| probiotics to minimize the disruption of faecal microbiota in healthy subjects undergoing antibiotic therapy. | a novel combination of culturing and dna-based terminal restriction fragment length polymorphism (trflp) analysis was used to investigate the effect of probiotics on antibiotic-induced gut microbiota alterations to determine if a probiotic preparation containing bifidobacteria and lactobacilli, taken during and after antibiotic therapy, can minimize antibiotic disturbance of faecal microbiota. healthy subjects administered amoxicillin/clavulanate were randomized and concomitantly received a plac ... | 2009 | 19369530 |
| differential cold-adaptation among protein components of the thioredoxin system in the psychrophilic eubacterium pseudoalteromonas haloplanktis tac 125. | thioredoxin and thioredoxin reductase from the psychrophilic eubacterium pseudoalteromonas haloplanktis were obtained as recombinant his-tagged proteins (rphtrx and rphtrxr, respectively). rphtrxr is organised as a homodimeric flavoenzyme, whereas rphtrx is a small monomeric protein, both containing a functional disulfide bridge. however, three additional cysteines are present as free thiols in purified rphtrxr. when individually tested in specific assays, rphtrxr and rphtrx display a full activ ... | 2009 | 19381366 |
| de novo sequence analysis of n-terminal sulfonated peptides after in-gel guanidination. | in this protocol, we describe an approach in which two-dimensional electrophoresis (2de)-separated proteins are guanidinated in-gel prior to enzymatic cleavage. in contrast to previously described techniques, this procedure allows the extracted tryptic peptides to be n-terminally sulfonated without any further sample purification. the protocol was applied on a proteomic study of 2de-separated proteins from halorhodospira halophila, an extremophilic eubacterium with an unsequenced genome at the m ... | 2009 | 19381605 |
| the role of ph in determining the species composition of the human colonic microbiota. | the ph of the colonic lumen varies with anatomical site and microbial fermentation of dietary residue. we have investigated the impact of mildly acidic ph, which occurs in the proximal colon, on the growth of different species of human colonic bacteria in pure culture and in the complete microbial community. growth was determined for 33 representative human colonic bacteria at three initial ph values (approximately 5.5, 6.2 and 6.7) in anaerobic ycfa medium, which includes a mixture of short-cha ... | 2009 | 19397676 |
| the bioavailability of apigenin-7-glucoside is influenced by human intestinal microbiota in rats. | we investigated the impact of human intestinal microbiota on bioavailability of the flavone apigenin-7-glucoside (a7g) by comparing germ-free and human microbiota-associated (hma) rats. first, the ability of the human intestinal microbiota to convert a7g was proven in vitro by incubating a7g with fecal suspensions. apigenin, naringenin, and 3-(4-hydroxyphenyl)propionic acid were formed as main metabolites. after application of a7g to germ-free rats, apigenin, luteolin, and their conjugates were ... | 2009 | 19403720 |
| role of aggregatibacter actinomycetemcomitans in glutathione catabolism. | our previous studies demonstrated that three enzymes, gamma-glutamyltransferase (ggt), cysteinylglycinase (cgase) and cystalysin, are required for the catabolism of glutathione to produce hydrogen sulfide (h(2)s) in treponema denticola. in this study, we examined glutathione catabolism in aggregatibacter actinomycetemcomitans. | 2009 | 19416454 |
| [bacterial diversity of disused thermal vents in tibetan yangbajing region]. | to study the bacterial diversity in sediment and water from two disused thermal vents in yangbajing, tibet, china. | 2009 | 19445178 |
| an rrna-based analysis for evaluating the effect of heat stress on the rumen microbial composition of holstein heifers. | we performed a set of heifer feeding trials to investigate the effect of heat and humidity stresses on the rumen bacterial molecular diversity of holstein heifers (tajima k, nonaka i, higuchi k, takusari n, kurihara m, takenaka a, et al. anaerobe 2007;13:57-64). to further characterize the response of the microbial community to the physiological changes caused by the stresses, we evaluated changes in the ruminal bacterial community composition in the same trials by applying an rna-based method ( ... | 2010 | 19446029 |
| aquifex aeolicus trna (n2,n2-guanine)-dimethyltransferase (trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in trna. | transfer rna (n2,n2-guanine)-dimethyltransferase (trm1) catalyzes n2,n2-dimethylguanine formation at position 26 (m(2)(2)g26) in trna. in the reaction, n2-guanine at position 26 (m(2)g26) is generated as an intermediate. the trm1 genes are found only in archaea and eukaryotes, although it has been reported that aquifex aeolicus, a hyper-thermophilic eubacterium, has a putative trm1 gene. to confirm whether a. aeolicus trm1 has trna methyltransferase activity, we purified recombinant trm1 protein ... | 2009 | 19491098 |
| gut microbiology: fitting into the intestinal neighbourhood. | microbes inhabiting the gut affect our health in profound and unexpected ways: new studies now show that these effects depend on synergistic and competitive interactions between the bacteria, which are influenced by diet. | 2009 | 19515354 |
| pig manure contamination marker selection based on the influence of biological treatment on the dominant fecal microbial groups. | the objective of this study was to identify a microbial marker for pig manure contamination. we quantified the persistence of four dominant bacterial groups from the pig intestinal tract throughout manure handling at 10 livestock operations (including aerobic digestion) by using molecular typing. the partial 16s rrna genes of bacteroides-prevotella, eubacterium-clostridiaceae, bacillus-streptococcus-lactobacillus (bsl), and bifidobacterium group isolates were amplified and analyzed by capillary ... | 2009 | 19525269 |
| bacterial diversity of darfiyeh, a lebanese artisanal raw goat's milk cheese. | in order to contribute to the preservation of the lebanese dairy heritage, the aim of this study was to characterize the darfiyeh cheese, a traditional variety made from raw goat's milk and ripened in goat's skin. three independent batches of darfiyeh production were analyzed after 20, 40 and 60 days of ripening. mesophilic lactobacilli, thermophilic coccal-shaped lactic acid bacteria (lab) and thermophilic lactobacilli were enumerated. in order to explore the darfiyeh natural ecosystem, a combi ... | 2009 | 19527841 |
| starvation response and growth in serum of fusobacterium nucleatum, peptostreptococcus anaerobius, prevotella intermedia, and pseudoramibacter alactolyticus. | the microbiota inhabiting the untreated root canal differ markedly from those found in post-treatment disease, yet there is limited information on the microbial characteristics distinguishing the different infections. we hypothesized that starvation survival is a key microbial property in species selection. this study analyzed starvation-survival behavior over 60 days of species representative of the untreated root canal infection: fusobacterium nucleatum, peptostreptococcus anaerobius, prevotel ... | 2009 | 19540450 |
| risk assessment of ciprofloxacin, flavomycin, olaquindox and colistin sulfate based on microbiological impact on human gut biota. | trace levels of veterinary antibiotics that reside in livestock products may disturb the balance of human intestinal microbiota and impair the colonized barrier function, which is critical to protect against the invasion or overgrowth of exogenous pathogens. we investigated the colonization barrier disruption effect of ciprofloxacin, flavomycin, olaquindox and colistin sulfate by the minimum inhibitory concentration (mic) assay in pure culture of human gut bacteria and evaluated the no-observed- ... | 2009 | 19545513 |
| the mo-se active site of nicotinate dehydrogenase. | nicotinate dehydrogenase (ndh) from eubacterium barkeri is a molybdoenzyme catalyzing the hydroxylation of nicotinate to 6-hydroxynicotinate. reactivity of ndh critically depends on the presence of labile (nonselenocysteine) selenium with an as-yet-unidentified form and function. we have determined the crystal structure of ndh and analyzed its active site by multiple wavelengths anomalous dispersion methods. we show that selenium is bound as a terminal mo=se ligand to molybdenum and that it occu ... | 2009 | 19549881 |
| crystal structure and putative mechanism of 3-methylitaconate-delta-isomerase from eubacterium barkeri. | 3-methylitaconate-delta-isomerase (mii) participates in the nicotinate fermentation pathway of the anaerobic soil bacterium eubacterium barkeri (order clostridiales) by catalyzing the reversible conversion of (r)-3-methylitaconate (2-methylene-3-methylsuccinate) to 2,3-dimethylmaleate. the enzyme is also able to catalyze the isomerization of itaconate (methylenesuccinate) to citraconate (methylmaleate) with ca 10-fold higher k(m) but > 1000-fold lower k(cat). the gene mii from e. barkeri was clo ... | 2009 | 19559030 |
| effects of chloride ion binding on the photochemical properties of salinibacter sensory rhodopsin i. | microbial organisms utilize light not only as energy sources but also as signals by which rhodopsins (containing retinal as a chromophore) work as photoreceptors. sensory rhodopsin i (sri) is a dual photoreceptor that regulates both negative and positive phototaxis in microbial organisms, such as the archaeon halobacterium salinarum and the eubacterium salinibacter ruber. these organisms live in highly halophilic environments, suggesting the possibility of the effects of salts on the function of ... | 2009 | 19560470 |
| comparison between polymerase chain reaction-based and checkerboard dna hybridization techniques for microbial assessment of subgingival plaque samples. | to compare polymerase chain reaction (pcr) with subsequent reverse hybridization (micro-ident test) and checkerboard dna-dna hybridization for the identification of 13 bacterial species in subgingival plaque samples. | 2009 | 19563330 |
| bacterial ortholog of mammalian translocator protein (tspo) with virulence regulating activity. | the translocator protein (tspo), previously designated as peripheral-type benzodiazepine receptor, is a protein mainly located in the outer mitochondrial membrane of eukaryotic cells. tspo is implicated in major physiological functions and functionally associated with other proteins such as the voltage-dependent anionic channel, also designated as mitochondrial porin. surprisingly, a tspo-related protein was identified in the photosynthetic bacterium rhodobacter sphaeroides but it was initially ... | 2009 | 19564920 |
| molecular analysis of persistent periradicular lesions and root ends reveals a diverse microbial profile. | the microbial etiology of periradicular lesions is recognized; however, the bacterial profile of these lesions is not well elucidated. the purpose of this study was to determine the frequency of bacterial colonization in these lesions and to characterize the bacterial community present in root ends and periradicular lesions. | 2009 | 19567313 |
| interaction between phenolics and gut microbiota: role in human health. | dietary phenolic compounds are often transformed before absorption. this transformation modulates their biological activity. different studies have been carried out to understand gut microbiota transformations of particular polyphenol types and identify the responsible microorganisms. although there are potentially thousands of different phenolic compounds in the diet, they are typically transformed to a much smaller number of metabolites. the aim of this review was to discuss the current inform ... | 2009 | 19580283 |
| enhancement of carotenoid biosynthesis in transplastomic tomatoes by induced lycopene-to-provitamin a conversion. | carotenoids are essential pigments of the photosynthetic apparatus and an indispensable component of the human diet. in addition to being potent antioxidants, they also provide the vitamin a precursor beta-carotene. in tomato (solanum lycopersicum) fruits, carotenoids accumulate in specialized plastids, the chromoplasts. how the carotenoid biosynthetic pathway is regulated and what limits total carotenoid accumulation in fruit chromoplasts is not well understood. here, we have introduced the lyc ... | 2009 | 19587100 |
| towards the human intestinal microbiota phylogenetic core. | the paradox of a host specificity of the human faecal microbiota otherwise acknowledged as characterized by global functionalities conserved between humans led us to explore the existence of a phylogenetic core. we investigated the presence of a set of bacterial molecular species that would be altogether dominant and prevalent within the faecal microbiota of healthy humans. a total of 10 456 non-chimeric bacterial 16s rrna sequences were obtained after cloning of pcr-amplified rdna from 17 human ... | 2009 | 19601958 |
| microbiological profile of untreated subjects with localized aggressive periodontitis. | the microbial profile of localized aggressive periodontitis (lagp) has not yet been determined. therefore, the aim of this study was to evaluate the subgingival microbial composition of lagp. | 2009 | 19637996 |
| human gut bacterial communities are altered by addition of cruciferous vegetables to a controlled fruit- and vegetable-free diet. | in the human gut, commensal bacteria metabolize food components that typically serve as energy sources. these components have the potential to influence gut bacterial community composition. cruciferous vegetables, such as broccoli and cabbage, contain distinctive compounds that can be utilized by gut bacteria. for example, glucosinolates can be hydrolyzed by certain bacteria, and dietary fibers can be fermented by a range of species. we hypothesized that cruciferous vegetable consumption would a ... | 2009 | 19640972 |
| proposal to unify clostridium orbiscindens winter et al. 1991 and eubacterium plautii (séguin 1928) hofstad and aasjord 1982, with description of flavonifractor plautii gen. nov., comb. nov., and reassignment of bacteroides capillosus to pseudoflavonifractor capillosus gen. nov., comb. nov. | we isolated several strains from various clinical samples (five samples of blood, four of intra-abdominal pus and one of infected soft tissue) that were anaerobic, motile or non-motile and gram-positive rods. some of the strains formed spores. phylogenetic analysis of the 16s rrna gene sequence showed that these organisms could be placed within clostridial cluster iv as defined by collins et al. [(1994). int j syst bacteriol 44, 812-826] and shared more than 99 % sequence similarity with clostri ... | 2010 | 19654357 |
| clinical spectrum of gram-positive infections in lung transplantation. | gram-positive (gp) organisms are among the most common cause of infections in early postsurgical and immunocompromised populations. patients recovering from lung transplantation (lt) are particularly susceptible owing to the physiologic stress imposed by surgery and induction with intense immunosuppression. sites, types, and timing of gp infections following lt are not well documented. this report describes the clinical spectrum of gp infections and their effects on surgical airway complications ... | 2009 | 19659672 |
| assessment of intraradicular bacterial composition by terminal restriction fragment length polymorphism analysis. | the aim of the study was to assess the bacterial community structures associated with endodontic infections using terminal restriction fragment length polymorphism (t-rflp), and to investigate the correlation of whole community profiles with the manifestation of particular clinical features. | 2009 | 19702949 |
| a photochromic photoreceptor from a eubacterium. | sensory rhodopsin i (sri) is one of the most interesting photo- sensory receptors because of its function in using the photochromic reaction to mediate opposing signals which depend on the color of light. it was initially thought that sri exists only in the archaea, but we recently reported for the first time a newly functional sri from a eubacterium, salinibacter ruber (srsri). the amino acid sequence of srsri shows 43% identity with the well-known sri (hssri) and contains most of the amino aci ... | 2008 | 19704876 |
| the growth of the flavonoid-degrading intestinal bacterium, eubacterium ramulus, is stimulated by dietary flavonoids in vivo. | a human study was performed to investigate the influence of different dietary flavonoids on the faecal population of the flavonoid-degrading bacterium eubacterium ramulus. twenty-eight healthy subjects, divided into five groups, consumed for 6 days a flavonoid-free diet. on day 4 of this intervention period the study participants ingested a single dose of quercetin (14 mg kg(-1) body mass (bm)), rutin (pure or as buckwheat leaves, 28 mg kg(-1) bm) or a placebo. during the first 3 days of the int ... | 2002 | 19709232 |
| design and evaluation of group-specific oligonucleotide probes for quantitative analysis of intestinal ecosystems: their application to assessment of equine colonic microflora. | nine oligonucleotide probes complementary to conserved regions of small subunit rrna from phylogenetically defined clusters of intestinal anaerobic bacteria were designed and evaluated for use in quantitative analysis of intestinal microflora. optimum wash temperatures (t(w)) were determined according to the temperature of dissociation (t(d)) of each probe and target group specificity was demonstrated by comparing hybridisation to target and non-target rrna immobilised on nylon membranes. three ... | 2003 | 19719641 |
| gastrointestinal microbial community shifts observed following oral administration of a lactobacillus fermentum strain to mice. | the indigenous gastrointestinal microbiota acts as an integral defense against the colonisation of orally introduced microbes. whilst this can be important in host protection, some introduced species, including lactobacilli, can have a positive impact on existing microbial communities. the interaction of a candidate probiotic strain of lactobacillus fermentum within the gastrointestinal tract was monitored in a mouse model and its effect on the indigenous microbiota observed. l. fermentum kld wa ... | 2003 | 19719673 |
| comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. | this study compared the subgingival microbiota of subjects with refractory periodontitis (rp) to those in subjects with treatable periodontitis (grs = good responders) or periodontal health (ph) using the human oral microbe identification microarray (homim). | 2009 | 19722792 |
| lactate has the potential to promote hydrogen sulphide formation in the human colon. | high concentrations of sulphide are toxic for the gut epithelium and may contribute to bowel disease. lactate is a favoured cosubstrate for the sulphate-reducing colonic bacterium desulfovibrio piger, as shown here by the stimulation of sulphide formation by d. piger dsm749 by lactate in the presence of sulphate. sulphide formation by d. piger was also stimulated in cocultures with the lactate-producing bacterium bifidobacterium adolescentis l2-32. other lactate-utilizing bacteria such as the bu ... | 2009 | 19732152 |
| characterization of a signaling complex composed of sensory rhodopsin i and its cognate transducer protein from the eubacterium salinibacter ruber. | sensory rhodopsin i (sri) exists in the cell membranes of microorganisms such as the archaeon halobacterium salinarum and is a photosensor responsible for positive and negative phototaxis. sri forms a signaling complex with its cognate transducer protein, htri, in the membrane. that complex transmits light signals to the flagellar motor through changes in protein-protein interactions with the kinase chea and the adaptor protein chew, which controls the direction of the rotation of the flagellar ... | 2009 | 19778064 |
| tributyltin sensitivity of vacuolar-type na(+)-transporting atpase from enterococcus hirae. | tributyltin chloride (tbt), an environmental pollutant, is toxic to a variety of eukaryotic and prokaryotic organisms. some members of f-atp synthase (f-atpase)/vacuolar type atpase (v-atpase) superfamily have been identified as the molecular target of this compound. tbt inhibited the activities of h(+)-transporting or na(+)-transporting f-atpase as well as h(+)-transporting v-atpase originated from various organisms. however, the sensitivity to tbt of na(+)-transporting v-atpase has not been in ... | 2009 | 19797867 |
| molecular and functional characterization of polynucleotide phosphorylase from the antarctic eubacterium pseudoalteromonas haloplanktis. | polyribonucleotide phosphorilase from the psychrophilic antarctic eubacterium pseudoalteromonas haloplanktis (phpnpase) has been purified. this enzyme catalyzes both the rna polymerisation and degradation reaction, showing the highest activity at temperatures below 40 degrees c. phpnpase is quite sensitive to heat treatment and it is endowed with remarkable halotolerance. | 2009 | 19799549 |
| diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-coa:acetate coa-transferase gene. | butyrate-producing bacteria play an important role in the human colon, supplying energy to the gut epithelium and regulating host cell responses. in order to explore the diversity and culturability of this functional group, we designed degenerate primers to amplify butyryl-coa:acetate coa-transferase sequences from faecal samples provided by 10 healthy volunteers. eighty-eight per cent of amplified sequences showed >98% dna sequence identity to coa-transferases from cultured butyrate-producing b ... | 2010 | 19807780 |
| a role for tungsten in the biology of campylobacter jejuni: tungstate stimulates formate dehydrogenase activity and is transported via an ultra-high affinity abc system distinct from the molybdate transporter. | the food-borne pathogen campylobacter jejuni possesses no known tungstoenzymes, yet encodes two abc transporters (cj0300-0303 and cj1538-1540) homologous to bacterial molybdate (modabc) uptake systems and the tungstate transporter (tupabc) of eubacterium acidaminophilum respectively. the actual substrates and physiological role of these transporters were investigated. tryptophan fluorescence spectroscopy and isothermal titration calorimetry of the purified periplasmic binding proteins of each sy ... | 2009 | 19818021 |
| bacterial origin recognition complexes direct assembly of higher-order dnaa oligomeric structures. | eukaryotic initiator proteins form origin recognition complexes (orcs) that bind to replication origins during most of the cell cycle and direct assembly of prereplication complexes (pre-rcs) before the onset of s phase. in the eubacterium escherichia coli, there is a temporally similar nucleoprotein complex comprising the initiator protein dnaa bound to three high-affinity recognition sites in the unique origin of replication, oric. at the time of initiation, this high-affinity dnaa-oric comple ... | 2009 | 19833870 |
| quantitative differences in intestinal faecalibacterium prausnitzii in obese indian children. | gut bacteria contribute to energy conservation in man through their ability to ferment unabsorbed carbohydrate. the present study examined the composition of predominant faecal microbiota in obese and non-obese children. the participants (n 28) aged 11-14 years provided fresh faecal samples and completed a dietary survey consisting of 24 h diet recall and a ffq of commonly used foods taken over the previous 3 months. faecal bacteria were quantitated by real-time pcr using primers targeted at 16s ... | 2010 | 19849869 |
| characterization of an o-desmethylangolensin-producing bacterium isolated from human feces. | a bacterium that converted daidzein to o-desmethylangolensin was isolated from the feces of healthy humans. it was an obligately anaerobic, nonsporeforming, nonmotile and gram-positive rod. the isolate used glucose, sucrose, raffinose, maltose, and fructose as carbon sources. it did not hydrolyze gelatin, esculin, or starch. the strain was urease, acid phosphatase, and arginine dihydrolase positive. it was catalase, oxidase, h(2)s, and indole negative. the major products of glucose fermentation ... | 2010 | 19904524 |
| acute appendicitis is characterised by local invasion with fusobacterium nucleatum/necrophorum. | acute appendicitis is a local intestinal inflammation with unclear origin. the aim was to test whether bacteria in appendicitis differ in composition to bacteria found in caecal biopsies from healthy and disease controls. | 2011 | 19926616 |
| n7-methylguanine at position 46 (m7g46) in trna from thermus thermophilus is required for cell viability at high temperatures through a trna modification network. | n(7)-methylguanine at position 46 (m(7)g46) in trna is produced by trna (m(7)g46) methyltransferase (trmb). to clarify the role of this modification, we made a trmb gene disruptant (deltatrmb) of thermus thermophilus, an extreme thermophilic eubacterium. the absence of trmb activity in cell extract from the deltatrmb strain and the lack of the m(7)g46 modification in trna(phe) were confirmed by enzyme assay, nucleoside analysis and rna sequencing. when the deltatrmb strain was cultured at high t ... | 2010 | 19934251 |
| bacterial contamination rate of the anterior chamber during cataract surgery using conventional culture and eubacterial pcr. | to evaluate the incidence of anterior chamber bacterial contamination during phacoemulsification cataract surgery using eubacterial polymerase chain reaction and conventional cultures. | 2010 | 19967676 |
| the red clover isoflavone irilone is largely resistant to degradation by the human gut microbiota. | intestinal bacteria may influence bioavailability and physiological activity of dietary isoflavones. we therefore investigated the ability of human intestinal microbiota to convert irilone and genistein in vitro. in contrast to genistein, irilone was largely resistant to transformation by fecal slurries of ten human subjects. the fecal microbiota converted genistein to dihydrogenistein, 6'-hydroxy-o-desmethylangolensin, and 2-(4-hydroxyphenyl)-propionic acid. however, considerable interindividua ... | 2010 | 19998384 |
| composition and dynamics of sulfate-reducing bacteria during the waterflooding process in the oil field application. | the composition and dynamics of sulfate-reducing bacteria (srb) during the waterflooding process of daqing oilfield were investigated in this study. pcr-dgge analysis indicated that the microbial communities were significantly different in each treatment unit, and the dominant members were mainly close to clostridium sp., thauera sp., hydrogenophaga sp., pseudomonas sp., eubacterium sp. and arcobacter sp. however, the members belonging to srb were relatively few and mainly consisted of desulfovi ... | 2010 | 20005702 |
| amino acid transport in thermophiles: characterization of an arginine-binding protein in thermotoga maritima. | members of the periplasmic binding protein superfamily are involved in the selective passage of ligands through bacterial cell membranes. the hyperthermophilic eubacterium thermotoga maritima was found to encode a highly stable and specific periplasmic arginine-binding protein (tm0593). following signal sequence removal and overexpression in escherichia coli, tm0593 was purified by thermoprecipitation and affinity chromatography. the ultra-stable protein with a monomeric molecular weight of 27.7 ... | 2010 | 20024076 |
| crystal structure of a thermophilic grpe protein: insight into thermosensing function for the dnak chaperone system. | a homodimeric grpe protein functions as a nucleotide exchange factor of the eubacterium dnak molecular chaperone system. the co-chaperone grpe accelerates adp dissociation from, and promotes atp binding to, dnak, which cooperatively facilitates the dnak chaperone cycle with another co-chaperone, dnaj. grpe characteristically undergoes two-step conformational changes in response to elevation of the environmental temperature. in the first transition at heat-shock temperatures, a fully reversible a ... | 2010 | 20036249 |
| unique features of animal mitochondrial translation systems. the non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases. | in animal mitochondria, several codons are non-universal and their meanings differ depending on the species. in addition, the trna structures that decipher codons are sometimes unusually truncated. these features seem to be related to the shortening of mitochondrial (mt) genomes, which occurred during the evolution of mitochondria. these organelles probably originated from the endosymbiosis of an aerobic eubacterium into an ancestral eukaryote. it is plausible that these events brought about the ... | 2010 | 20075606 |
| structure of intact thermus thermophilus v-atpase by cryo-em reveals organization of the membrane-bound v(o) motor. | the eubacterium thermus thermophilus uses a macromolecular assembly closely related to eukaryotic v-atpase to produce its supply of atp. this simplified v-atpase offers several advantages over eukaryotic v-atpases for structural analysis and investigation of the mechanism of the enzyme. here we report the structure of the complex at approximately 16 a resolution as determined by single particle electron cryomicroscopy (cryo-em). the resolution of the map and our use of cryo-em, rather than negat ... | 2010 | 20080582 |
| polymerase chain reaction-denaturing gradient gel electrophoresis, cloning, and sequence analysis of bacteria associated with acute periapical abscesses in children. | polymerase chain reaction-denaturing gradient gel electrophoresis (pcr-dgge), cloning, and sequencing were applied to the microbiologic study of acute periapical abscesses of endodontic origin in children to examine the predominant bacteria. | 2010 | 20113778 |
| in vitro evaluation of the prebiotic properties of almond skins (amygdalus communis l.). | in this study we investigated the potential prebiotic effect of natural (ns) and blanched (bs) almond skins, the latter being a byproduct of the almond-processing industry. a full model of the gastrointestinal tract, including in vitro gastric and duodenal digestion, followed by colonic fermentation using mixed faecal bacterial cultures, was used. both ns and bs significantly increased the population of bifidobacteria and clostridium coccoides/eubacterium rectale group, resulting in a prebiotic ... | 2010 | 20146750 |
| a role for a bacterial ortholog of the ro autoantigen in starvation-induced rrna degradation. | cellular adaptations to stress often involve changes in rna metabolism. one rna-binding protein that has been implicated in rna handling during environmental stress in both animal cells and prokaryotes is the ro autoantigen. however, the function of ro in stress conditions has been unknown. we report that a ro protein in the radiation-resistant eubacterium deinococcus radiodurans participates in ribosomal rna (rrna) degradation during growth in stationary phase, a form of starvation. levels of t ... | 2010 | 20160119 |
| effect of a new synbiotic mixture on atopic dermatitis in infants: a randomized-controlled trial. | clinical trials investigating the therapeutic effect of probiotics on atopic dermatitis (ad) show inconsistent results. better results can possibly be achieved by combining probiotics with prebiotics, i.e. synbiotics. | 2010 | 20184604 |
| prebiotic effect of fruit and vegetable shots containing jerusalem artichoke inulin: a human intervention study. | the present study aimed to determine the prebiotic effect of fruit and vegetable shots containing inulin derived from jerusalem artichoke (ja). a three-arm parallel, placebo-controlled, double-blind study was carried out with sixty-six healthy human volunteers (thirty-three men and thirty-three women, age range: 18-50 years). subjects were randomised into three groups (n 22) assigned to consume either the test shots, pear-carrot-sea buckthorn (pcs) or plum-pear-beetroot (ppb), containing ja inul ... | 2010 | 20187995 |
| preventive effects of enzyme-treated rice fiber in a restraint stress-induced irritable bowel syndrome model. | irritable bowel syndrome (ibs) is a common health issue that is characterized by abdominal pain, abnormal bowel movements, altered visceral perception, and abnormal metabolism of 5-hydroxy triptamine (serotonin; 5ht). the use of prebiotics or probiotics treatment for ibs has become increasingly important as an adjunct to pharmaceutical options. the aim of this study was to determine the efficacy of enzyme-treated rice fiber (erf) on an ibs model. we obtained a new prebiotic from defatted rice br ... | 2010 | 20198303 |
| detection of periodontopathogenic bacteria in pregnant women by traditional anaerobic culture method and by a commercial molecular genetic method. | to culture facultative and strict anaerobic bacteria is a well-established method for analyzing subgingival plaque samples. micro-ident and micro-ident plus (hain lifescience gmbh, nehren, germany) tests are two commercially available rapid pcr-based methods for the identification and quantification of putative periodontopathogen bacteria. in this study, we compared these commercial pcr-based hybridization methods with conventional anaerobic culture technique. a total of 36 subgingival plaque sa ... | 2010 | 20219690 |
| decontamination and detoxification strategies for the fusarium mycotoxin deoxynivalenol in animal feed and the effectiveness of microbial biodegradation. | trichothecenes are a group of mycotoxins mainly produced by fungi of the fusarium genus. deoxynivalenol (don) is one of the most abundant and important trichothecenes in food and feed, and is a significant contaminants due to its frequent occurrence in toxicologically relevant concentrations worldwide. since toxin production depends strongly on environmental conditions, such as temperature and humidity, fusarium toxin contamination can not be avoided completely. therefore, exposure to this toxin ... | 2010 | 20234966 |
| effect of apple intake on fecal microbiota and metabolites in humans. | the effects of apple intake on the fecal flora, water content, ph, and metabolic activities in eight healthy volunteers and the utilization of apple pectin in vitro were investigated. although several isolates of bifidobacterium, lactobacillus, enterococcus, and the bacteroides fragilis group utilized apple pectin, most isolates of escherichia coli, collinsela aerofaciense, eubacterium limosum, and clostridium perfringens could not. when fecal samples from healthy adults were incubated in liquid ... | 2010 | 20304079 |
| profiling of subgingival plaque biofilm microflora from periodontally healthy subjects and from subjects with periodontitis using quantitative real-time pcr. | qualitative and quantitative changes of the subgingival plaque biofilm microflora in periodontal pockets are thought to be associated with the development and progression of periodontitis. the aims of the present study were to quantify the proportions of nine periodontitis-associated bacterial species and four streptococcus species in subgingival plaque, and to evaluate their relationship with periodontitis quantitatively. | 2010 | 20337892 |
| changes in bacterial communities from swine feces during continuous culture with starch. | bacteria from swine feces were grown in continuous culture with starch as the sole carbohydrate in order to monitor changes during fermentation and to determine how similar fermenter communities were to each other. dna extracted from fermenter samples was analyzed by denaturing gradient gel electrophoresis (dgge). a significant decrease in diversity was observed, the shannon-weaver index dropped from 1.92 to 1.13 after 14 days of fermentation. likewise, similarity of fermenter communities to tho ... | 2010 | 20371295 |
| consumption of human milk oligosaccharides by gut-related microbes. | human milk contains large amounts of complex oligosaccharides that putatively modulate the intestinal microbiota of breast-fed infants by acting as decoy binding sites for pathogens and as prebiotics for enrichment of beneficial bacteria. several bifidobacterial species have been shown to grow well on human milk oligosaccharides. however, few data exist on other bacterial species. this work examined 16 bacterial strains belonging to 10 different genera for growth on human milk oligosaccharides. ... | 2010 | 20394371 |
| molecular factors controlling photosynthetic light harvesting by carotenoids. | carotenoids are naturally occurring pigments that absorb light in the spectral region in which the sun irradiates maximally. these molecules transfer this energy to chlorophylls, initiating the primary photochemical events of photosynthesis. carotenoids also regulate the flow of energy within the photosynthetic apparatus and protect it from photoinduced damage caused by excess light absorption. to carry out these functions in nature, carotenoids are bound in discrete pigment-protein complexes in ... | 2010 | 20446691 |
| the tertiary structure of group ii introns: implications for biological function and evolution. | group ii introns are some of the largest ribozymes in nature, and they are a major source of information about rna assembly and tertiary structural organization. these introns are of biological significance because they are self-splicing mobile elements that have migrated into diverse genomes and played a major role in the genomic organization and metabolism of most life forms. the tertiary structure of group ii introns has been the subject of many phylogenetic, genetic, biochemical and biophysi ... | 2010 | 20446804 |
| low levels of faecal lactobacilli in women with iron-deficiency anaemia in south india. | fe deficiency in women contributes significantly to maternal and child morbidity in india. the intestinal bacterial flora may facilitate absorption of fe from the caecum and proximal colon. the present study investigated the possibility that intestinal microbiota of anaemic young women may differ from that of women with normal hb levels. the microbiota was quantified by real-time pcr in faeces of eight anaemic (hb ≤ 100 g/l) and twenty-six normohaemic (hb ≥ 120 g/l) women aged 18-25 years. seque ... | 2010 | 20447323 |
| the influence of pomegranate by-product and punicalagins on selected groups of human intestinal microbiota. | we have examined the gut bacterial metabolism of pomegranate by-product (pomx) and major pomegranate polyphenols, punicalagins, using ph-controlled, stirred, batch culture fermentation systems reflective of the distal region of the human large intestine. incubation of pomx or punicalagins with faecal bacteria resulted in formation of the dibenzopyranone-type urolithins. the time course profile confirmed the tetrahydroxylated urolithin d as the first product of microbial transformation, followed ... | 2010 | 20452076 |
| through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. | age-related physiological changes in the gastrointestinal tract, as well as modifications in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbiota, resulting in a greater susceptibility to infections. | 2010 | 20498852 |
| effects of age and region on fecal microflora in elderly subjects living in bama, guangxi, china. | intestinal microflora analysis was performed on 52 healthy elderly subjects of different ages and in different regions in bama county, guangxi, china. the participants were assigned to three groups depending on their age and location: longevous (group m; mean age = 98 years; n = 21); rural younger elderly (group s; mean age = 70 years; n = 18); and urban elderly (group c; mean age = 82 years; n = 13). ten groups of bacteria were quantified using real-time pcr. age-related differences were observ ... | 2011 | 20509028 |
| diversity and abundance of the bacterial 16s rrna gene sequences in forestomach of alpacas (lama pacos) and sheep (ovis aries). | two bacterial 16s rrna gene clone libraries were constructed from the forestomach of alpacas and sheep fed alfalfa. after the amplification using the universal 16s rrna gene primers, equal quantities of pcr products from the same species were mixed and used to construct the two libraries. sequence analysis showed that the 60 clones from alpacas were divided into 27 phylotypes with 25% clones affiliated with eubacterium sp. f1. the 60 clones from sheep were divided into 21 phylotypes with 7 phylo ... | 2010 | 20558310 |
| microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for bacteroidetes and clostridium cluster ix. | dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. these reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. we therefore investigated the microbial colonization process ... | 2010 | 20562281 |
| the codon specificity of eubacterial release factors is determined by the sequence and size of the recognition loop. | the two codon-specific eubacterial release factors (rf1: uaa/uag and rf2: uaa/uga) have specific tripeptide motifs (pxt/spf) within an exposed recognition loop shown in recent structures to interact with stop codons during protein synthesis termination. the motifs have been inferred to be critical for codon specificity, but this study shows that they are insufficient to determine specificity alone. swapping the motifs or the entire loop between factors resulted in a loss of codon recognition rat ... | 2010 | 20584893 |
| analysis of the microflora in the stomach of mongolian gerbils infected with helicobacter pylori. | mongolian gerbils are frequently used to study helicobacter pylori-induced gastritis and its consequences. the presence of some gastric flora with a suppressive effect on h. pylori suggests inhibitory microflora against h. pylori infection. the aim of the present study was to analyze the microflora in the stomach of mongolian gerbils with h. pylori infection. | 2010 | 20586850 |
| a eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. | comparative sequence analyses of bacterial genomes are revealing many structured rna motifs that function as metabolite-binding riboswitches. we have identified an rna motif frequently positioned in the 5' utrs of folate transport and biosynthesis genes in firmicute genomes. biochemical experiments confirm that representatives of this new-found rna class selectively bind derivatives of the vitamin folate, including di- and tetrahydrofolate coenzymes. in addition, representatives of this aptamer ... | 2010 | 20659680 |
| dominant and diet-responsive groups of bacteria within the human colonic microbiota. | the populations of dominant species within the human colonic microbiota can potentially be modified by dietary intake with consequences for health. here we examined the influence of precisely controlled diets in 14 overweight men. volunteers were provided successively with a control diet, diets high in resistant starch (rs) or non-starch polysaccharides (nsps) and a reduced carbohydrate weight loss (wl) diet, over 10 weeks. analysis of 16s rrna sequences in stool samples of six volunteers detect ... | 2011 | 20686513 |
| sunflower seed oil and oleic acid utilization for the production of rhamnolipids by thermus thermophilus hb8. | the potential production of rhamnolipids was demonstrated using the thermophilic eubacterium thermus thermophilus hb8 and sunflower seed oil or oleic acid as carbon sources. sunflower seed oil was directly hydrolyzed by secretion of lipase and became a favorable carbon source for rhamnolipids production. rhamnolipids levels were attainted high values, comparable to those produced by pseudomonas strains from similar sources. rhamnolipids synthesis in oleic acid exhibited a long period of inductio ... | 2010 | 20703873 |
| highlighting new phylogenetic specificities of crohn's disease microbiota. | recent studies suggest that gastrointestinal (gi) microbes play a part in the pathogenesis of crohn's disease (cd). | 2011 | 20722058 |
| structure and flexibility in cold-adapted iron superoxide dismutases: the case of the enzyme isolated from pseudoalteromonas haloplanktis. | superoxide dismutases (sods) are metalloenzymes catalysing the dismutation of superoxide anion radicals into molecular oxygen and hydrogen peroxide. here, we present the crystal structure of a cold-adapted fe-sod from the antarctic eubacterium pseudoalteromonas haloplanktis (phsod), and that of its complex with sodium azide. the structures were compared with those of the corresponding homologues having a high sequence identity with phsod, such as the mesophilic sod from escherichia coli (ecsod) ... | 2010 | 20732427 |
| cloning and characterization of a thermostable and halo-tolerant endoglucanase from thermoanaerobacter tengcongensis mb4. | a β-1,4-endoglucanase (cel5a) was cloned from the genomic dna of saccharolytic thermophilic eubacterium thermoanaerobacter tengcongensis mb4 and functionally expressed in escherichia coli. substrate specificity analysis revealed that cel5a cleaves specifically the β-1,4-glycosidic linkage in cellulose with high activity (294 u mg(-1); carboxymethyl cellulose sodium (cmc)). on cmc, kinetics of cel5a was determined (k (m) 1.39 ± 0.12 g l(-1); k (cat)/k (m) 1.41 ± 0.13 g(-1) s(-1)). cel5a displays ... | 2011 | 20803139 |
| bacterial 16s sequence analysis of severe caries in young permanent teeth. | previous studies have confirmed the association of the acid producers streptococcus mutans and lactobacillus spp. with childhood caries, but they also suggested these microorganisms are not sufficient to explain all cases of caries. in addition, health-associated bacterial community profiles are not well understood, including the importance of base production and acid catabolism in ph homeostasis. the bacterial community composition in health and in severe caries of the young permanent dentition ... | 2010 | 20826648 |
| a 6-month study of the effects of 0.3% triclosan/copolymer dentifrice on dental implants. | supportive therapy to maintain dental implants is increasingly important. this study examined the effect of a 0.3% triclosan/2% copolymer dentifrice on oral biofilms and gingival inflammation (gi) on dental implants and peri-implant tissues. | 2011 | 20831669 |
| distinct microbiome in pouchitis compared to healthy pouches in ulcerative colitis and familial adenomatous polyposis. | pouchitis occurs in up to 50% of patients with ulcerative colitis (uc) undergoing ileal pouch anal anastomosis (ipaa). pouchitis rarely occurs in patients with familial adenomatous polyposis (fap) who undergo ipaa. our aim was to compare mucosal and luminal flora in patients with uc-associated pouchitis (ucp), healthy uc pouches (huc), and healthy fap pouches (fap). | 2011 | 20845425 |
| dysbiosis of fecal microbiota in crohn's disease patients as revealed by a custom phylogenetic microarray. | a custom phylogenetic microarray composed of small subunit ribosomal rna probes, representing ≈500 bacterial species from the human and animal gut, was developed and evaluated for analysis of gut microbial diversity using fecal samples from healthy subjects and crohn's disease (cd) patients. | 2010 | 20848492 |
| rrna-based analysis to monitor succession of faecal bacterial communities in holstein calves. | to quantitatively analyse the faecal bacterial communities of holstein calves and track their succession up to 12 weeks of age. | 2010 | 20849397 |
| association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. | to investigate the correlations between self-reported symptoms of irritable bowel syndrome (ibs) and the gastrointestinal (gi) microbiota composition. | 2010 | 20857523 |
| revisiting the structures of several antibiotics bound to the bacterial ribosome. | the increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental pr ... | 2010 | 20876130 |
| gradual adaptive changes of a protein facing high salt concentrations. | several experimental techniques were applied to unravel fine molecular details of protein adaptation to high salinity. we compared four homologous enzymes, which suggested a new halo-adaptive state in the process of molecular adaptation to high-salt conditions. together with comparative functional studies, the structure of malate dehydrogenase from the eubacterium salinibacter ruber shows that the enzyme shares characteristics of a halo-adapted archaea-bacterial enzyme and of non-halo-adapted en ... | 2010 | 20888835 |
| effect of β -glucanase and xylanase supplementation of barley- and rye-based diets on caecal microbiota of broiler chickens. | 1. the aim was to investigate the effect of grain type (barley or rye) and exogenous enzymes (β-glucanase or xylanase) on the composition of chicken caecal microbiota as examined by classical culturing and molecular techniques (fluorescent in-situ hybridisation (fish) and terminal-restriction fragment-length polymorphism (t-rflp)). 2. plate counting revealed higher total numbers of anaerobic bacteria, lactic acid bacteria and yeasts in caecal contents of birds fed with rye-based diets than in bi ... | 2010 | 20924850 |
| interaction of co dehydrogenase with the cytoplasmic membrane monitored by fluorescence correlation spectroscopy. | we have investigated the interaction of carbon monoxide dehydrogenase (codh), an enzyme that catalyses the oxidation of co in the aerobic eubacterium oligotropha carboxidovorans, with the cytoplasmic membrane by using fluorescence correlation spectroscopy (fcs). our results reveal that in vitro this interaction of codh is specific for cytoplasmic membranes from co-grown bacteria. | 2010 | 20979125 |
| complete genome sequence of a carbon monoxide-utilizing acetogen, eubacterium limosum kist612. | eubacterium limosum kist612 is an anaerobic acetogenic bacterium that uses co as the sole carbon/energy source and produces acetate, butyrate, and ethanol. to evaluate its potential as a syngas microbial catalyst, we have sequenced the complete 4.3-mb genome of e. limosum kist612. | 2010 | 21036996 |
| specified species in gingival crevicular fluid predict bacterial diversity. | analysis of gingival crevicular fluid (gcf) samples may give information of unattached (planktonic) subgingival bacteria. our study represents the first one targeting the identity of bacteria in gcf. | 2010 | 21049043 |
| role of alkyltransferase-like (atl) protein in repair of methylated dna lesions in thermus thermophilus. | thermus thermophilus is an extremely thermophilic eubacterium that grows optimally at 70-75°c. it does not have a gene encoding o(6)-alkylguanine-dna alkyltransferase (agt) for the repair of o(6)-methylguanine (o(6)-meg), but it has a homologous gene atl encoding alkyltransferase-like (atl) proteins in which the cysteine residue in the active site of the pchr motif conserved in agt is replaced by alanine (i.e. lack of methyltransferase activity). to investigate the role of atl protein in the rep ... | 2010 | 21059809 |
| pseudouridine at position 55 in trna controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium thermus thermophilus. | pseudouridine at position 55 (ψ55) in eubacterial trna is produced by trub. to clarify the role of the ψ55 modification, we constructed a trub gene disruptant (δtrub) strain of thermus thermophilus which is an extreme-thermophilic eubacterium. unexpectedly, the δtrub strain exhibited severe growth retardation at 50 °c. we assumed that these phenomena might be caused by lack of rna chaperone activity of trub, which was previously hypothetically proposed by others. to confirm this idea, we replace ... | 2010 | 21097467 |
| resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. | to systematically develop dietary strategies based on resistant starch (rs) that modulate the human gut microbiome, detailed in vivo studies that evaluate the effects of different forms of rs on the community structure and population dynamics of the gut microbiota are necessary. the aim of the present study was to gain a community wide perspective of the effects of rs types 2 (rs2) and 4 (rs4) on the fecal microbiota in human individuals. | 2010 | 21151493 |
| identification, cloning, heterologous expression, and characterization of a nadph-dependent 7β-hydroxysteroid dehydrogenase from collinsella aerofaciens. | a gene encoding an nadph-dependent 7β-hydroxysteroid dehydrogenase (7β-hsdh) from collinsella aerofaciens dsm 3979 (atcc 25986, formerly eubacterium aerofaciens) was identified and cloned in this study. sequence comparison of the translated amino acid sequence suggests that the enzyme belongs to the short-chain dehydrogenase superfamily. this enzyme was expressed in escherichia coli with a yield of 330 mg (5,828 u) per liter of culture. the enzyme catalyzes both the oxidation of ursodeoxycholic ... | 2010 | 21181147 |
| asymmetric atp hydrolysis cycle of the heterodimeric multidrug abc transport complex tmrab from thermus thermophilus. | atp-binding cassette (abc) systems translocate a wide range of solutes across cellular membranes. the thermophilic gram-negative eubacterium thermus thermophilus, a model organism for structural genomics and systems biology, discloses ∼46 abc proteins, which are largely uncharacterized. here, we functionally analyzed the first two and only abc half-transporters of the hyperthermophilic bacterium, tmra and tmrb. the abc system mediates uptake of the drug hoechst 33342 in inside-out oriented vesic ... | 2010 | 21190941 |
| [current clinical significance of anaerobic bacteremia]. | to estimate tje current clinical significance of anaerobic bacteremia in a group of czech hospitals. | 2010 | 21191873 |
| melatonin-mitochondria interplay in health and disease. | although two main hypotheses of mitochondrial origin have been proposed, i.e., the autogenous and the endosymbiotic, only the second is being seriously considered currently. the 'hydrogen hypothesis' invokes metabolic symbiosis as the driving force for a symbiotic association between an anaerobic, strictly hydrogen-dependent (the host) and an eubacterium (the symbiont) that was able to respire, but which generated molecular hydrogen as an end product of anaerobic metabolism. the resulting proto- ... | 2010 | 21192780 |
| quantification of butyryl coa:acetate coa-transferase genes reveals different butyrate production capacity in individuals according to diet and age. | the gastrointestinal microbiota produces short-chain fatty acids, especially butyrate, which affect colonic health, immune function and epigenetic regulation. to assess the effects of nutrition and aging on the production of butyrate, the butyryl-coa:acetate coa-transferase gene and population shifts of clostridium clusters lv and xlva, the main butyrate producers, were analysed. faecal samples of young healthy omnivores (24 ± 2.5 years), vegetarians (26 ± 5 years) and elderly (86 ± 8 years) omn ... | 2011 | 21204931 |
| [spatial characteristics of microbial groups associated with the groundwater flow in a small watershed]. | few reports of microbial groups associated with the groundwater flow system are available in china. 16s rrna gene library was constructed by the cultured-independent approach to investigate gene sequences of microorganism in groundwater samples from the recharge (r), intermediate (m) and discharge (d) zones of an experimental watershed at zhuhai campus of sun yat-sen university. proteobacterium, candidate division opx, uncultured archaeon (uncultured crenarchaeote and euryarchaeote) and actinoba ... | 2010 | 21229735 |