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Diversity analysis of methanogens in rumen of Bubalus bubalis by 16S riboprinting and sequence analysis.The molecular diversity of rumen methanogens was investigated by 16S rDNA gene library prepared from the rumen contents obtained from Murrah buffaloes in India. Genomic DNA was isolated from adult male fistulated buffaloes and PCR conditions were set up using specific primers. Amplified product was cloned into a suitable vector, and the positive clones were selected assuming based on blue-white screening and sequenced. Positive clones were reamplified and the resulting PCR products were further ...201222155312
contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen.methanobrevibacter smithii is the most abundant archaeon in the human colon. as most of its neighbors are bacterial species, it is expected that lateral gene acquisition from bacteria might have contributed to the evolution and adaptation of this archaeon. we performed a tree-based genome-wide survey of putative lateral gene transfer products in m. smithii, using a phylogenetic pipeline. over 15% of the coding genes of m. smithii are inferred to be bacterial in origin, based on this analysis. la ...201222056789
detection of methanogenic archaea in the pitchers of the northern pitcher plant ( sarracenia purpurea ).carnivorous plants of the genus sarracenia rely on microorganisms in their pitchers to decompose drowned insects. the environment inside pitchers is considered to be aerobic; however, there might be zones, such as at the bottom of the pitcher, where anaerobic conditions develop. samples of the sediment at the bottom of sarracenia purpurea pitchers were analyzed for the presence of archaea, using pcr and sequencing of the 16s rrna gene. archaeal dna was detected in 20% of sampled pitchers. al ...201222263906
Relationship between rumen methanogens and methane production in dairy cows fed diets supplemented with a feed enzyme additive.To investigate the relationship between ruminal methanogen community and host enteric methane (CH(4) ) production in lactating dairy cows fed diets supplemented with an exogenous fibrolytic enzyme additive.201121848695
degradation of lignified secondary cell walls of lucerne (medicago sativa l.) by rumen fungi growing in methanogenic co-culture.to compare the abilities of the monocentric rumen fungi neocallimastix frontalis, piromyces communis and caecomyces communis, growing in coculture with methanobrevibacter smithii, to colonize and degrade lignified secondary cell walls of lucerne (alfalfa) hay.201121848807
Immunogenic properties of archaeal species found in bioaerosols.The etiology of bioaerosol-related pulmonary diseases remains poorly understood. Recently, archaea emerged as prominent airborne components of agricultural environments, but the consequences of airway exposure to archaea remain unknown. Since subcomponents of archaea can be immunogenic, we used a murine model to study the pulmonary immune responses to two archaeal species found in agricultural facilities: Methanobrevibacter smithii (MBS) and Methanosphaera stadtmanae (MSS). Mice were administere ...201121858070
Evaluation of the nifH Gene Marker of Methanobrevibacter smithii for the Detection of Sewage Pollution in Environmental Waters in Southeast Queensland, Australia.This study aimed at evaluating the host-specificity and -sensitivity of the nifH gene marker of Methanobrevibacter smithii by screening 272 fecal and wastewater samples from 11 animal species including humans in Southeast Queensland (SEQ), Australia. In addition, environmental water samples (n=21) were collected during the dry and wet weather conditions and tested for the presence of the nifH marker along with other sewage-associated markers, namely, enterococci surface protein (esp) found in En ...201122070524
Molecular diversity of methanogens in fecal samples from Bactrian camels (Camelusbactrianus) at two zoos.Animals are dependent on mutualistic microbial communities that reside in their gastrointestinal track for essential physiological functions such as nutrition and pathogen resistance. The composition of microbial communities in an animal is influenced by various factors, including species, diet and geographical location. In this preliminary study, the population structure of fecal methanogens in Bactrian camels (Camelus bactrianus) from two zoos was studied using separate 16S rRNA gene libraries ...201121917280
culture-based indicators of fecal contamination and molecular microbial indicators rarely correlate with campylobacter spp. in recreational waters.campylobacter spp. are the leading cause of gastroenteritis worldwide. most human infections result from contaminated food; however, infections are also caused by recreational waterway contamination. campylobacter culture is technically challenging and enumeration by culture-based methods is onerous. thus, we employed qpcr to quantify campylobacter spp. in fresh- and marine-water samples, raw sewage and animal feces. multiplex pcr determined whether campylobacter jejuni or c. coli, most commonly ...201122048429
methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions.the prototypical representatives of the euryarchaeota-the methanogens-are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. however, we found methanogens of the genera methanosarcina and methanocella to be present in many types of upland soils (including dryland soils) sampled globally. these methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any add ...201122071343
toxicity of methylated bismuth compounds produced by intestinal microorganisms to bacteroides thetaiotaomicron, a member of the physiological intestinal microbiota.methanoarchaea have an outstanding capability to methylate numerous metal(loid)s therefore producing toxic and highly mobile derivatives. here, we report that the production of methylated bismuth species by the methanoarchaeum methanobrevibacter smithii, a common member of the human intestine, impairs the growth of members of the beneficial intestinal microbiota at low concentrations. the bacterium bacteroides thetaiotaomicron, which is of great importance for the welfare of the host due to its ...201121966291
methyl coenzyme m reductase (mcra) gene based phylogenetic analysis of methanogens population in murrah buffaloes (bubalus bubalis).the aim of the present study was to decipher the diversity of methanogens in rumen of murrah buffaloes so that effective strategies can be made in order to mitigate methane emission from these methanogens. in the present study diversity of rumen methanogens in murrah buffaloes (bubalus bubalis) from north india was evaluated by using mcr-a gene library obtained from the pooled pcr product from four animals and by using mega4 software. a total of 104 clones were examined, revealing 26 different m ...201121887637
diversity and abundance of the rumen and fecal methanogens in altay sheep native to xinjiang and the influence of diversity on methane emissions.this study aims to investigate the influence of diet roughage proportion on the methanogenic communities from the rumen and fecal samples in altay local sheep native to xinjiang and better understand the association of methanogenic diversity or abundance with methane emissions of the ruminants. in this study, the high roughage diet was found to cause more methane emissions for either maintenance or ad-lib group, but the total methanogenic abundance was not influenced by roughage proportion and s ...201122038025
a1ao-atp synthase of methanobrevibacter ruminantium couples sodium ions for atp synthesis under physiological conditions.an unresolved question in the bioenergetics of methanogenic archaea is how the generation of proton-motive and sodium-motive forces during methane production is used to synthesize atp by the membrane-bound a(1)a(o)-atp synthase, with both proton- and sodium-coupled enzymes being reported in methanogens. to address this question, we investigated the biochemical characteristics of the a(1)a(o)-atp synthase (mbbra(1)a(o)) of methanobrevibacter ruminantium m1, a predominant methanogen in the rumen. ...201121953465
a novel fingerprint method to assess the diversity of methanogens in microbial systems.understanding the ecology of methanogens in natural and engineered environments is a prerequisite to predicting or managing methane emissions. in this study, a novel high-throughput fingerprint method was developed for determining methanogen diversity and relative abundance within environmental samples. the method described here, designated amplicon length heterogeneity pcr of the mcra gene (lh-mcra), is based on the natural length variation in the mcra gene. the mcra gene encodes the alpha-subu ...201122093027
bacteria and archaea community structure in the rumen microbiome of goats (capra hircus) from the semiarid region of brazil.most studies present in the literature about the rumen microbiome have focused on cattle and sheep. this is the first report of the characterization of the bacterial and archaeal communities present in the liquid and solid-associated fractions of the rumen from free ranging moxotó breed goats using 16s rrna gene libraries. pcr was used to amplify the 16s rrna gene with bacterial and archaeal universal primers and sequences from each library constructed were obtained. sequences of bacteria from t ...201121575735
terrestrial sources homogenize bacterial water quality during rainfall in two urbanized watersheds in santa barbara, ca.microbiological contamination from runoff is a human health concern in urbanized coastal environments, but the contamination sources are often unknown. this study quantified fecal indicator bacteria and compared the distributions of human-specific genetic markers and bacterial community composition during dry and wet weather in urban creeks draining two neighboring watersheds in santa barbara, ca. in a prior study conducted during exclusively dry weather, the creeks were contaminated with human ...201121617896
impact of high-concentrate feeding and low ruminal ph on methanogens and protozoa in the rumen of dairy cows.non-lactating dairy cattle were transitioned to a high-concentrate diet to investigate the effect of ruminal ph suppression, commonly found in dairy cattle, on the density, diversity, and community structure of rumen methanogens, as well as the density of rumen protozoa. four ruminally cannulated cows were fed a hay diet and transitioned to a 65% grain and 35% hay diet. the cattle were maintained on an high-concentrate diet for 3 weeks before the transition back to an hay diet, which was fed for ...201121625972
sewage exfiltration as a source of storm drain contamination during dry weather in urban watersheds.separating storm drains and sanitary sewers is expected to control sewage pollution, for example from combined sewer overflows, and to reduce excessive stormwater flow to wastewater treatment plants. however, sewage contamination has been found in municipal separate storm drain systems in urban areas during dry weather flow. to determine if transmission of sewage is occurring from leaking sanitary sewers directly to leaking separated storm drains, field experiments were performed in three waters ...201121786744
a 'universal' type ii chaperonin pcr detection system for the investigation of archaea in complex microbial communities.bacteria and archaea are evolutionarily and biochemically distinct domains found together in many environments. robust 'universal' pcr primer sets targeting both the bacterial 16s rrna gene and the type i chaperonin gene have been established. however, 'universal' pcr primers for archaea are currently limited to the 16s rrna gene. we investigated the type ii chaperonin (known as the thermosome, tf55, cct or tcp-1) as a potential universal target (ut) for archaea. reproducible amplification of th ...201121776031
abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon.hydrogenotrophic microbiota have a significant impact on colonic health; however, little is known about their diversity and ecology in situ. here, molecular-based methods and multivariate analyses were used to examine the abundance and diversity of mucosa-associated hydrogenotrophic microbes in 90 biopsies collected from right colon, left colon and rectum of 25 healthy subjects. functional genes of all three hydrogenotrophic groups were detected in at least one colonic region of all subjects. me ...201121753800
differences in the rumen methanogen populations of lactating jersey and holstein dairy cows under the same diet regimen.in the dairy cattle industry, holstein and jersey are the breeds most commonly used for production. they differ in performance by various traits, such as body size, milk production, and milk composition. with increased concerns about the impact of agriculture on climate change, potential differences in other traits, such as methane emission, also need to be characterized further. since methane is produced in the rumen by methanogenic archaea, we investigated whether the population structure of m ...201121705541
the antimicrobial resistance pattern of cultured human methanogens reflects the unique phylogenetic position of archaea.objectives methanogenic archaea are constant members of the human oral and digestive microbiota retrieved, in particular, from periodontitis lesions. the objective of the study was to determine their susceptibility to antimicrobials. methods using the macrodilution method in hungate tubes with optical microscope observation combined with monitoring methane production, we determined the antibiotic resistance characteristics of eight methanogenic archaea. results methanobrevibacter smithii strains ...201121680581
isolation of natural cultures of anaerobic fungi and indigenously associated methanogens from herbivores and their bioconversion of lignocellulosic materials to methane.this study aimed to obtain natural cultures of anaerobic fungi and their indigenously associated methanogens from herbivores and investigate their ability to degrade lignocelluloses to methane. eight natural cultures were obtained by hungate roll tube technique. the fungi were identified as belonging to piromyces, anaeromyces and neocallimastix respectively by microscopy, and the methanogens as methanobrevibacter spp. by 16s rrna gene sequencing. in vitro studies with rice straw showed that thes ...201121719276
obesity-associated gut microbiota is enriched in lactobacillus reuteri and depleted in bifidobacterium animalis and methanobrevibacter smithii.background:obesity is associated with increased health risk and has been associated with alterations in bacterial gut microbiota, with mainly a reduction in bacteroidetes, but few data exist at the genus and species level. it has been reported that the lactobacillus and bifidobacterium genus representatives may have a critical role in weight regulation as an anti-obesity effect in experimental models and humans, or as a growth-promoter effect in agriculture depending on the strains.objectives an ...201121829158
methanogen community structure in the rumens of farmed sheep, cattle and red deer fed different diets.development of inhibitors and vaccines that mitigate rumen-derived methane by targeting methanogens relies on knowledge of the methanogens present. we investigated the composition of archaeal communities in the rumens of farmed sheep (ovis aries), cattle (bos taurus) and red deer (cervus elaphus) using denaturing gradient gel electrophoresis (dgge) to generate fingerprints of archaeal 16s rrna genes. the total archaeal communities were relatively constant across species and diets, and were less ...201121255054
phylogenetic analysis of methanogens in the pig feces.in order to assess methanogen diversity in feces of pigs, archaeal 16s rrna gene clone libraries were constructed from feces of the pig. after the amplification by pcr using primers met86f and met1340r, equal quantities of pcr products from each of the five pigs were mixed together and used to construct the library. sequence analysis showed that the 74 clones were divided into ten phylotypes as defined by rflp analysis. phylogenetic analysis showed that three phylotypes were most closely affilia ...201121259005
pan-genome of the dominant human gut-associated archaeon, methanobrevibacter smithii, studied in twins.the human gut microbiota harbors three main groups of h(2)-consuming microbes: methanogens including the dominant archaeon, methanobrevibacter smithii, a polyphyletic group of acetogens, and sulfate-reducing bacteria. defining their roles in the gut is important for understanding how hydrogen metabolism affects the efficiency of fermentation of dietary components. we quantified methanogens in fecal samples from 40 healthy adult female monozygotic (mz) and 28 dizygotic (dz) twin pairs, analyzed b ...201121317366
prevalence and microbiological diversity of archaea in peri-implantitis subjects by 16s ribosomal rna clonal analysis.this study evaluated the prevalence and the molecular diversity of archaea in the subgingival biofilm samples of subjects with peri-implantitis.201121338359
archaea as emerging organisms in complex human microbiomes.in this work, we review the state of knowledge of archaea associated with the human microbiome. these prokaryotes, initially discovered in extreme environments, were named archaea because these environments were thought to be the most primitive on earth. further research revealed that this terminology is misleading because these organisms were later found in various non-extreme environments, including the human host. further examination of the human microbiome has enabled the isolation of three ...201121420503
structure modeling and inhibitor prediction ofnadp oxidoreductase enzyme from methanobrevibacter smithii.the f420-dependent nadp oxidoreductase enzyme from methanobrevibacter smithii catalyzes the important electron transfer step during methanogenesis. therefore, it may act as potential target for blocking the process of methane formation. its protein sequence is available in genbank (accession number: abq86254.1) however no report has been found about its 3d protein structure. in this work, we first time claim 3d model structure of f420-dependent nadp oxidoreductase enzyme from methanobrevibacter ...201121464839
diversity and quantitative analysis of archaea in aggressive periodontitis and periodontally healthy subjects.matarazzo f, ribeiro ac, feres m, faveri m, mayer mpa. diversity and quantitative analysis of archaea in aggressive periodontitis and periodontally healthy subjects. j clin peridontol 2011; doi: 10.1111/j.1600-051x.2011.01734.x. abstract: aim: to investigate the diversity, levels and proportions of archaea in the subgingival biofilm of generalized aggressive periodontitis (gagp; n=30) and periodontally healthy (ph; n=30) subjects. materials and methods: diversity was determined by sequencing arc ...201121539593
archaeosome adjuvant overcomes tolerance to tumor-associated melanoma antigens inducing protective cd8 t cell responses.vesicles comprised of the ether glycerolipids of the archaeon methanobrevibacter smithii (archaeosomes) are potent adjuvants for evoking cd8(+) t cell responses. we therefore explored the ability of archaeosomes to overcome immunologic tolerance to self-antigens. priming and boosting of mice with archaeosome-antigen evoked comparable cd8(+) t cell response and tumor protection to an alternate boosting strategy utilizing live bacterial vectors for antigen delivery. vaccination with melanoma antig ...201021318177
microbial equol production attenuates colonic methanogenesis and sulphidogenesis in vitro.hydrogen gas produced during colonic fermentation is excreted in breath and flatus, or removed by hydrogen-consuming bacteria such as methanogens and sulphate-reducing bacteria. however, recent research has shown that h2 is also consumed by equol-producing bacteria during the reduction of daidzein into equol. in this study, the interactions between methanogens, sulphate-reducing, and equol-producing bacteria were investigated under in vitro simulated intestinal conditions. in the presence of dai ...201020298796
antigenic group ii chaperonin in methanobrevibacter oralis may cross-react with human chaperonin cct.methanobrevibacter oralis is an archaeal species frequently isolated from sites of severe periodontitis. however, its pathogenic roles remain unclear. here, we aimed to isolate group ii chaperonin from m. oralis and examine its antigenicity. the genes encoding two chaperonin subunits (cpn-1 and cpn-2) were cloned from m. oralis using polymerase chain reaction and genome walking procedures. recombinant proteins cpn-1 and cpn-2 were generated, and the reactivities of sera from patients with period ...201020331799
characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by pcr-denaturing gradient gel electrophoresis analysis.understanding ruminal methanogens is essential for greenhouse gas mitigation, as well as for improving animal performance in the livestock industry. it has been speculated that ruminal methanogenic diversity affects host feed efficiency and results in differences in methane production. this study examined methanogenic profiles in the rumen using culture-independent pcr-denaturing gradient gel electrophoresis (pcr-dgge) analysis for 56 beef cattle which differed in feed efficiency, as well as die ...201020418436
formate-driven growth coupled with h(2) production.although a common reaction in anaerobic environments, the conversion of formate and water to bicarbonate and h(2) (with a change in gibbs free energy of δg° = +1.3 kj mol(-1)) has not been considered energetic enough to support growth of microorganisms. recently, experimental evidence for growth on formate was reported for syntrophic communities of moorella sp. strain amp and a hydrogen-consuming methanothermobacter species and of desulfovibrio sp. strain g11 and methanobrevibacter arboriphilus ...201020844539
molecular profiling and identification of methanogenic archaeal species from rabbit caecum.during a comparison of 16s rdna pcr-denaturant gradient gel electrophoresis (dgge) profiles of methanogenic archaea from rumen fluid, rabbit caecum and pig feces, a unique band common to all rabbit caecum samples was observed. dgge profiling also showed that the methanogen community from the new zealand white adult rabbits is different and less complex than the methanogen communities from the rumen and pig feces. small subunit ribosomal gene sequences of methanogenic archaea were subsequently re ...201020950344
lack of correlation between enterococcal counts and the presence of human specific fecal markers in mississippi creek and coastal waters.the objective of this study was to determine whether statistically valid correlations could be shown between enterococcal counts of samples from creek and coastal sites and the presence of two molecular, library-independent markers that specify human and/or sewage pollution. four hundred ninety samples were collected between august 2007 and april 2009 to determine enterococcal counts and the presence of genetic markers for the sewage indicator organisms methanobrevibacter smithii and bacteroidal ...201020950837
a real-time qpcr assay for the detection of the nifh gene of methanobrevibacter smithii, a potential indicator of sewage pollution.to develop a quantitative, real-time pcr assay to detect the nifh gene of methanobrevibacter smithii. methanobrevibacter smithii is a methanogenic archaea found in the intestinal tract of humans that may be a useful indicator of sewage pollution in water.201021070516
the discussion goes on: what is the role of euryarchaeota in humans?the human body (primarily the intestinal tract, the oral cavity, and the skin) harbours approximately 1,000 different bacterial species. however, the number of archaeal species known to colonize man seems to be confined to a handful of organisms within the class euryarchaeota (including methanobrevibacter smithii, m. oralis, and methanosphaera stadtmanae). in contrast to this conspicuously low diversity of archaea in humans their unique physiology in conjunction with the growing number of report ...201021253553
performance of a three-stage membrane bioprocess treating the organic fraction of municipal solid waste and evolution of its archaeal and bacterial ecology.a novel three-stage bioprocess achieved 75% volatile solids (vs) removal at an organic loading rate (olr) of 4g vsl(-1)day, a solids retention time (srt) of 66days, a hydraulic retention time (hrt) of 20days, at a temperature of 35 degrees c. the bioprocess consisted of an anaerobic hydrolytic reactor (hr) where the solids and liquid fractions of the organic fraction of the municipal solid waste (ofmsw) were separated with a mesh. the leachate was pumped to a submerged anaerobic membrane bioreac ...201019857960
the genome sequence of the rumen methanogen methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions.methane (ch(4)) is a potent greenhouse gas (ghg), having a global warming potential 21 times that of carbon dioxide (co(2)). methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. technologies to reduce these emissions are lacking. ruminant methane is formed by the action of methanogenic archaea typified by methanobrevibacter ruminantium, which is present in ...201020126622
microbial population dynamics during startup of a full-scale anaerobic digester treating industrial food waste in kyoto eco-energy project.the microbial community in a full-scale anaerobic digester (2300m3) treating industrial food waste in the kyoto eco-energy project was analyzed using terminal restriction fragment length polymorphism for eubacterial and archaeal 16s rrna genes. both thermophilic and mesophilic sludge of treated swine waste were seeded to the digestion tank. during the 150-day startup period, coffee grounds as a main food waste, along with potato, kelp and boiled beans, tofu, bean curd lees, and deep-fried bean c ...201020129780
development of a vaccine to mitigate greenhouse gas emissions in agriculture: vaccination of sheep with methanogen fractions induces antibodies that block methane production in vitro.to develop an understanding of the immune responses of ruminants to methanogens, and to provide proof of a concept that harnessing the immune system of ruminants is a potentially viable approach to mitigate greenhouse gas emissions from agriculture.201020200573
the role of methane in intestinal diseases.the volume of human intestinal gas is about 200 ml, and it is derived from complex physiological processes including swallowed air, diffusion from bloodstream into the lumen, and particularly intraluminal production by chemical reactions and bacterial fermentation. gas is continuously removed by eructation, anal evacuation, absorption through the intestinal mucosa, and bacterial consumption. more than 99% of it is composed of hydrogen, oxygen, carbon dioxide, nitrogen, and other odoriferous gase ...201020216536
[phylogenetic analysis of symbiotic archaea in the gut of reticulitermes chinensis snyder].to analyze the phylotypes of symbiotic archaea in the gut of reticulitermes chinensis snyder by using non-cultivating method.200920222453
molecular diversity of the rumen microbiome of norwegian reindeer on natural summer pasture.the molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female norwegian reindeer (rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern norway (71.00 degrees n, 25.30 degrees e). mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using quantitative real-time polymerase chain reaction (pcr), were 3.17x10(9), 5.17x10(11) and 4.02x10(7), respective ...200918604648
thermophilic degradation of phenolic compounds in lab scale hybrid up flow anaerobic sludge blanket reactors.this study describes the feasibility of anaerobic degradation of united states environmental protection agency (usepa) listed 4-chloro-2-nitrophenol (4c-2-np), 2-chloro-4-nitrophenol (2c-4-np), 2-chloro-5-methylphenol (2c-5-mp) from a simulated wastewater using four identical 7l bench scale hybrid up flow anaerobic sludge blankets (huasbs) at five different hydraulic retention times (hrts) under thermophilic condition (55+/-3 degrees c). the substrate to co-substrate ratios were maintained betwe ...200918986764
long-term monensin supplementation does not significantly affect the quantity or diversity of methanogens in the rumen of the lactating dairy cow.a long-term monensin supplementation trial involving lactating dairy cattle was conducted to determine the effect of monensin on the quantity and diversity of rumen methanogens in vivo. fourteen cows were paired on the basis of days in milk and parity and allocated to one of two treatment groups, receiving (i) a control total mixed ration (tmr) or (ii) a tmr with 24 mg of monensin premix/kg of diet dry matter. rumen fluid was obtained using an ororuminal probe on day -15 (baseline) and days 20, ...200919028912
quantitative detection of culturable methanogenic archaea abundance in anaerobic treatment systems using the sequence-specific rrna cleavage method.a method based on sequence-specific cleavage of rrna with ribonuclease h was used to detect almost all known cultivable methanogens in anaerobic biological treatment systems. to do so, a total of 40 scissor probes in different phylogeny specificities were designed or modified from previous studies, optimized for their specificities under digestion conditions with 32 methanogenic reference strains, and then applied to detect methanogens in sludge samples taken from 6 different anaerobic treatment ...200919212429
quantification of human polyomaviruses jc virus and bk virus by taqman quantitative pcr and comparison to other water quality indicators in water and fecal samples.in the united states, total maximum daily load standards for bodies of water that do not meet bacterial water quality standards are set by each state. the presence of human polyomaviruses (hpyvs) can be used as an indicator of human-associated sewage pollution in these waters. we have developed and optimized a taqman quantitative pcr (qpcr) assay based on the conserved t antigen to both quantify and simultaneously detect two hpyvs; jc virus and bk virus. the qpcr assay was able to consistently q ...200919346361
rumen-like methanogens identified from the crop of the folivorous south american bird, the hoatzin (opisthocomus hoazin).the hoatzin is the only known avian species with foregut fermentation. it is a primarily folivorous feeder and has a distended crop and lower/distal esophagus, which has evolved for the microbial fermentation of ingested feed. crop samples collected from 10 individual animals from the apure river area, apure state, venezuela were examined for the presence and density of methanogens using 16s rrna gene clone libraries and real-time pcr prepared from pooled and individual pcr products. a total of ...200919387486
molecular diversity analysis of rumen methanogenic archaea from goat in eastern china by dgge methods using different primer pairs.to screen a pair of primers suitable for denaturing gradient gel electrophoretic (dgge) analysis of ruminal methanogenic archaea and to detect the archaeal communities in the rumen of goat.200919416460
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.200919567313
prevalence and molecular diversity of archaea in subgingival pockets of periodontitis patients.the aim of this study was to investigate the prevalence and molecular diversity of archaea in the subgingival crevices of patients with chronic periodontitis.200919572899
validation and field testing of library-independent microbial source tracking methods in the gulf of mexico.water quality is frequently impacted by microbial pollution from human and animal feces. microbial source tracking (mst) can identify dominant pollution sources and improve assessment of health risk compared to indicator bacteria alone. this study aims to standardize and validate mst methods across laboratories in coastal gulf of mexico states. three laboratories evaluated library-independent mst methods for human sewage detection via conventional pcr: (1) human-associated bacteroidales, (2) hum ...200919595426
innovations in host and microbial sialic acid biosynthesis revealed by phylogenomic prediction of nonulosonic acid structure.sialic acids (sias) are nonulosonic acid (nulo) sugars prominently displayed on vertebrate cells and occasionally mimicked by bacterial pathogens using homologous biosynthetic pathways. it has been suggested that sias were an animal innovation and later emerged in pathogens by convergent evolution or horizontal gene transfer. to better illuminate the evolutionary processes underlying the phenomenon of sia molecular mimicry, we performed phylogenomic analyses of biosynthetic pathways for sias and ...200919666579
t-rflp-based mcra gene analysis of methanogenic archaea in association with oral infections and evidence of a novel methanobrevibacter phylotype.increasing evidence suggests a role for methanogenic archaea (methanogens) in human health and disease via syntrophic interactions with bacteria. here we assessed the prevalence and distribution of methanogens and possible associations with bacteria in oral biofilms.200919702957
assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies.cattle with high feed efficiencies (designated "efficient") produce less methane gas than those with low feed efficiencies (designated "inefficient"); however, the role of the methane producers in such difference is unknown. this study investigated whether the structures and populations of methanogens in the rumen were associated with differences in cattle feed efficiencies by using culture-independent methods. two 16s rrna libraries were constructed using approximately 800-bp amplicons generate ...200919717632
high prevalence of methanobrevibacter smithii and methanosphaera stadtmanae detected in the human gut using an improved dna detection protocol.the low and variable prevalence of methanobrevibacter smithii and methanosphaera stadtmanae dna in human stool contrasts with the paramount role of these methanogenic archaea in digestion processes. we hypothesized that this contrast is a consequence of the inefficiencies of current protocols for archaeon dna extraction. we developed a new protocol for the extraction and pcr-based detection of m. smithii and m. stadtmanae dna in human stool.200919759898
monitoring bacterial community of human gut microbiota reveals an increase in lactobacillus in obese patients and methanogens in anorexic patients.studies of the bacterial communities of the gut microbiota have revealed a shift in the ratio of firmicutes and bacteroidetes in obese patients. determining the variations of microbial communities in feces may be beneficial for the identification of specific profiles in patients with abnormal weights. the roles of the archaeon methanobrevibacter smithii and lactobacillus species have not been described in these studies.200919774074
design and development of the anaerochip microarray for investigation of methanogenic communities.the aim of this study was to design a microarray targeting methanogens found in anaerobic digesters, and to apply this chip together with a cloning approach to investigate the methanogenic community present in an anaerobic digester. oligonucleotide probes were designed based on sequence differences in the 16s rrna genes in order to target microorganisms in situ. for microarray hybridisations, dna was subjected to pcr amplification of the 16s rrna gene and cy5-labeled. the microarray was tested w ...200919799937
effect of tea saponin on methanogenesis, microbial community structure and expression of mcra gene, in cultures of rumen micro-organisms.to determine the in-vitro effect and mode of action of tea saponin on the rumen microbial community and methane production.200819146532
identification of endosymbiotic methanogen and ectosymbiotic spirochetes of gut protists of the termite coptotermes formosanus.prokaryotic associations with gut protists of the termite coptotermes formosanus were investigated based on 16s rrna gene sequences. an endosymbiotic methanogen of spirotrichonympha leidyi phylogenetically grouped with endosymbionts of other gut protists in the genus methanobrevibacter, seemed to be unrelated to the host protist phylogeny. three different lineages of ectosymbiotic spirochetes in the genus treponema were identified in single cells of holomastigotoides mirabile, indicating their s ...200821558694
evaluation of methanogenic strains and their ability to endure aeration and water stress.during periods of drainage, both water stress and oxygen can cause damage to indigenous methanogens. in the present study, we evaluated the tolerance of seven methanogenic strains (methanobrevibacter arboriphilicus, methanobacterium formicicum, methanococcus vannielii, methanospirillum hungatei, methanoculleus olentangyi, methanoplanus limicola, and methanosarcina mazei) to long-term exposure to air/nitrogen and drying. we found that these methanogenic strains except for m. limicola and m. olent ...200817990030
evidence of increased diversity of methanogenic archaea with plant extract supplementation.this study evaluated the effects of selected essential oils on archaeal communities using the ovine rumen model. forty weaned canadian arcott ewes, fed with barley-based diet, were allotted to one of three essential oil supplementation treatments or a control (10 ewes per treatment) for 13 weeks. the treatments were cinnamaldehyde, garlic oil, juniper berry oil, and a control with no additive. rumen content was sampled after slaughter and grouped by treatment by combining subsamples from each an ...200818075710
evaluations of different hypervariable regions of archaeal 16s rrna genes in profiling of methanogens by archaea-specific pcr and denaturing gradient gel electrophoresis.different hypervariable (v) regions of the archaeal 16s rrna gene (rrs) were compared systematically to establish a preferred v region(s) for use in archaea-specific pcr-denaturing gradient gel electrophoresis (dgge). the pcr products of the v3 region produced the most informative dgge profiles and permitted identification of common methanogens from rumen samples from sheep. this study also showed that different methanogens might be detected when different v regions are targeted by pcr-dgge. die ...200818083874
methanobrevibacter phylotypes are the dominant methanogens in sheep from venezuela.rumen methanogens in sheep from venezuela were examined using 16s rrna gene libraries and denaturing gradient gel electrophoresis (dgge) profiles prepared from pooled and individual pcr products from the rumen contents from 10 animals. a total of 104 clones were examined, revealing 14 different 16s rrna gene sequences or phylotypes. of the 14 phylotypes, 13 (99 of 104 clones) belonged to the genus methanobrevibacter, indicating that the genus methanobrevibacter is the most dominant component of ...200818165875
[molecular diversity of rumen archaea from jinnan cattle].molecular diversities of rumen archaea of jinnan (south shanxi province, china) cattle was analyzed and compared by 16s rrna gene sequencing from three clone libraries generated using three different archaea-specific primer sets, respectively. dna from rumen of 4 jinnan cattle was extracted, and methanogen 16s rrna gene was amplified using archaea-specific primer sets. three clone libraries were generated by using vector pgem-t and cloning into e.coli jm109. one hundred clones were randomly pick ...200818338569
archaeosome adjuvants: immunological capabilities and mechanism(s) of action.archaeosomes (liposomes comprised of glycerolipids of archaea) constitute potent adjuvants for the induction of th1, th2 and cd8(+) t cell responses to the entrapped soluble antigen. archaeal lipids are uniquely constituted of ether-linked isoprenoid phytanyl cores conferring stability to the membranes. additionally, varied head groups displayed on the glycerol-lipid cores facilitate unique immunostimulating interactions with mammalian antigen-presenting cells (apcs). the polar lipid from the ar ...200818343538
volatilisation of metals and metalloids: an inherent feature of methanoarchaea?as shown by recent studies, anaerobic members of archaea and bacteria are involved in processes that transform ionic species of metals and metalloids (arsenic, antimony, bismuth, selenium, tellurium and mercury) into volatile and mostly toxic derivatives (mainly methyl derivatives or hydrides). since the fact that these transformations proceed in both environmental settings and in parts of the human body, we have to consider that these processes also interfere directly with human health. the div ...200818396004
human methanogen diversity and incidence in healthy and diseased colonic groups using mcra gene analysis.the incidence and diversity of human methanogens are insufficiently characterised in the gastrointestinal tract of both health and disease. a pcr and clone library methodology targeting the mcra gene was adopted to facilitate the two-fold aim of surveying the relative incidence of methanogens in health and disease groups and also to provide an overview of methanogen diversity in the human gastrointestinal tract.200818492229
structural characterization of archaeal lipid mucosal vaccine adjuvant and delivery (amvad) formulations prepared by different protocols and their efficacy upon intranasal immunization of mice.intranasal administration of ovalbumin (ova) formulated in an archaeal lipid mucosal vaccine adjuvant and delivery (amvad) system prepared by the addition of cacl2 to small unilamellar archaeosomes (liposomes made from archaeal polar lipids) containing encapsulated ova, was recently shown to elicit strong and sustained ova-specific mucosal and systemic immune responses. in this study, we show that the centrifugation/washing and antigen quantization steps required in the standard protocol for obt ...200818569448
relationships between anaerobic consortia and removal efficiencies in an uasb reactor degrading 2,4 dichlorophenol (dcp).to gain more insight into the interactions between anaerobic bacteria and reactor performances (chemical oxygen demand-cod, 2,4 dichlorophenol-2,4 dcp removals, volatile fatty acid-vfa, and methane gas productions) and how they depended on operational conditions the microbial variations in the anaerobic granular sludge from an upflow anaerobic sludge blanket (uasb) reactor treating 2,4 dcp was studied. the study was composed of two parts. in the first part, the numbers of methanogens and acedoge ...200817379394
a putative new order of methanogenic archaea inhabiting the human gut, as revealed by molecular analyses of the mcra gene.the diversity of methanogenic archaea from the gut of 6 humans was investigated by targeting mcra, a molecular metabolic marker of methanogenesis. three operational taxonomic units (otus) were recovered from about 400 clones analyzed, two of which were attributed to the expected methanobacteriales methanobrevibacter smithii (4 volunteers) and methanosphaera stadtmanae (1 volunteer). the third otu (1 volunteer) corresponded to a distant phylotype that does not cluster with any of the five methano ...200818644435
distribution of archaea in japanese patients with periodontitis and humoral immune response to the components.there is controversy regarding the existence of archaeal pathogens. periodontitis is one of the human diseases in which archaea have been suggested to have roles as pathogens. this study was performed to investigate the distribution of archaea in japanese patients with periodontitis and to examine the serum igg responses to archaeal components. subgingival plaque samples were collected from 111 periodontal pockets of 49 patients (17 with aggressive periodontitis and 32 with chronic periodontitis ...200818707623
syntrophic growth on formate: a new microbial niche in anoxic environments.anaerobic syntrophic associations of fermentative bacteria and methanogenic archaea operate at the thermodynamic limits of life. the interspecies transfer of electrons from formate or hydrogen as a substrate for the methanogens is key. contrary requirements of syntrophs and methanogens for growth-sustaining product and substrate concentrations keep the formate and hydrogen concentrations low and within a narrow range. since formate is a direct substrate for methanogens, a niche for microorganism ...200818708519
functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome.bile salt hydrolases (bshs) catalyze the "gateway" reaction in a wider pathway of bile acid modification by the gut microbiota. because bile acids function as signaling molecules regulating their own biosynthesis, lipid absorption, cholesterol homeostasis, and local mucosal defenses in the intestine, microbial bsh activity has the potential to greatly influence host physiology. however, the function, distribution, and abundance of bsh enzymes in the gut community are unknown. here, we show that ...200818757757
diversity of the resident microbiota in a thermophilic municipal biogas plant.biogas plants continuously convert biological wastes mainly into a mixture of methane, co2 and h2o-a conversion that is carried out by a consortium of bacteria and archaea. especially in the municipal plants dedicated towards waste treatment, the reactor feed may vary considerably, exposing the resident microbiota to a changing variety of substrates. to evaluate how and if such changes influence the microbiology, an established biogas plant (6,600 m3, up to 600 m3 biogas per h) was followed over ...200818820906
safety of intranasally administered archaeal lipid mucosal vaccine adjuvant and delivery (amvad) vaccine in mice.the safety profile of a recently described novel archaeal lipid mucosal vaccine adjuvant and delivery (amvad) system capable of eliciting robust antigen-specific mucosal and systemic immune responses was evaluated in female balb/c mice (10/group) using ovalbumin (ova) antigen. mice were intranasally immunized (0, 7, and 21 days) with a vaccine comprising 1 microg ova (0.05 mg/kg body weight) formulated in 0.04 mg total polar lipids extract (2.17 mg/kg body weight) of methanobrevibacter smithii c ...200818821397
effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding g protein-coupled receptor, gpr41.the distal human intestine harbors trillions of microbes that allow us to extract calories from otherwise indigestible dietary polysaccharides. the products of polysaccharide fermentation include short-chain fatty acids that are ligands for gpr41, a g protein-coupled receptor expressed by a subset of enteroendocrine cells in the gut epithelium. to examine the contribution of gpr41 to energy balance, we compared gpr41-/- and gpr41+/+ mice that were either conventionally-raised with a complete gut ...200818931303
identification and quantification of methanogenic archaea in adult chicken ceca.by using molecular methods for the identification and quantification of methanogenic archaea in adult chicken ceca, 16s rrna genes of 11 different phylotypes, 10 of which were 99% similar to methanobrevibacter woesei, were found. methanogen populations, as assessed by cultivation, and the 16s rrna copy number were between 6.38 and 8.23 cells/g (wet weight) and 5.50 and 7.19 log(10)/g (wet weight), respectively.200717085694
phylogenetic analysis of bacterial and archaeal species in symptomatic and asymptomatic endodontic infections.phylogenetic analysis of bacterial and archaeal 16s rrna was used to examine polymicrobial communities within infected root canals of 20 symptomatic and 14 asymptomatic patients. nucleotide sequences from approximately 750 clones amplified from each patient group with universal bacterial primers were matched to the ribosomal database project ii database. phylotypes from 37 genera representing actinobacteria, bacteroidetes, firmicutes, fusobacteria and proteobacteria were identified. results were ...200717172525
rapid clonal expansion and prolonged maintenance of memory cd8+ t cells of the effector (cd44highcd62llow) and central (cd44highcd62lhigh) phenotype by an archaeosome adjuvant independent of tlr2.vaccines capable of eliciting long-term t cell immunity are required for combating many diseases. live vectors can be unsafe whereas subunit vaccines often lack potency. we previously reported induction of cd8(+) t cells to ag entrapped in archaeal glycerolipid vesicles (archaeosomes). in this study, we evaluated the priming, phenotype, and functionality of the cd8(+) t cells induced after immunization of mice with ova-methanobrevibacter smithii archaeosomes (ms-ova). a single injection of ms-ov ...200717277146
molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an offshore oilfield.the microbial community and its diversity in production water from a high-temperature, water-flooded petroleum reservoir of an offshore oilfield in china were characterized by 16s rrna gene sequence analysis. the bacterial and archaeal 16s rrna gene clone libraries were constructed from the community dna and, using sequence analysis, 388 bacterial and 220 archaeal randomly selected clones were clustered with 60 and 28 phylotypes, respectively. the results showed that the 16s rrna genes of bacter ...200717286581
analysis of methanogen diversity in the rumen using temporal temperature gradient gel electrophoresis: identification of uncultured methanogens.a temporal temperature gradient gel electrophoresis (ttge) method was developed to determine the diversity of methanogen populations in the rumen. tests with amplicons from genomic dna from 12 cultured methanogens showed single bands for all strains, with only two showing apparently comigrating bands. fingerprints of methanogen populations were analyzed from dna extracted from rumen contents from two cattle and four sheep grazing pasture. for one sheep, dilution cultures selective for methanogen ...200717431710
phylogenetic analysis and fluorescence in situ hybridization detection of archaeal and bacterial endosymbionts in the anaerobic ciliate trimyema compressum.the anaerobic free-living ciliate, trimyema compressum, is known to harbor both methanogenic archaeal and bacterial symbionts in the cytoplasm. to clarify their phylogenetic belongings, a full-cycle rrna approach was applied to this symbiosis. phylogenetic analysis showed that the methanogenic symbiont was related to methanobrevibacter arboriphilicus, which was distantly related to symbionts found in other trimyema species. this result suggested that trimyema species do not require very specific ...200717468963
molecular diversity of methanogens in feedlot cattle from ontario and prince edward island, canada.the molecular diversity of rumen methanogens in feedlot cattle and the composition of the methanogen populations in these animals from two geographic locations were investigated using 16s rrna gene libraries prepared from pooled pcr products from 10 animals in ontario (127 clones) and 10 animals from prince edward island (114 clones). a total of 241 clones were examined, with methanobrevibacter ruminantium accounting for more than one-third (85 clones) of the clones identified. from these 241 cl ...200717483285
postinoculation protozoan establishment and association patterns of methanogenic archaea in the ovine rumen.association patterns between archaea and rumen protozoa were evaluated by analyzing archaeal 16s rrna gene clone libraries from ovine rumen inoculated with different protozoa. five protozoan inoculation treatments, fauna free (negative control), holotrich and cellulolytic protozoa, isotricha and dasytricha spp., entodinium spp., and total fauna (type a) were tested. we used denaturing gradient gel electrophoresis, quantitative pcr, and phylogenetic analysis to evaluate the impact of the protozoa ...200717513586
genomic and metabolic adaptations of methanobrevibacter smithii to the human gut.the human gut is home to trillions of microbes, thousands of bacterial phylotypes, as well as hydrogen-consuming methanogenic archaea. studies in gnotobiotic mice indicate that methanobrevibacter smithii, the dominant archaeon in the human gut ecosystem, affects the specificity and efficiency of bacterial digestion of dietary polysaccharides, thereby influencing host calorie harvest and adiposity. metagenomic studies of the gut microbial communities of genetically obese mice and their lean litte ...200717563350
say hello to our little friends. 200717633442
methanobrevibacter ruminantium as an indicator of domesticated-ruminant fecal pollution in surface waters.a pcr-based assay (mrnif) targeting the nifh gene of methanobrevibacter ruminantium was developed to detect fecal pollution from domesticated ruminants in environmental water samples. the assay produced the expected amplification product only when the reaction mixture contained dna extracted from m. ruminantium culture, bovine (80%), sheep (100%), and goat (75%) feces, and water samples from a bovine waste lagoon (100%) and a creek contaminated with bovine lagoon waste (100%). the assay appears ...200717827308
quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane.methyl coenzyme-m reductase a (mcra) clone libraries were generated from microbial dna extracted from the rumen of cattle fed a roughage diet with and without supplementation of the antimethanogenic compound bromochloromethane. bromochloromethane reduced total methane emissions by c. 30%, with a resultant increase in propionate and branched chain fatty acids. the mcra clone libraries revealed that methanobrevibacter spp. were the dominant species identified. a decrease in the incidence of methan ...200717949432
simultaneous methanogenesis and oxygen reduction by methanobrevibacter cuticularis at low oxygen fluxes.methanogenic archaea are often encountered in habitats that are not entirely anoxic in space or time. recent biochemical and genomic studies have revealed the capacity of methanogens to reduce molecular oxygen. o(2) reduction by methanobrevibacter species was investigated. cell suspensions incubated in agar tubes under a headspace of h(2)-co(2) and increasing concentrations of o(2) formed a distinct growth band, which coincided with the oxic-anoxic interface and indicated that the influx of o(2) ...200717961173
methanobrevibacter millerae sp. nov. and methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth.four formate-utilizing methanogens were isolated from ovine (strain km1h5-1p(t)) and bovine (strains ak-87, ocp and za-10(t)) rumen contents. based on 16s rrna gene sequence analysis, the methanogen strains were found to belong to the order methanobacteriales in the genus methanobrevibacter. strains za-10(t) and km1h5-1p(t) gained energy for growth by the reduction of co(2) to ch(4) using h(2) or formate exclusively as electron donors. increasing formate concentrations to 220 mm in batch culture ...200717329767
[detection and diversity analysis of rumen methanogens in the co-cultures with anaerobic fungi].rumen methanogen diversity in the co-cultures with anaerobic fungi from goat rumen was analyzed. mix-cultures of anaerobic fungi and methanogens were obtained from goat rumen using anaerobic fungal medium and the addition of penicillin and streptomycin and then subcultured 62 times by transferring cultures every 3 - 4d. total dna from the original rumen fluid and subcultured fungal cultures was used for pcr/dgge and rflp analysis. 16s rdna of clones corresponding to representative otus were sequ ...200617302147
a humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism.our colons harbor trillions of microbes including a prominent archaeon, methanobrevibacter smithii. to examine the contributions of archaea to digestive health, we colonized germ-free mice with bacteroides thetaiotaomicron, an adaptive bacterial forager of the polysaccharides that we consume, with or without m. smithii or the sulfate-reducing bacterium desulfovibrio piger. whole-genome transcriptional profiling of b. thetaiotaomicron, combined with mass spectrometry, revealed that, unlike d. pig ...200616782812
detection of the nifh gene of methanobrevibacter smithii: a potential tool to identify sewage pollution in recreational waters.the goal of this study was to develop and test the efficacy of a pcr assay for the environmental detection of the nifh gene of methanobrevibacter smithii, a methanogen found in human faeces and sewage.200616834590
carriage, quantification, and predominance of methanogens and sulfate-reducing bacteria in faecal samples.to determine carriage rates and densities of methanogens and sulfate-reducing bacteria in adults and children using molecular methods, and to also determine if a reciprocal relationship exists between these organisms.200616834722
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