recently described clinically important anaerobic bacteria: taxonomic aspects and update.a new method of identifying bacteria, phylogenetic 16s rrna sequencing, has led to major reorganizations among most genera of anaerobic bacteria. the pigmented prevotella species now comprise seven species including p. nigrescens and p. tannerae; p. intermedia/p. nigrescens-like organisms await inclusion. the former mitsuokella dentalis and hallella seregens were transferred to prevotella as one species, p. dentalis. p. enoeca is a new nonpigmenting prevotella. the genus porphyromonas currently ...19979310640
phylogenic and phenotypic evidence for the transfer of eubacterium fossor to the genus atopobium as atopobium fossor comb. nov.the 16s rrna primary structure of eubacterium fossor was determined by sequencing in vitro amplified rdna. sequence comparisons indicated that e. fossor has a specific phylogenetic association with the atopobium species and is far from e. limosum, the type species of the genus eubacterium. phenotypic characters of e. fossor resemble those of the genus atopobium. therefore, we propose that e. fossor should be transferred to the genus atopobium as atopobium fossor comb. nov.199910449244
diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients.the primary purpose of the present study was to compare the microbial profiles of the tongue dorsa of healthy subjects and subjects with halitosis by using culture-independent molecular methods. our overall goal was to determine the bacterial diversity on the surface of the tongue dorsum as part of our ongoing efforts to identify all cultivable and not-yet-cultivated species of the oral cavity. tongue dorsum scrapings were analyzed from healthy subjects with no complaints of halitosis and subjec ...200312574246
new bacterial species associated with chronic periodontitis.recent investigations of the human subgingival oral flora based on ribosomal 16s cloning and sequencing have shown many of the bacterial species present to be novel species or phylotypes. the purpose of the present investigation was to identify potential periodontal pathogens among these newly identified species and phylotypes. species-specific ribosomal 16s primers for pcr amplification were developed for detection of new species. associations with chronic periodontitis were observed for severa ...200312709498
usefulness of the microseq 500 16s ribosomal dna-based bacterial identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles.due to the inadequate automation in the amplification and sequencing procedures, the use of 16s rrna gene sequence-based methods in clinical microbiology laboratories is largely limited to identification of strains that are difficult to identify by phenotypic methods. in this study, using conventional full-sequence 16s rrna gene sequencing as the "gold standard," we evaluated the usefulness of the microseq 500 16s ribosomal dna (rdna)-based bacterial identification system, which involves amplifi ...200312734240
association of atopobium vaginae, a recently described metronidazole resistant anaerobe, with bacterial vaginosis.bacterial vaginosis (bv) is a polymicrobial syndrome characterized by a change in vaginal flora away from predominantly lactobacillus species. the cause of bv is unknown, but the condition has been implicated in diverse medical outcomes. the bacterium atopobium vaginae has been recognized only recently. it is not readily identified by commercial diagnostic kits. its clinical significance is unknown but it has recently been isolated from a tuboovarian abcess.200415018635
cloning of 16s rrna genes amplified from normal and disturbed vaginal microflora suggests a strong association between atopobium vaginae, gardnerella vaginalis and bacterial vaginosis.the pathogenesis of bacterial vaginosis remains largely elusive, although some microorganisms, including gardnerella vaginalis, are suspected of playing a role in the etiology of this disorder. recently culture-independent analysis of microbial ecosystems has proven its efficacy in characterizing the diversity of bacterial populations. here, we report on the results obtained by combining culture and pcr-based methods to characterize the normal and disturbed vaginal microflora.200415102329
detection of novel organisms associated with salpingitis, by use of 16s rdna polymerase chain reaction.although chlamydia trachomatis and neisseria gonorrhoeae are established causes of salpingitis, the majority of cases have no known etiology. we used broad-range 16s rdna polymerase chain reaction to identify novel, possibly uncultivable, bacteria associated with salpingitis and identified bacterial 16s sequences in fallopian-tube specimens from 11 (24%) of 45 consecutive women with laparoscopically confirmed acute salpingitis (the case patients) and from 0 of 44 women seeking tubal ligations (t ...200415551209
use of species-directed 16s rrna gene pcr primers for detection of atopobium vaginae in patients with bacterial vaginosis.recent studies suggest that the association between a metronidazole-resistant anaerobe, atopobium vaginae, and bacterial vaginosis (bv) warrants further investigation. in the present study, specific primers enhanced detection of a. vaginae and provided additional evidence that this bacterium is prevalent among patients with bv but absent among patients with normal vaginal flora.200415583334
novel bacterial phylotypes in endodontic infections.although molecular studies have revealed potential oral pathogens among the phyla spirochaetes and deferribacteres, their occurrence in endodontic infections has not been consistently investigated. in this study, we devised a nested pcr-dgge approach to survey samples from infected root canals for the presence of members of these two phyla, and to examine their diversity. the primers used also amplified dna from atopobium species. eight of 10 cases showed bands representative of the target bacte ...200515914596
identification of candidate periodontal pathogens and beneficial species by quantitative 16s clonal analysis.most studies of the bacterial etiology of periodontitis have used either culture-based or targeted dna approaches, and so it is likely that pathogens remain undiscovered. the purpose of this study was to use culture-independent, quantitative analysis of biofilms associated with chronic periodontitis and periodontal health to identify pathogens and beneficial species. samples from subjects with periodontitis and controls were analyzed using ribosomal 16s cloning and sequencing. several genera, ma ...200516081935
a preliminary survey of atopobium vaginae in women attending the dunedin gynaecology out-patients clinic: is the contribution of the hard-to-culture microbiota overlooked in gynaecological disorders?preliminary studies have indicated that the recently described bacterium atopobium vaginae may have an association with bacterial vaginosis (bv). fifty-five women attending the gynaecology out-patient's clinic were tested for the presence of this micro-organism, gardnerella vaginalis, mobiluncus and bacteroides species by polymerase chain reaction (pcr)-based assays. the frequency of detection was 40%. pcr detection of gardnerella vaginalis with a. vaginae, occurred in 50% of a. vaginae-positive ...200516171487
comparison between gram stain and culture for the characterization of vaginal microflora: definition of a distinct grade that resembles grade i microflora and revised categorization of grade i microflora.the microbiological diagnosis of bacterial vaginosis is usually made using nugent's criteria, a useful but rather laborious scoring system based on counting bacterial cell types on gram stained slides of vaginal smears. ison and hay have simplified the score system to three categories and added a fourth category for microflora with a predominance of the streptococcus cell type. because in the nugent system several cell types are not taken into account for a final score, we carried out a detailed ...200516225680
throwing the dice for the diagnosis of vaginal complaints?vaginitis is among the most common conditions women are seeking medical care for. although these infections can easily be treated, the relapse rate is high. this may be due to inadequate use of the diagnostic potential.200616503990
[topics on anaerobic bacteria and anaerobic infection].considerable information has been accumulated in the field of anaerobic bacteria and anaerobic infections in the last ten years. here we tried to briefly introduce several selected topics of clinical importance in this field: proposal of the term "nanaerobe", changes of classification and nomenclature of anaerobes, anaerobic bacteremia, lemierre's syndrome as a revival anaerobic infection, atopobium vaginae as bacterial vaginosis-associated bacteria, and new actions of the clostridium perfringen ...200616629490
catabacter hongkongensis gen. nov., sp. nov., isolated from blood cultures of patients from hong kong and canada.four bacterial isolates were recovered from the blood cultures of four patients, two of whom were from hong kong and two of whom were from canada. the two hong kong strains were isolated from a 48-year-old man with intestinal obstruction and secondary sepsis (strain hku16t) and from a 39-year-old man with acute appendicitis (strain hku17), while the two canadian strains were isolated from a 74-year-old man with biliary sepsis (strain ca1) and from a 66-year-old woman with metastatic carcinoma an ...200717122022
antibiotic susceptibility of atopobium vaginae.previous studies have indicated that a recently described anaerobic bacterium, atopobium vaginae is associated with bacterial vaginosis (bv). thus far the four isolates of this fastidious micro-organism were found to be highly resistant to metronidazole and susceptible for clindamycin, two antibiotics preferred for the treatment of bv.200616542416
intestinal bacterial communities that produce active estrogen-like compounds enterodiol and enterolactone in humans.lignans are dietary diphenolic compounds which require activation by intestinal bacteria to exert possible beneficial health effects. the intestinal ecosystem plays a crucial role in lignan metabolism, but the organisms involved are poorly described. to characterize the bacterial communities responsible for secoisolariciresinol (seco) activation, i.e., the communities that produce the enterolignans enterodiol (ed) and enterolactone (el), a study with 24 human subjects was undertaken. seco activa ...200516204524
quantification of mucosa-adhered microbiota of lambs and calves by the use of culture methods and fluorescent in situ hybridization coupled with flow cytometry techniques.the intestinal mucosa-associated microbiota could play important biological roles due to its close proximity with the animal host, but knowledge on its composition is still limited. the aim of this study was to characterize the microbial communities tightly associated with different parts (rumen, duodenum and colon) of the gastrointestinal tract (git) of healthy lambs and calves by using both cultural, and fluorescent in situ hybridization-flow cytometry (fcm-fish) techniques. lactic acid bacter ...200717218070
quantitative analysis of the intestinal bacterial community in one- to three-week-old commercially reared broiler chickens fed conventional or antibiotic-free vegetable-based explore the effect of drug-free poultry production on the intestinal microflora of broiler chickens, the bacterial community of this environment was quantitatively profiled in both conventionally reared birds and birds reared without antibiotic growth promotants (agps) on a vegetable-based diet.200717381758
differences between the fecal microbiota of coeliac infants and healthy controls.coeliac disease (cd) is an immune-mediated enteropathy with a multifactorial aetiology, characterized by chronic inflammation of the small intestinal mucosa. although evidence suggests that the gut microbiota contributes to other chronic inflammatory disorders, its possible role in cd has not been determined. in this study, the composition of the fecal microbiota of coeliac children and age-matched controls was investigated by culture-dependent and -independent methodologies, using fluorescent i ...200717489434
microbial and immunological responses relative to high-altitude exposure in mountaineers.high-altitude exposure is often associated with gastrointestinal disorders, inflammation, and an increased risk of infection. we suspected microbial and immunological responses to high-altitude exposure in mountaineers resulting from changes in the balance of the intestinal microflora.200516118577
modulation of the fecal microbiota by the intake of a lactobacillus johnsonii la1-containing product in human volunteers.lactobacillus johnsonii la1 (la1) is a probiotic strain capable of stimulating the immune system of the host and interfering with gastrointestinal pathogens. this study evaluates how the ingestion of different amounts of la1 influences the main bacterial populations of the fecal microbiota. eight asymptomatic volunteers participated in the study. after a basal period, they ingested daily 100 ml of a product containing 10(8) cfu ml(-1) of la1 during the first week, 200 ml during the second week a ...200515970400
use of 16s rrna gene-targeted group-specific primers for real-time pcr analysis of predominant bacteria in human feces.16s rrna gene-targeted group-specific primers were designed and validated for specific detection and quantification of the clostridium leptum subgroup and the atopobium cluster. to monitor the predominant bacteria in human feces by real-time pcr, we used these specific primers together with four sets of group-specific primers for the clostridium coccoides group, the bacteroides fragilis group, bifidobacterium, and prevotella developed in a previous study (t. matsuki, k. watanabe, j. fujimoto, y. ...200415574920
imbalance in intestinal microflora constitution could be involved in the pathogenesis of inflammatory bowel disease.since genetically engineered animal models of inflammatory bowel disease (ibd) do not develop colitis under germ-free conditions, the intestinal microflora is thought to be one of the most important environmental factors associated with ibd. to understand the involvement of intestinal microflora in the pathogenesis of ibd, we analyzed the constituents of intestinal microflora in ibd. faecal samples from 73 patients with ulcerative colitis (uc) and 23 patients with crohn's disease (cd) were analy ...200817897884
evolving issues in understanding and treating bacterial vaginosis.bacterial vaginosis is a synergistic polymicrobial syndrome characterized by depletion of lactobacillus spp., especially those that produce hydrogen peroxide, and an intense increase in the quantity of commensal vaginal anaerobic bacteria to 100- to 1000-fold above normal levels. while the bacterial spectrum of these organisms has long been known to include gardnerella vaginalis, prevotella spp., anaerobic gram-positive cocci, mobiluncus spp. and mycoplasma hominis, innovative use of molecular d ...200415566334
effect of a milk formula containing probiotics on the fecal microbiota of asian infants at risk of atopic diseases.the fecal microbiota of 37 infants with (n = 20) or without (n = 17) probiotic administration was evaluated on d 3, and at 1, 3, and 12 mo by fluorescence in situ hybridization-flow cytometry (fish-fc), pcr, and bacteriological culture methods. they represent consecutive subjects of an ongoing double-blind, placebo-controlled trial on a probiotic formula (lgg and bifidobacterium longum) administered during the first 6 mo of life. despite varying composition in each baby, there was a general bact ...200717957155
culture-independent analysis of vaginal microflora: the unrecognized association of atopobium vaginae with bacterial vaginosis.although the pathogenesis of bacterial vaginosis remains elusive, a few microorganisms, such as gardnerella vaginalis, are considered markers on gram stain or culture. culture-independent analysis of vaginal microflora using 16s rdna cloning and sequencing of total bacterial communities reveals the gram-positive atopobium vaginae as a predominant species in disturbed vaginal flora.200415507931
characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods.the normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the aetiology of these diseases. common wisdom is that lactobacilli dominate the normal vaginal microflora of post-pubertal women. however, this conclusion is based on methods that require cultivation of microbial populations; an approach that is known to yield a b ...200415289553
detection of atopobium vaginae in postmenopausal women by cultivation-independent methods warrants further investigation.we sequenced 16s rrna genes from the vaginal swab contents of a postmenopausal woman with asymptomatic bacterial vaginosis (bv). sequences from atopobium vaginae were the most commonly detected. in a survey of 35 other postmenopausal women, this organism was detected in 44% with bv but not in any subjects deemed healthy.200415071062
tuboovarian abscess caused by atopobium vaginae following transvaginal oocyte recovery.a 39-year-old woman with tubarian sterility fell ill with acute pelvic inflammatory disease 2 months after transvaginal oocyte recovery. laparotomy revealed a large tuboovarian abscess, from which atopobium vaginae, an anaerobic gram-positive coccoid bacterium of hitherto unknown clinical significance, was isolated. the microbial etiology and the risk of pelvic infections following transvaginal punctures are discussed.200312791933
[a case of bacteremia by atopobium rimae in a patient with liver cirrhosis].atopobium rimae, previously lactobacillus rimae, is a strictly anaerobic, non-spore forming grampositive rod which was frequently isolated from odontogenic infection. we report a case of a. rimae bacteremia. a 47-yr-old man with liver cirrhosis was admitted to the hospital via emergency room due to fever and chill. his abdominal and pelvic computed tomography revealed a small abscess near the left adrenal gland. three sets of blood cultures were taken and non-spore forming, grampositive rods wer ...200718094600
characterization of the gastrointestinal mucosa-associated microbiota of pigs and chickens using culture-based and molecular methodologies.the microbiota of the gastrointestinal tract (git) can play an important role in the healthy status of farm animals and in the safety of the whole food chain. in this study, the mucosa-associated microbiota of the git of pigs and chickens was analyzed by culture methods and fluorescence in situ hybridization combined with flow cytometry (fcm-fish). in all pig git sections, lactic acid bacteria, enterobacteriaceae, atopobium, bacteroides, and clostridium histolyticum were the predominant bacteria ...200718095433
bacteria of dental caries in primary and permanent teeth in children and young adults.although streptococcus mutans has been implicated as a major etiological agent of dental caries, our cross-sectional preliminary study indicated that 10% of subjects with rampant caries in permanent teeth do not have detectable levels of s. mutans. our aims were to use molecular methods to detect all bacterial species associated with caries in primary and permanent teeth and to determine the bacterial profiles associated with different disease states. plaque was collected from 39 healthy control ...200818216213
ammonia production by ruminal microorganisms and enumeration, isolation, and characterization of bacteria capable of growth on peptides and amino acids from the sheep rumen.excessive nh(3) production in the rumen is a major nutritional inefficiency in ruminant animals. experiments were undertaken to compare the rates of nh(3) production from different substrates in ruminal fluid in vitro and to assess the role of asaccharolytic bacteria in nh(3) production. ruminal fluid was taken from four rumen-fistulated sheep receiving a mixed hay-concentrate diet. the calculated rate of nh(3) production from trypticase varied from 1.8 to 19.7 nmol mg of protein(-1) min(-1) dep ...200212324340
bacterial profiles of root caries in elderly patients.culture-based studies have shown that streptococcus mutans and lactobacilli are associated with root caries (rc). the purpose of the present study was to assess the bacterial diversity of rc in elderly patients by use of culture-independent molecular techniques and to determine the associations of specific bacterial species or bacterial communities with healthy and carious roots. plaque was collected from root surfaces of 10 control subjects with no rc and from 11 subjects with rc. the bacterial ...200818385433
the lower genital tract microbiota in relation to cytokine-, slpi- and endotoxin levels: application of checkerboard dna-dna hybridization (cdh).in the present study the lower genital tract microbiota in asymptomatic fertile women (n=34) was identified and quantified by culturing vaginal secretions. also, vaginal and cervical samples were analyzed by a semiquantitative checkerboard dna-dna hybridization technique (cdh) based on genomic probes prepared from 13 bacterial species (bacteroides ureolyticus, escherichia coli, fusobacterium nucleatum, gardnerella vaginalis, mobiluncus curtisii ss curtisii, prevotella bivia, prevotella disiens, ...200818397461
atopobium vaginae triggers an innate immune response in an in vitro model of bacterial vaginosis.bacterial vaginosis is the most common vaginal disorder among women of reproductive age. the pathogenesis of bacterial vaginosis is poorly understood, but is defined by a transition in the vaginal flora from the predominant lactobacillus species to other bacterial species such as atopobium vaginae and gardnerella vaginalis. this change is associated with an increase in vaginal cytokine secretion. we hypothesize that vaginal epithelial cells respond to bacterial vaginosis-associated bacteria by t ...200818403235
in vitro fermentation of oat and barley derived beta-glucans by human faecal microbiota.fermentation of beta-glucan fractions from barley [average molecular mass (mm), of 243, 172, and 137 kda] and oats (average mm of 230 and 150 kda) by the human faecal microbiota was investigated. fractions were supplemented to ph-controlled anaerobic batch culture fermenters inoculated with human faecal samples from three donors, in triplicate, for each substrate. microbiota changes were monitored by fluorescent in situ hybridization; groups enumerated were: bifidobacterium genus, bacteroides an ...200818430007
molecular quantification of gardnerella vaginalis and atopobium vaginae loads to predict bacterial vaginosis.bacterial vaginosis (bv) is a poorly detected public health problem that is associated with preterm delivery and for which no reliable diagnostic tool exists.200818513147
characterisation of eubacterium-like strains isolated from oral infections.the genus eubacterium currently includes a heterogeneous group of gram-positive, non-spore-forming anaerobic bacilli, many of which are slow growing, fastidious and generally unreactive in biochemical tests. as a consequence, cultivation and identification of isolates are difficult and the taxonomy of the group remains indifferent. in this study, 105 isolates from odontogenic infections, infections associated with dental implants or saliva from healthy subjects and provisionally assigned to the ...200111699590
characterization of novel human oral isolates and cloned 16s rdna sequences that fall in the family coriobacteriaceae: description of olsenella gen. nov., reclassification of lactobacillus uli as olsenella uli comb. nov. and description of olsenella profusa sp. nov.the diversity of organisms present in the subgingival pockets of patients with periodontitis and acute necrotizing ulcerative gingivitis (anug) were examined previously. the 16s rrna genes of subgingival plaque bacteria were amplified using pcr with a universal forward primer and a spirochaete-selective reverse primer. the amplified dna was cloned into escherichia coli. in one subject with anug, 70 clones were sequenced. seventy-five per cent of the clones were spirochaetal, as expected. twelve ...200111594611
sepsis associated with a new atopobium species, provisionally named atopobium detroiti: case report and review of the current status of the species atopobium.this paper reports a case of sepsis associated with a previously unknown atopobium species and highlights the role of 16s ribosomal subunit sequencing in the rapid identification of slow-growing or atypical organisms in the clinical laboratory.200818979609
clinical characteristics of bacterial vaginosis among women testing positive for fastidious the aetiology of bacterial vaginosis (bv) is not well understood, this study sought to determine the relationships between several fastidious microbes, bv and selected clinical characteristics of bv.200919004865
new in vitro colonic fermentation model for salmonella infection in the child this study, a new in vitro continuous colonic fermentation model of salmonella infection with immobilized child fecal microbiota and salmonella serovar typhimurium was developed for the proximal colon. this model was then used to test the effects of two amoxicillin concentrations (90 and 180 mg day(-1)) on the microbial composition and metabolism of the gut microbiota and on salmonella serovar typhimurium during a 43-day fermentation. addition of gel beads (2%, v/v) colonized with salmonella ...200919087202
changes in vaginal bacterial concentrations with intravaginal metronidazole therapy for bacterial vaginosis as assessed by quantitative pcr.several fastidious bacteria have been associated with bacterial vaginosis (bv) using broad-range bacterial pcr methods such as consensus sequence 16s rrna gene pcr, but their role in bv remains poorly defined. we describe changes in vaginal bacterial concentrations following metronidazole therapy for bv. vaginal swabs were collected from women with bv diagnosed using amsel clinical criteria, and vaginal fluid was assessed by gram stain to generate nugent scores. follow-up swabs were collected 1 ...200919144794
human case of atopobium rimae bacteremia. 200919193298
development of 16s rrna-based probes for the coriobacterium group and the atopobium cluster and their application for enumeration of coriobacteriaceae in human feces from volunteers of different age groups.two 16s rrna-targeted probes were developed: one for the coriobacterium group and the other for the atopobium cluster (which comprises most of the coriobacteriaceae species, including the coriobacterium group). the new probes were based on sequences of three new coriobacteriaceae strains isolated from human feces and clinical material and sequences from databases. application of the probes to fecal samples showed that formula-fed infants had higher numbers of coriobacterium group cells in their ...200011010909
establishment of an analytical system for the human fecal microbiota, based on reverse transcription-quantitative pcr targeting of multicopy rrna analytical system based on rrna-targeted reverse transcription-quantitative pcr (rt-qpcr) was established for the precise evaluation of human intestinal microbiota. group- and species-specific primer sets for clostridium perfringens, lactobacillus spp. (six subgroups and three species), enterococcus spp., and staphylococcus spp. targeting 16s rrna gene sequences were newly developed for the quantitative analysis of such subdominant populations in human intestines. they were used together with ...200919201979
temperature-dependent variation in api 50 ch fermentation profiles of lactobacillus species.api 50 ch fermentation profiles of 45 lactobacillus, one atopobium, and three weissella strains incubated at 30 degrees c and 37 degrees c were evaluated. atopobium uli and ten species of lactobacillus showed stable patterns despite the change in temperature. the rest of the type strains showed discrepancy between the two incubation temperatures: 18 strains lost, 12 additionally fermented another sugar, and 7 others fermented a different one in lieu. the variation was maximum in l. delbrueckii s ...200010919394
phylogenetic evidence for the transfer of eubacterium lentum to the genus eggerthella as eggerthella lenta gen. nov., comb. nov.eubacterium lentum has unique phenotypic characters within the genus eubacterium. the 16s rrna sequence of eubacterium lentum was determined and its phylogenetic position was defined. this micro-organism is a member of the genus eubacterium but it is not closely related to eubacterium limosum, the type species of the genus eubacterium, and is nearer to collinsella aerofaciens and coriobacterium glomerans. a pcr-based identification system using species-specific primers designed on the basis of d ...199910555354
microflora of the penile skin-lined neovagina of transsexual women.the microflora of the penile skin-lined neovagina in male-to-female transsexuals is a recently created microbial niche which thus far has been characterized only to a very limited extent. yet the knowledge of this microflora can be considered as essential to the follow-up of transsexual women. the primary objective of this study was to map the neo-vaginal microflora in a group of 50 transsexual women for whom a neovagina was constructed by means of the inverted penile skin flap technique. second ...200919457233
characterization of a novel atopobium isolate from the human vagina: description of atopobium vaginae sp. nov.phenotypic and phylogenetic studies were performed on a hitherto undescribed micro-organism isolated from the human vagina. comparative 16s rrna gene sequencing studies demonstrated that the unknown strain constituted a new subline within the genus atopobium. the unknown bacterium was readily distinguished from other atopobium species by biochemical tests and electrophoretic analysis of whole-cell proteins. based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium ...199910555338
comparative sequence analyses of the 16s rrna genes of lactobacillus minutus, lactobacillus rimae and streptococcus parvulus: proposal for the creation of a new genus atopobium.16s rrna gene sequencing was performed on the species lactobacillus minutus, lactobacillus rimae and streptococcus parvulus in order to clarify their taxonomic position. based on comparative sequence analyses these organisms represent a hitherto unknown line of descent within the lactic acid group of bacteria for which a new genus, atopobium gen. nov., is proposed.19921382033
cultivation-independent analysis of changes in bacterial vaginosis flora following metronidazole treatment.pcr was used to survey bacterial vaginosis flora before and after metronidazole treatment. the species composition for pretreatment patients was variable. lactobacillus iners was prominent in all patients posttreatment. atopobium vaginae concentrations were highest for patients who failed or responded incompletely to treatment and lowest for patients who were cured.200717202272
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
clinical study comparing probiotic lactobacillus gr-1 and rc-14 with metronidazole vaginal gel to treat symptomatic bacterial vaginosis.bacterial vaginosis (bv) is particularly common in black women, and in nigeria it is often caused by mycoplasma, as well as atopobium, prevotella and gardnerella sp. antimicrobial metronidazole oral therapy is poorly effective in eradicating the condition and restoring the lactobacillus microbiota in the vagina. in this study, 40 women diagnosed with bv by discharge, fishy odor, sialidase positive test and nugent gram stain scoring, were randomized to receive either two dried capsules containing ...200617045832
[atopobium vaginae: characterization and association with pathogenesis of bacterial vaginosis].atopobium vaginae was described in 1999 by rodriguez et al. it is a gram-positive bacterium producing organic acids (lactic acid, acetic acid, formic acid) as a results of glucose fermentation. it was first found in vaginal swab taken from a healthy woman using 16s rrna analysis. a. vaginae is associated with bacterial vaginosis and its consequences in upper part of women reproductive organs.200616958231
multiplex detection of bacteria associated with normal microbiota and with bacterial vaginosis in vaginal swabs by use of oligonucleotide-coupled fluorescent microspheres.bacterial vaginosis (bv) is a recurrent condition that is associated with a range of negative outcomes, including the acquisition of human immunodeficiency virus and other sexually transmitted diseases, preterm births, and pelvic inflammatory disease. in contrast to the lactobacillus-dominated normal vaginal microbiota, bv is characterized by a lack of lactobacilli and an abundance of anaerobic and gram-negative organisms, including gardnerella vaginalis and atopobium vaginae. to date, the labor ...200919794034
the association of atopobium vaginae and gardnerella vaginalis with bacterial vaginosis and recurrence after oral metronidazole therapy.we investigated associations between atopobium vaginae and bacterial vaginosis (bv) and the role that a. vaginae plays in recurrent bv after oral metronidazole therapy.200616941351
high vaginal concentrations of atopobium vaginae and gardnerella vaginalis in women undergoing preterm estimate the relationship between vaginal quantification of the main microorganisms related with bacterial vaginosis and the risk of preterm delivery among women with preterm labor.201020027045
prevalence of gardnerella vaginalis and atopobium vaginae in virginal women.the objectives of this study was to determine the prevalence of gardnerella vaginalis and atopobium vaginae in virginal women and to establish if nonpenetrative sexual activity is associated with these organisms.200616601662
bacterial flora of the female genital tract: function and immune regulation.the use of non-culture gene amplification techniques has improved our understanding of the composition of the vaginal bacterial ecosystem. in most healthy women in the reproductive period the predominant vaginal bacteria are one or more of the following species of lactobacillus: l. crispatus, l. iners and l. gasseri. however, in other apparently healthy women lactobacilli may be deficient or absent, being replaced by other lactic-acid-producing bacteria: atopobium, megasphaera and/or leptotrichi ...200717215167
studies on the effect of system retention time on bacterial populations colonizing a three-stage continuous culture model of the human large gut using fish techniques.fluorescence in situ hybridization was used to quantitate bacteria growing in a three-stage continuous culture system inoculated with human faeces, operated at two system retention times (60 and 20 h). twenty-three different 16s rrna gene oligonucleotide probes of varying specificities were used to detect bacteria. organisms belonging to genera bacteroides and bifidobacterium, together with the eubacterium rectale/clostridium coccoides group, the atopobium, faecalibacterium prausnitzii and eubac ...200616420637
molecular methodology in determining vaginal flora in health and disease: its time has come.the microbial flora of the human vagina can affect the health of women, their fetuses, and newborns. conventional cultivation methods fail to detect some fastidious vaginal bacteria, leading to an incomplete census. recent advances in molecular biology have facilitated the detection and identification of bacteria without cultivation, and the advantages and limitations of this approach are described. molecular studies of the vaginal flora have discovered many uncultivated bacterial species. for i ...200516225785
rapid characterization of the normal and disturbed vaginal microbiota by application of 16s rrna gene terminal rflp fingerprinting.bacterial vaginosis (bv) is a prevalent infection in women of reproductive age associated with numerous sequelae, including preterm delivery, amniotic fluid infections and an increased risk of acquiring sexually transmitted diseases. the vaginal microbiota in bv patients is characterized by a shift from lactobacilli to a diverse spectrum of mostly anaerobic bacteria. in this study, terminal restriction fragment length polymorphism (t-rflp) was used to characterize the vaginal bacterial communiti ...200717510259
[the bacterial vaginosis--treatment problems].the changes in vaginal ecosystem (decreasing number of h2o2 producing lactobacillus spp. and increasing number of mobiluncus spp., gardnerella vaginalis, atopobium vaginae, prevotella spp., mycoplasma hominis, peptostreptococcus spp.) appears to be a major cause of bacterial vaginosis (bv). bacterial vaginosis is associated with infectious complications in pregnant and non-pregnant women and increasing risk of sti. the preventive role of natural vaginal microflora and problems of bv treatment ar ...200717607971
targeted pcr for detection of vaginal bacteria associated with bacterial vaginosis.several novel bacterial species have been detected in subjects with bacterial vaginosis (bv) by using broad-range pcr assays, but this approach is insensitive for detecting minority species. we developed a series of taxon-directed 16s rrna gene pcr assays for more sensitive detection of key vaginal bacteria. we sought to determine the prevalence of each species in the vagina, its association with bv, and the utility of pcr for the microbiological diagnosis of bv. targeted pcr assays were develop ...200717687006
rapid detection of atopobium vaginae and association with organisms implicated in bacterial vaginosis.atopobium vaginae, a fastidious, anaerobic, gram-positive cocci-shaped bacterium that generates large quantities of lactic acid, is associated with bacterial vaginosis (bv). published nucleic acid amplification tests for identifying a. vaginae are directed toward the 16s ribosomal dna with suboptimal specificity and require isolation of the organism. here, sequencing of an a. vaginae genomic library has led to the development of a highly specific and sensitive real-time pcr test for detection of ...200817913456
an adherent gardnerella vaginalis biofilm persists on the vaginal epithelium after standard therapy with oral metronidazole.the purpose of this study was to determine the efficacy of standard treatment with oral metronidazole in the eradication of the bacterial vaginosis biofilm.200818005928
imbalance in the composition of the duodenal microbiota of children with coeliac disease.coeliac disease (cd) is the most common immune-mediated enteropathy characterized by chronic inflammation of the small intestinal mucosa. the ingestion of gluten is responsible for the symptoms of cd, but other environmental factors are also thought to play a role in this disorder. in this study, the composition of the duodenal microbiota of coeliac children with active disease, symptom-free cd patients on a gluten-free diet and control children was determined. bacteriological analyses of duoden ...200718033837
differences in the composition of vaginal microbial communities found in healthy caucasian and black women.the maintenance of a low ph in the vagina through the microbial production of lactic acid is known to be an important defense against infectious disease in reproductive age women. previous studies have shown that this is largely accomplished through the metabolism of lactic acid bacteria, primarily species of lactobacillus. despite the importance of this defense mechanism to women's health, differences in the species composition of vaginal bacterial communities among women have not been well def ...200718043622
rrna-based analysis to monitor succession of faecal bacterial communities in holstein quantitatively analyse the faecal bacterial communities of holstein calves and track their succession up to 12 weeks of age.201020849397
rifaximin modulates the colonic microbiota of patients with crohn's disease: an in vitro approach using a continuous culture colonic model system.rifaximin, a rifamycin derivative, has been reported to induce clinical remission of active crohn's disease (cd), a chronic inflammatory bowel disorder. in order to understand how rifaximin affects the colonic microbiota and its metabolism, an in vitro human colonic model system was used in this study.201020852272
quantitative determination by real-time pcr of four vaginal lactobacillus species, gardnerella vaginalis and atopobium vaginae indicates an inverse relationship between l. gasseri and l. iners.most studies of the vaginal microflora have been based on culture or on qualitative molecular techniques. here we applied existing real-time pcr formats for lactobacillus crispatus, l. gasseri and gardnerella vaginalis and developed new formats for atopobium vaginae, l. iners and l. jensenii to obtain a quantitative non culture-based determination of these species in 71 vaginal samples from 32 pregnant and 28 non-pregnant women aged between 18 and 45 years.200718093311
response of gardnerella vaginalis biofilm to 5 days of moxifloxacin treatment.polymicrobial communities are often recalcitrant to antibiotics. we tested whether the polymicrobial gardnerella vaginalis biofilm can be eradicated with moxifloxacin. twenty women with bacterial vaginosis were treated with 400 mg moxifloxacin for 5 days. the changes in the occurrence and proportions of gardnerella, atopobium and lactobacillus spp. were assessed using fish. the bacterial biofilm was investigated using desquamated epithelial cells of spontaneously voided urine and sections of vag ...201020955467
microbiota of dentinal caries as assessed by reverse-capture checkerboard analysis.this study aimed to identify the microbiota of different layers of dentinal caries by using a culture-independent molecular biology approach.201021160186
molecular identification of bacteria on the tongue dorsum of subjects with and without the microbial profiles on the tongue dorsum in patients with halitosis and control subjects in a uk population using culture-independent techniques.200818336372
microarray-based identification of clinically relevant vaginal bacteria in relation to bacterial vaginosis.the objective was to examine the use of a tailor-made dna microarray containing probes representing the vaginal microbiota to examine bacterial vaginosis.201121272848
effects of resistant starch type iii polymorphs on human colon microbiota and short chain fatty acids in human gut models.this study probed the possible effects of type iii resistant starch (rs) crystalline polymorphism on rs fermentability by human gut microbiota and the short chain fatty acids production in vitro. human fecal ph-controlled batch cultures showed rs induces an ecological shift in the colonic microbiota with polymorph b inducing bifidobacterium spp. and polymorph a inducing atopobium spp. interestingly, polymorph b also induced higher butyrate production to levels of 0.79 mm. in addition, human gut ...200818543927
quantitative variations in the vaginal bacterial population associated with asymptomatic infections: a real-time polymerase chain reaction study.the real-time polymerase chain reaction (pcr) quantification of several vaginal bacterial groups in healthy women and patients developing asymptomatic bacterial vaginosis (bv) and candidiasis (ca) was performed. statistical analysis revealed that the bv condition is characterised by a great variability among subjects and that it is associated with a significant increase of prevotella, atopobium, veillonella and gardnerella vaginalis, and a drop in lactobacillus. on the contrary, the vaginal micr ...200918762999
gene polymorphisms of toll-like and related recognition receptors in relation to the vaginal carriage of gardnerella vaginalis and atopobium genetic factors have previously been found to act as determinants of differential susceptibility to major infectious diseases. it is less clear whether such polymorphisms may also impose on pathogen recognition in mucosal overgrowth conditions such as bacterial vaginosis, an anaerobic overgrowth condition characterised by the presence of a vaginal biofilm consisting of the gram-positive anaerobes gardnerella vaginalis and atopobium vaginae. we selected 34 single nucleotide polymorphisms per ...200919200604
bacterial populations in the vaginas of healthy adolescent women.given that the microbiota of the healthy vagina plays an important role in the maintenance of health, it follows that an understanding of its composition and development may offer insights into the etiology and prevention of disease. in contrast to previous studies, this study exclusively investigated the structure and composition of adolescent vaginal bacterial communities. in this report, the vaginal bacterial communities of 90 menarcheal adolescents, ages 13-18y, were characterized using term ...200919232297
the human vaginal bacterial biota and bacterial vaginosis.the bacterial biota of the human vagina can have a profound impact on the health of women and their neonates. changes in the vaginal microbiota have been associated with several adverse health outcomes including premature birth, pelvic inflammatory disease, and acquisition of hiv infection. cultivation-independent molecular methods have provided new insights regarding bacterial diversity in this important niche, particularly in women with the common condition bacterial vaginosis (bv). pcr method ...200919282975
determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five european centres.although it is well established that early infant feeding has a major influence on the establishment of the gut microbiota, very little is understood about how the introduction of first solid food influences the colonization process. this study aimed to determine the impact of weaning on the faecal microbiota composition of infants from five european countries (sweden, scotland, germany, italy and spain) which have different lifestyle characteristics and infant feeding practices. faecal samples ...201121330436
fluorescent hybridisation combined with flow cytometry and hybridisation of total rna to analyse the composition of microbial communities in human faeces using 16s rrna determine the structure of human faecal microbiota, faecal samples from 23 healthy individuals were analysed with a similar set of probes targeting six phylogenetic groups using rrna dot-blot hybridisation and whole cell fluorescent in situ hybridisation (fish) combined with flow cytometry. when microbiota compositions derived by each method were compared, the results were not statistically different for clostridium coccoides, fusobacterium prausnitzii, bifidobacterium spp. and enterobacteria ...200319719684
exopolysaccharides produced by bifidobacterium longum ipla e44 and bifidobacterium animalis subsp. lactis ipla r1 modify the composition and metabolic activity of human faecal microbiota in ph-controlled batch cultures.exopolysaccharides (eps) isolated from two bifidobacterium strains, one of human intestinal origin (bifidobacterium longum subsp. longum ipla e44) and the other from dairy origin (bifidobacterium animalis subsp. lactis ipla r1), were subjected to in vitro chemically simulated gastrointestinal digestion, which showed the absence of degradation of both polymers in these conditions. polymers were then used as carbon sources in ph-controlled faecal batch cultures and compared with the non-prebiotic ...200919735956
strong correspondence in bacterial loads between the vagina and rectum of pregnant women.we sampled the vagina and rectum in 71 pregnant women and bacterial loads of lactobacillus crispatus, l. jensenii, l. gasseri, l. iners, gardnerella vaginalis and atopobium vaginae were determined by culture and quantitative pcr (qpcr). culture and qpcr results differed substantially with regard to the evaluation of vaginal and rectal occurrence of the six species tested. the vaginal-rectal prevalence of l. crispatus, l. jensenii, l. gasseri, l. iners, g. vaginalis and a. vaginae as established ...201121513795
self-collected vaginal swabs for the quantitative real-time polymerase chain reaction assay of atopobium vaginae and gardnerella vaginalis and the diagnosis of bacterial vaginosis.the aim of this study was to assess the feasibility of using self-collected vaginal specimens for the quantitative real-time polymerase chain reaction (qpcr) assays of bacterial vaginosis (bv)-associated bacteria versus practitioner-collected swabs. a cross-sectional study included 190 pregnant women enrolled before 20 weeks' gestation from september 2008 to november 2009. self- and practitioner-collected swabs were taken during the same prenatal visit for each woman, qpcr assays performed for e ...201121789604
intravaginal microbial flora by the 16s rrna gene sequencing.objective: conventional diagnosis of bacterial vaginosis contains some controversial points. to understand accurately the relationship between clinical stages and the microbiotas, the intravaginal microbial flora was analyzed by the clone library method. study design: vaginal fluid samples from 31 patients were examined. lactobacillary grade, nugent score, culture-based method, and clone library analysis using the 16srrna gene sequencing were performed and were compared with each other. results: ...201121783170
vanb-type resistant clostridium clostridioforme and atopobium minutum clinical isolates in france.acquired vancomycin resistance in gram-positive anaerobes has been reported only in australia and canada from rare vanb-positive stool samples in absence of vre. we report the emergence of vanb-type resistance in clostridium clostridioforme and atopobium minutum involved in human infections in france.201121775552
investigation of the faecal microbiota associated with canine chronic diarrhoea.diarrhoea is a common problem in dogs and can result in disturbance of the normal intestinal microbiota. however, little is known about the gastrointestinal microbiota of dogs with chronic diarrhoea and controlled canine studies of dietary management are scarce. the aims of this study were to investigate the predominant faecal microbiota of chronic diarrhoea dogs and to examine the effect(s) of a fibre blend on the canine faecal microbiota. a 3-week fibre supplementation feeding study was perfor ...201020002179
differential induction of apoptosis in human colonic carcinoma cells (caco-2) by atopobium, and commensal, probiotic and enteropathogenic bacteria: mediation by the mitochondrial pathway.the induction of apoptosis in mammalian cells by bacteria is well reported. this process may assist infection by pathogens whereas for non-pathogens apoptosis induction within carcinoma cells protects against colon cancer. here, apoptosis induction by a major new gut bacterium, atopobium minutum, was compared with induction by commensal (escherichia coli k-12 strains), probiotic (lactobacillus rhamnosus, bifidobacterium latis) and pathogenic (e. coli: epec and vtec) gut bacteria within the colon ...201020036023
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 ...201020187995
prevalence and diversity of microbes in the amniotic fluid, the fetal inflammatory response, and pregnancy outcome in women with preterm pre-labor rupture of membranes.the role played by microbial invasion of the amniotic cavity (miac) in preterm pre-labor rupture of membranes (pprom) is inadequately characterized, in part because of reliance on cultivation-based methods.201020331587
olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of olsenella, olsenella uli and olsenella profusa.strain a2 is an anaerobic, variably gram-stain-positive, non-spore-forming, small and irregularly rod-shaped bacterium from the ruminal fluid of a sheep that has been described informally as a representative of 'olsenella (basonym atopobium) oviles'. three phenotypically similar bacterial strains (lac15, lac16 and lac31(t)) were isolated in concert with veillonella magna lac18(t) from the mucosal jejunum of a pig. a phylogenetic analysis based on 16s rrna gene sequences revealed that strains a2, ...201120435744
intestinal microbiota of 6-week-old infants across europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics.: there are many differences in diet and lifestyle across europe that may influence the development of the infant gut microbiota. this work aimed to assess the impact of geographic area, mode of delivery, feeding method, and antibiotic treatment on the fecal microbiota of infants from 5 european countries with different lifestyle characteristics: sweden, scotland, germany, italy, and spain.201020479681
a double-blind, placebo-controlled, cross-over study to establish the bifidogenic effect of a very-long-chain inulin extracted from globe artichoke (cynara scolymus) in healthy human subjects.there is growing interest in the use of inulins as substrates for the selective growth of beneficial gut bacteria such as bifidobacteria and lactobacilli because recent studies have established that their prebiotic effect is linked to several health benefits. in the present study, the impact of a very-long-chain inulin (vlci), derived from globe artichoke (cynara scolymus), on the human intestinal microbiota compared with maltodextrin was determined. a double-blind, cross-over study was carried ...201020591206
is there a correlation between bacterial vaginosis and preterm labour in women in the otago region of new zealand?while an association between bacterial vaginosis and preterm labour has been established, the relative contribution of this condition remains controversial.201020618238
In vitro fermentation of alternansucrase raffinose-derived oligosaccharides by human gut bacteria.In this work, in vitro fermentation of alternansucrase raffinose-derived oligosaccharides, previously fractionated according to their degree of polymerization (DP; from DP4 to DP10), was carried out using small-scale pH-controlled batch cultures at 37 °C under anaerobic conditions with human feces. Bifidogenic activity of oligosaccharides with DP4-6 similar to that of lactulose was observed; however, in general, a significant growth of lactic acid bacteria Bacteroides , Atopobium cluster, and ...201121913653
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