically cleaves oligonucleotides and structured rnas at locations that are partly overlapping or completely different when compared to the positions of e. coli rnase e and rnase g cleavage sites. the efficiency of cleavage by a. ... | 2005 | 15629127 |
| monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism. | terminal restriction fragment length polymorphism (t-rflp) was investigated as a tool for monitoring the human intestinal microflora during antibiotic treatment and during ingestion of a probiotic product. fecal samples from eight healthy volunteers were taken before, during, and after administration of clindamycin. during treatment, four subjects were given a probiotic, and four subjects were given a placebo. changes in the microbial intestinal community composition and relative abundance of sp ... | 2005 | 15640226 |
| identification of candidate periodontal pathogens and beneficial species by quantitative 16s clonal analysis. | most studies of the bacterial etiology of periodontitis have used either culture-based or targeted dna approaches, and so it is likely that pathogens remain undiscovered. the purpose of this study was to use culture-independent, quantitative analysis of biofilms associated with chronic periodontitis and periodontal health to identify pathogens and beneficial species. samples from subjects with periodontitis and controls were analyzed using ribosomal 16s cloning and sequencing. several genera, ma ... | 2005 | 16081935 |
| design and validation of 16s rrna probes to enumerate members of the clostridium leptum subgroup in human faecal microbiota. | among human faecal bacteria, many members of the clostridium leptum subgroup are fibrolytic and butyrate producing microorganisms thereby contributing to processes important to colonic health. yet this phylogenetic subgroup remains poorly described to date. to improve detection and description of members of the c. leptum subgroup, the clep 866 group probe was developed. its association with probes targeting the clostridium viride cluster (cvir 1414) and eubacterium desmolans species (edes 635) a ... | 2005 | 15946290 |
| the maintenance in the oral cavity of children of tetracycline-resistant bacteria and the genes encoding such resistance. | to investigate the maintenance of tetracycline-resistant oral bacteria and the genes encoding tetracycline resistance in these bacteria in children (aged 4--6 years) over a period of 12 months. | 2005 | 16027144 |