The Experts below are selected from a list of 51204 Experts worldwide ranked by ideXlab platform
Wang Wei - One of the best experts on this subject based on the ideXlab platform.
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ESTABLISHMENT OF REAL-TIME FLUORESCENCE PCR FOR Bacteroides
Modern Preventive Medicine, 2010Co-Authors: Wang WeiAbstract:[Objective] To develop a detection method of Bacteroides with TaqMan real-time PCR for the rapid enumeration of Bacteroides. [Methods] Through homology comparison of 16S rRNA gene sequences of Bacteroides downloaded from GenBank, conservative regions were selected for the designation of primers and probe. After optimization of reaction conditions of real-time PCR, the sensitivity, specificity and reproducibility of the method were evaluated. A recombinant plasmids were constructed for the establishment of standard curve. [Results] Linear regression coefficient (R) of real-time PCR assay was 0.995 7. The sensitivity was down to level of 103CFU / mL. The time of detection was no more than 2 hours. The coefficient variation (CV) of reproducibility experiments were between 1.19% and 2.21%. [Conclusion] The established TaqMan real-time PCR assay for the rapid enumeration of Bacteroides demonstrates high sensitivity, specificity and reproducibility. It could be applied in the rapid diagnosis of clinical Bacteroides infection and the counts of intestinal Bacteroides in different samples.
Yoshimi Benno - One of the best experts on this subject based on the ideXlab platform.
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Bacteroides chinchillae sp nov and Bacteroides rodentium sp nov isolated from chinchilla chinchilla lanigera faeces
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Maki Kitahara, Mitsuo Sakamoto, Yoshimi Benno, Sayaka Tsuchida, Koh Kawasumi, Hiromi Amao, Moriya OhkumaAbstract:Gram-negative anaerobic rods were isolated from chinchilla (Chinchilla lanigera) faeces and three strains, ST170T, ST180 and ST28T, were investigated taxonomically. On the basis of phylogenetic analyses and specific phenotypic characteristics, the three strains belonged to the genus Bacteroides. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strains ST170T and ST180 formed a single cluster and a distinct line of descent. Strain ST170T exhibited 99.7 % 16S rRNA gene sequence similarity with strain ST180 and 95.1, 94.6 and 94.4 % 16S rRNA gene sequence similarity with Bacteroides massiliensis JCM 13223T, Bacteroides dorei JCM 13471T and Bacteroides vulgatus JCM 5826T, respectively. Strain ST28T also formed a distinct line of descent and exhibited the highest 16S rRNA gene sequence similarity with Bacteroides uniformis JCM 5828T (98.1 %). Low DNA–DNA relatedness (1 %) between strain ST28T and B. uniformis JCM 5828T clearly indicated that they belonged to different species. Analysis of hsp60 sequences also supported these relationships. The DNA G+C contents of strains ST170T and ST28T were 45.2 and 41.0 mol%, respectively. On the basis of phenotypic characteristics and phylogenetic data, two novel species, Bacteroides chinchillae sp. nov. (type strain ST170T = JCM 16497T = CCUG 59335T) and Bacteroides rodentium sp. nov. (type strain ST28T = JCM 16496T = CCUG 59334T), are proposed.
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hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes.
International journal of systematic and evolutionary microbiology, 2010Co-Authors: Mitsuo Sakamoto, Natsuko Suzuki, Yoshimi BennoAbstract:hsp60 gene sequences were determined for members of the genus Bacteroides and sequence similarities were compared with those obtained for the 16S rRNA gene. Among the 29 Bacteroides type strains, the mean sequence similarity of the hsp60 gene (84.5 %) was significantly less than that of the 16S rRNA gene (90.7 %), indicating a high discriminatory power of the hsp60 gene. Species of the genus Bacteroides were differentiated well by hsp60 gene sequence analysis, except for Bacteroides pyogenes JCM 6294(T), Bacteroides suis JCM 6292(T) and Bacteroides tectus JCM 10003(T). The hsp60 gene sequence analysis and the levels of DNA-DNA relatedness observed demonstrated that these three type strains are a single species. Consequently, B. suis and B. tectus are heterotypic synonyms of B. pyogenes. This study suggests that the hsp60 gene is an alternative phylogenetic marker for the classification of species of the genus Bacteroides.
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reclassification of Bacteroides distasonis Bacteroides goldsteinii and Bacteroides merdae as paraBacteroides distasonis gen nov comb nov paraBacteroides goldsteinii comb nov and paraBacteroides merdae comb nov
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Mitsuo Sakamoto, Yoshimi BennoAbstract:The characteristics of three Bacteroides species, Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae, were examined. 16S rRNA gene sequence analysis showed that B. distasonis, B. goldsteinii and B. merdae should not be classified as species within the genus Bacteroides. Although B. distasonis, B. goldsteinii and B. merdae were phylogenetically related to Tannerella forsythensis, the ratios of anteiso-C15 : 0 to iso-C15 : 0 in whole-cell methanolysates of the three species were different from that of T. forsythensis. In addition, whereas the major menaquinones of T. forsythensis were MK-10 and MK-11, the major menaquinones of B. distasonis, B. goldsteinii and B. merdae were MK-9 and MK-10. The three species were phenotypically similar to Bacteroides sensu stricto, but phylogenetically distinct. Furthermore, B. distasonis, B. goldsteinii and B. merdae could be differentiated from Bacteroides sensu stricto (predominant menaquinones: MK-10 and MK-11) by the menaquinone composition. This is an important chemotaxonomic characteristic of the three species. On the basis of these data, a novel genus, ParaBacteroides gen. nov., is proposed for B. distasonis, B. goldsteinii and B. merdae, with three species, ParaBacteroides distasonis gen. nov., comb. nov. (the type species), ParaBacteroides goldsteinii comb. nov. and ParaBacteroides merdae comb. nov. The type strains of P. distasonis, P. goldsteinii and P. merdae are JCM 5825T (=CCUG 4941T=DSM 20701T=ATCC 8503T), JCM 13446T (=CCUG 48944T) and JCM 9497T (=CCUG 38734T=ATCC 43184T), respectively.
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reclassification of Bacteroides forsythus tanner et al 1986 as tannerella forsythensis corrig gen nov comb nov
International Journal of Systematic and Evolutionary Microbiology, 2002Co-Authors: Mitsuo Sakamoto, Masahito Suzuki, Makoto Umeda, Isao Ishikawa, Yoshimi BennoAbstract:The characteristics of the fusiform species Bacteroides forsythus, isolated from human periodontal pockets, were examined. 165 rDNA sequence analysis confirmed that B. forsythus was not a species within the genus Bacteroides sensu stricto. Although B. forsythus was phylogenetically related to Bacteroides distasonis and Bacteroides merdae in the phylogenetic tree, the ratio of anteiso-15:0 to iso-15:0 in whole-cell methanolysates of B. forsythus was different from those of B. distasonis, B. merdae and other Bacteroides species. B. forsythus did not grow on medium containing 20% bile, but members of the Bacteroides fragilis group did. B. forsythus was the only species tested that was trypsin-positive in API ZYM tests. The dehydrogenase enzyme pattern was of no use for the differentiation of B. forsythus and the B. fragilis group. On the basis of these data, a new genus, Tannerella, is proposed for Bacteroides forsythus, with one species, Tannerella forsythensis corrig., gen. nov., comb. nov. The type strain of Tannerella forsythensis is JCM 10827T (= ATCC 43037T).
Sydney M. Finegold - One of the best experts on this subject based on the ideXlab platform.
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Application of quantitative real-time PCR for rapid identification of Bacteroides fragilis group and related organisms in human wound samples
Anaerobe, 2011Co-Authors: Jia Tong, Huaxi Xu, Paula Summanen, Sydney M. FinegoldAbstract:Our goal was to establish a quantitative real-time PCR (QRT-PCR) method to detect Bacteroides fragilis group and related organisms from clinical specimens. Compared to conventional anaerobic culture, QRT-PCR can provide accurate and more rapid detection and identification of B. fragilis group and similar species. B. fragilis group and related organisms are the most frequently isolated anaerobic pathogens from clinical samples. However, culture and phenotypic identification is quite time-consuming. We designed specific primers and probes based on the 16S rRNA gene sequences of Bacteroides caccae, Bacteroides eggerthii, B. fragilis, Bacteroides ovatus, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Odoribacter splanchnicus (Bacteroides splanchnicus), ParaBacteroides distasonis (Bacteroides distasonis) and ParaBacteroides merdae (Bacteroides merdae), and detected these species by means of QRT-PCR in 400 human surgical wound infection samples or closed abscesses. The target bacteria were detected from 31 samples (8%) by culture, but from 132 samples (33%) by QRT-PCR (p-value < 0.001). B. uniformis was the most common species (44 positive samples) according to QRT-PCR while culture showed it to be B. fragilis (16 positive samples). Additionally, for each species QRT-PCR detected higher counts than culture did; this may reflect detecting DNA of dead organisms by QRT-PCR. QRT-PCR is a rapid and sensitive method which has great potential for detection of B. fragilis group and related organisms in wound samples.
Steven D Siciliano - One of the best experts on this subject based on the ideXlab platform.
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detection and quantification of the human specific hf183 Bacteroides 16s rrna genetic marker with real time pcr for assessment of human faecal pollution in freshwater
Environmental Microbiology, 2005Co-Authors: Sylvie Seurinck, Tom Defoirdt, Willy Verstraete, Steven D SicilianoAbstract:The human-specific HF183 Bacteriodes 16S rRNA genetic marker can be used to detect human faecal pollution in water environments. However, there is currently no method to quantify the prevalence of this marker in environmental samples. We developed a real-time polymerase chain reaction (PCR) assay using SYBR Green I detection to quantify this marker in faecal and environmental samples. To decrease the amplicon length to a suitable size for real-time PCR detection, a new reverse primer was designed and validated on human and animal faecal samples. The use of the newly developed reverse primer in combination with the human-specific HF183 primer did not decrease the specificity of the real-time PCR assay but a melting curve analysis must always be included. This new assay was more sensitive than conventional PCR and highly reproducible with a coefficient of variation of less than 1% within an assay and 3% between assays. As the Bacteroides species that carries this human-specific marker has never been isolated, a bacteria real-time assay was used to determine the detection efficiency. The estimated detection efficiency in freshwater ranged from 78% to 91% of the true value with an average detection efficiency of 83+/-4% of the true value. Using a simple filtration method, the limit of quantification was 4.7+/-0.3x10(5) human-specific Bacteroides markers per litre of freshwater. The aerobic incubation of the human-specific Bacteroides marker in freshwater for up to 24 days at 4 and 12 degrees C, and up to 8 days at 28 degrees C, indicated that the marker persisted up to the end of the incubation period for all incubation temperatures.
Mitsuo Sakamoto - One of the best experts on this subject based on the ideXlab platform.
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Bacteroides chinchillae sp nov and Bacteroides rodentium sp nov isolated from chinchilla chinchilla lanigera faeces
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Maki Kitahara, Mitsuo Sakamoto, Yoshimi Benno, Sayaka Tsuchida, Koh Kawasumi, Hiromi Amao, Moriya OhkumaAbstract:Gram-negative anaerobic rods were isolated from chinchilla (Chinchilla lanigera) faeces and three strains, ST170T, ST180 and ST28T, were investigated taxonomically. On the basis of phylogenetic analyses and specific phenotypic characteristics, the three strains belonged to the genus Bacteroides. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strains ST170T and ST180 formed a single cluster and a distinct line of descent. Strain ST170T exhibited 99.7 % 16S rRNA gene sequence similarity with strain ST180 and 95.1, 94.6 and 94.4 % 16S rRNA gene sequence similarity with Bacteroides massiliensis JCM 13223T, Bacteroides dorei JCM 13471T and Bacteroides vulgatus JCM 5826T, respectively. Strain ST28T also formed a distinct line of descent and exhibited the highest 16S rRNA gene sequence similarity with Bacteroides uniformis JCM 5828T (98.1 %). Low DNA–DNA relatedness (1 %) between strain ST28T and B. uniformis JCM 5828T clearly indicated that they belonged to different species. Analysis of hsp60 sequences also supported these relationships. The DNA G+C contents of strains ST170T and ST28T were 45.2 and 41.0 mol%, respectively. On the basis of phenotypic characteristics and phylogenetic data, two novel species, Bacteroides chinchillae sp. nov. (type strain ST170T = JCM 16497T = CCUG 59335T) and Bacteroides rodentium sp. nov. (type strain ST28T = JCM 16496T = CCUG 59334T), are proposed.
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hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes.
International journal of systematic and evolutionary microbiology, 2010Co-Authors: Mitsuo Sakamoto, Natsuko Suzuki, Yoshimi BennoAbstract:hsp60 gene sequences were determined for members of the genus Bacteroides and sequence similarities were compared with those obtained for the 16S rRNA gene. Among the 29 Bacteroides type strains, the mean sequence similarity of the hsp60 gene (84.5 %) was significantly less than that of the 16S rRNA gene (90.7 %), indicating a high discriminatory power of the hsp60 gene. Species of the genus Bacteroides were differentiated well by hsp60 gene sequence analysis, except for Bacteroides pyogenes JCM 6294(T), Bacteroides suis JCM 6292(T) and Bacteroides tectus JCM 10003(T). The hsp60 gene sequence analysis and the levels of DNA-DNA relatedness observed demonstrated that these three type strains are a single species. Consequently, B. suis and B. tectus are heterotypic synonyms of B. pyogenes. This study suggests that the hsp60 gene is an alternative phylogenetic marker for the classification of species of the genus Bacteroides.
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reclassification of Bacteroides distasonis Bacteroides goldsteinii and Bacteroides merdae as paraBacteroides distasonis gen nov comb nov paraBacteroides goldsteinii comb nov and paraBacteroides merdae comb nov
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Mitsuo Sakamoto, Yoshimi BennoAbstract:The characteristics of three Bacteroides species, Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae, were examined. 16S rRNA gene sequence analysis showed that B. distasonis, B. goldsteinii and B. merdae should not be classified as species within the genus Bacteroides. Although B. distasonis, B. goldsteinii and B. merdae were phylogenetically related to Tannerella forsythensis, the ratios of anteiso-C15 : 0 to iso-C15 : 0 in whole-cell methanolysates of the three species were different from that of T. forsythensis. In addition, whereas the major menaquinones of T. forsythensis were MK-10 and MK-11, the major menaquinones of B. distasonis, B. goldsteinii and B. merdae were MK-9 and MK-10. The three species were phenotypically similar to Bacteroides sensu stricto, but phylogenetically distinct. Furthermore, B. distasonis, B. goldsteinii and B. merdae could be differentiated from Bacteroides sensu stricto (predominant menaquinones: MK-10 and MK-11) by the menaquinone composition. This is an important chemotaxonomic characteristic of the three species. On the basis of these data, a novel genus, ParaBacteroides gen. nov., is proposed for B. distasonis, B. goldsteinii and B. merdae, with three species, ParaBacteroides distasonis gen. nov., comb. nov. (the type species), ParaBacteroides goldsteinii comb. nov. and ParaBacteroides merdae comb. nov. The type strains of P. distasonis, P. goldsteinii and P. merdae are JCM 5825T (=CCUG 4941T=DSM 20701T=ATCC 8503T), JCM 13446T (=CCUG 48944T) and JCM 9497T (=CCUG 38734T=ATCC 43184T), respectively.
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reclassification of Bacteroides forsythus tanner et al 1986 as tannerella forsythensis corrig gen nov comb nov
International Journal of Systematic and Evolutionary Microbiology, 2002Co-Authors: Mitsuo Sakamoto, Masahito Suzuki, Makoto Umeda, Isao Ishikawa, Yoshimi BennoAbstract:The characteristics of the fusiform species Bacteroides forsythus, isolated from human periodontal pockets, were examined. 165 rDNA sequence analysis confirmed that B. forsythus was not a species within the genus Bacteroides sensu stricto. Although B. forsythus was phylogenetically related to Bacteroides distasonis and Bacteroides merdae in the phylogenetic tree, the ratio of anteiso-15:0 to iso-15:0 in whole-cell methanolysates of B. forsythus was different from those of B. distasonis, B. merdae and other Bacteroides species. B. forsythus did not grow on medium containing 20% bile, but members of the Bacteroides fragilis group did. B. forsythus was the only species tested that was trypsin-positive in API ZYM tests. The dehydrogenase enzyme pattern was of no use for the differentiation of B. forsythus and the B. fragilis group. On the basis of these data, a new genus, Tannerella, is proposed for Bacteroides forsythus, with one species, Tannerella forsythensis corrig., gen. nov., comb. nov. The type strain of Tannerella forsythensis is JCM 10827T (= ATCC 43037T).
