The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Katsuji Ueki - One of the best experts on this subject based on the ideXlab platform.
-
Prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from plant residue and rice roots in irrigated rice field soil
International Journal of Systematic and Evolutionary Microbiology, 2007Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji UekiAbstract:Two strictly anaerobic bacterial strains, KB7T and A42, were isolated from rice plant residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10–40 °C; optimum growth was observed at 30 °C and pH 5.7–6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. Menaquinones MK-11 and MK-11(H2) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8–92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9–92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7T and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7T (=JCM 13650T=DSM 17968T).
-
Prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from plant residue and rice roots in irrigated rice field soil
International Journal of Systematic and Evolutionary Microbiology, 2007Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji UekiAbstract:Two strictly anaerobic bacterial strains, KB7(T) and A42, were isolated from rice plant residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10-40 degrees C; optimum growth was observed at 30 degrees C and pH 5.7-6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), C(15 : 0) and iso-C(17 : 0) 3-OH. Menaquinones MK-11 and MK-11(H(2)) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8-92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9-92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7(T) and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7(T) (=JCM 13650(T)=DSM 17968(T)).
Atsuko Ueki - One of the best experts on this subject based on the ideXlab platform.
-
Prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from plant residue and rice roots in irrigated rice field soil
International Journal of Systematic and Evolutionary Microbiology, 2007Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji UekiAbstract:Two strictly anaerobic bacterial strains, KB7T and A42, were isolated from rice plant residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10–40 °C; optimum growth was observed at 30 °C and pH 5.7–6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. Menaquinones MK-11 and MK-11(H2) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8–92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9–92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7T and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7T (=JCM 13650T=DSM 17968T).
-
Prevotella paludivivens sp nov a novel strictly anaerobic gram negative hemicellulose decomposing bacterium isolated from plant residue and rice roots in irrigated rice field soil
International Journal of Systematic and Evolutionary Microbiology, 2007Co-Authors: Atsuko Ueki, Hiroshi Akasaka, Daisuke Suzuki, Atsuya Satoh, Katsuji UekiAbstract:Two strictly anaerobic bacterial strains, KB7(T) and A42, were isolated from rice plant residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10-40 degrees C; optimum growth was observed at 30 degrees C and pH 5.7-6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), C(15 : 0) and iso-C(17 : 0) 3-OH. Menaquinones MK-11 and MK-11(H(2)) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8-92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9-92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7(T) and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7(T) (=JCM 13650(T)=DSM 17968(T)).
Harry J. Flint - One of the best experts on this subject based on the ideXlab platform.
-
relative abundance of the Prevotella genus within the human gut microbiota of elderly volunteers determines the inter individual responses to dietary supplementation with wheat bran arabinoxylan oligosaccharides
BMC Microbiology, 2020Co-Authors: Wing Sun Faith Chung, A Walker, Douwina Bosscher, Vicenta Garciacampayo, Josef Wagner, Julian Parkhill, Sylvia H Duncan, Harry J. FlintAbstract:The human colon is colonised by a dense microbial community whose species composition and metabolism are linked to health and disease. The main energy sources for colonic bacteria are dietary polysaccharides and oligosaccharides. These play a major role in modulating gut microbial composition and metabolism, which in turn can impact on health outcomes. We investigated the influence of wheat bran arabinoxylan oligosaccharides (AXOS) and maltodextrin supplements in modulating the composition of the colonic microbiota and metabolites in healthy adults over the age of 60. Male and female volunteers, (n = 21, mean BMI 25.2 ± 0.7 kg/m2) participated in the double-blind, cross over supplement study. Faecal samples were collected for analysis of microbiota, short chain fatty acids levels and calprotectin. Blood samples were collected to measure glucose, cholesterol and triglycerides levels. There was no change in these markers nor in calprotectin levels in response to the supplements. Both supplements were well-tolerated by the volunteers. Microbiota analysis across the whole volunteer cohort revealed a significant increase in the proportional abundance of faecal Bifidobacterium species (P ≤ 0.01) in response to AXOS, but not maltodextrin, supplementation. There was considerable inter-individual variation in the other bacterial taxa that responded, with a clear stratification of volunteers as either Prevotella-plus (n = 8; > 0.1% proportional abundance) or Prevotella-minus (n = 13; ≤0.1% proportional abundance) subjects founded on baseline sample profiles. There was a significant increase in the proportional abundance of both faecal Bifidobacterium (P ≤ 0.01) and Prevotella species (P ≤ 0.01) in Prevotella-plus volunteers during AXOS supplementation, while Prevotella and Bacteroides relative abundances showed an inverse relationship. Proportional abundance of 26 OTUs, including bifidobacteria and Anaerostipes hadrus, differed significantly between baseline samples of Prevotella-plus compared to Prevotella-minus individuals. The wheat bran AXOS supplementation was bifidogenic and resulted in changes in human gut microbiota composition that depended on the initial microbiota profile, specifically the presence or absence of Prevotella spp. as a major component of the microbiota. Our data therefore suggest that initial profiling of individuals through gut microbiota analysis should be considered important when contemplating nutritional interventions that rely on prebiotics. Clinical trial registration number: NCT02693782 . Registered 29 February 2016 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT02693782?term=NCT02693782&rank=1
-
estimation of the relative abundance of different bacteroides and Prevotella ribotypes in gut samples by restriction enzyme profiling of pcr amplified 16s rrna gene sequences
Applied and Environmental Microbiology, 1998Co-Authors: Jacqueline Wood, Karen P Scott, Charles J. Newbold, Gorazd Avguštin, Harry J. FlintAbstract:We describe an approach for determining the genetic composition of Bacteroides and Prevotella populations in gut contents based on selective amplification of 16S rRNA gene sequences (rDNA) followed by cleavage of the amplified material with restriction enzymes. The relative contributions of different ribotypes to total Bacteroides and Prevotella 16S rDNA are estimated after end labelling of one of the PCR primers, and the contribution of Bacteroides and Prevotella sequences to total eubacterial 16S rDNA is estimated by measuring the binding of oligonucleotide probes to amplified DNA. Bacteroides and Prevotella 16S rDNA accounted for between 12 and 62% of total eubacterial 16S rDNA in samples of ruminal contents from six sheep and a cow. Ribotypes 4, 5, 6, and 7, which include most cultivated rumen Prevotella strains, together accounted for between 20 and 86% of the total amplified Bacteroides and Prevotella rDNA in these samples. The most abundant Bacteroides or Prevotella ribotype in four animals, however, was ribotype 8, for which there is only one known cultured isolate, while ribotypes 1 and 2, which include many colonic Bacteroides spp., were the most abundant in two animals. This indicates that some abundant Bacteroides and Prevotella groups in the rumen are underrepresented among cultured rumen Prevotella isolates. The approach described here provides a rapid, convenient, and widely applicable method for comparing the genotypic composition of bacterial populations in gut samples. Methods for enumerating gut bacteria that are based on cultivation, isolation, and biochemical testing are generally laborious and do not guarantee recovery of the less easily cultivated species. This is a particular problem for obligately anaerobic bacteria, which make up the great majority of organisms present in densely populated gut habitats such as the rumen and hind gut (13, 31). For this reason, there has been increasing interest in the rapid enumeration of microbial groupings by analysis of nucleic acids extracted from gut samples. Probing of extracted RNA with radiolabelled or fluorescently labelled oligonucleotide probes has been used in several studies (6, 14, 20, 30) but relies on developing panels of probes for different groups from available sequence data. Sequencing of random PCR-amplified 16S rRNA gene (rDNA) clones has provided valuable information on total eubacterial diversity for human fecal microflora (37). However, more rapid approaches to the study of diversity that allow the examination of large numbers of samples are required, and a semiquantitative PCR detection approach based on serial dilution has been reported for some of the predominant gut anaerobes (35). The approach we take here is to perform selective PCR amplification of 16S rRNA genes from the gram-negative anaerobic genera Bacteroides and Prevotella by using DNA extracted from gut samples and then to estimate the genotypic composition of samples from restriction enzyme cleavage patterns (restriction fragment length polymorphism [RFLP]) of the amplified DNA (PCR-RFLP). 16S rDNA PCR-RFLP approaches have proved valuable for typing isolated bacterial strains (see, e.g., refer
-
Phenotypic diversity among ruminal isolates of Prevotella ruminicola: proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and redefinition of Prevotella ruminicola.
International Journal of Systematic and Evolutionary Microbiology, 1997Co-Authors: Avgustin G, Wallace Rj, Harry J. FlintAbstract:Selected phenotypic characteristics of isolates of Prevotella ruminicola (formerly Bacteroides ruminicola) were studied in order to establish whether the characteristics of genotypic strain groups established previously on the basis of 16S ribosomal DNA sequences differed systematically. Among strains formerly considered P. ruminicola subsp. brevis, strains related to strain GA33T (T = type strain) typically failed to produce carboxymethyl cellulase (CMCase) activity detectable by plate assays and failed to ferment xylose, while strains related to strain B14T produced abundant CMCase and fermented xylose. We propose that strains related to GA33T, which have DNA G+C contents between 45 and 51 mol%, should be assigned to a new species, Prevotella brevis, and that strains related to B14T, which have DNA G+C contents between 39 and 43 mol%, should be assigned to another new species, Prevotella bryantii. Most of the isolates formerly classified as P. ruminicola subsp. ruminicola strains produced CMCase and had DNA G+C contents between 45 and 51 mol%, and we propose that these organisms should be placed in the redefined species P. ruminicola. A small group of isolates that have lower G+C contents are assigned to another new species, Prevotella albensis. Most P. brevis and P. bryantii strains produced abundant extracellular DNase activity. Proteinase activities (as determined by [14C] casein hydrolysis) varied widely between strains, and P. brevis strains exhibited the highest mean activity. All strains produced dipeptidyl peptidase activity, but the relative activities against different peptide substrates exhibited by P. bryantii, P. albensis, and P. brevis differed systematically. The phenotypic differences among the newly defined species suggest that they may occupy distinct niches within the rumen ecosystem.
William G Wade - One of the best experts on this subject based on the ideXlab platform.
-
description of alloPrevotella rava gen nov sp nov isolated from the human oral cavity and reclassification of Prevotella tannerae moore et al 1994 as alloPrevotella tannerae gen nov comb nov
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Julia Downes, Floyd E Dewhirst, Anne C. R. Tanner, William G WadeAbstract:Five strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. Phylogenetic analysis of full-length 16S rRNA gene sequences showed that these strains represented a novel group within the family Prevotellaceae , and the most closely related species was Prevotella tannerae . P. tannerae and the novel taxon are deeply branched from the genus Prevotella , with sequence identities to the type strain of the type species of Prevotella , Prevotella melaninogenica , of 82.2 and 85.6 %, respectively. The novel genus AlloPrevotella gen. nov. is proposed to accommodate the novel species AlloPrevotella rava gen. nov., sp. nov. and the previously named Prevotella tannerae Moore et al. 1994 as AlloPrevotella tannerae gen. nov., comb. nov. The type species is AlloPrevotella tannerae. The type strain of AlloPrevotella rava is 81/4-12T ( = DSM 22548T = CCUG 58091T) and the type strain of AlloPrevotella tannerae is ATCC 51259T = CCUG 34292T = CIP 104476T = NCTC 13073T. AlloPrevotella rava is weakly to moderately saccharolytic and produces moderate amounts of acetic acid and major amounts of succinic acid as end products of fermentation. Strains are sensitive to 20 % bile and hydrolyse gelatin. The principal cellular long-chain fatty acids are anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C17 : 0 and iso-C17 : 0 3-OH. The G+C content of the DNA of the type strain is 47 mol%.
-
Prevotella marshii sp nov and Prevotella baroniae sp nov isolated from the human oral cavity
International Journal of Systematic and Evolutionary Microbiology, 2005Co-Authors: Julia Downes, Anne C. R. Tanner, William G Wade, Iain C SutcliffeAbstract:Eleven strains of anaerobic Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise two homogeneous groups, designated E2 and E4. 16S rRNA gene sequence analysis revealed that members of both groups belonged to the genus Prevotella but were distinct from any species with validly published names. This distinction was confirmed by DNA-DNA hybridization and phenotypic tests. Two novel species are therefore proposed: Prevotella marshii sp. nov. (group E2) and Prevotella baroniae (group E4). Both species are saccharolytic; the end-products of fermentation for P. marshii are acetic, propionic and succinic acids, while P. baroniae produces acetic and succinic acids with minor amounts of isovaleric and isobutyric acids. The G+C content of the DNA of the type strain of Prevotella marshii is 51 mol% and that of Prevotella baroniae is 52 mol%. The type strain for P. marshii is E9.34(T) (=DSM 16973(T)=CCUG 50419(T)) and that for P. baroniae is E9.33(T) (=DSM 16972(T)=CCUG 50418(T)).
Yoko Shimazu - One of the best experts on this subject based on the ideXlab platform.
-
persistence of host specific bacteroides Prevotella 16s rrna genetic markers in environmental waters effects of temperature and salinity
Applied Microbiology and Biotechnology, 2007Co-Authors: Satoshi Okabe, Yoko ShimazuAbstract:Host-specific Bacteroides–Prevotella 16S rRNA genetic markers are promising alternative indicators for identifying the sources of fecal pollution because of their high abundance in the feces of warm-blooded animals and high host specificity. However, little is known about the persistence of these genetic markers in environments after being released into environmental waters. The persistence of feces-derived four different host-specific Bacteroides–Prevotella 16S rRNA genetic makers (total, human-, cow-, and pig-specific) in environmental waters was therefore investigated at different incubation temperatures (4, 10, 20, and 30°C) and salinities (0, 10, 20, and 30 ppt) and then compared with the survival of conventional fecal-indicator organisms. The host-specific genetic markers were monitored by using real-time polymerase chain reaction (PCR) assays with specific primer sets. Each host-specific genetic marker showed similar responses in non-filtered river water and seawater: They persisted longer at lower temperatures and higher salinities. In addition, these markers did not increase in all conditions tested. Decay rates for indicator organisms were lower than those for host-specific genetic markers at temperature above 10°C. Furthermore, we investigated whether the PCR-detectable 16S rRNA genetic markers reflect the presence of live target cells or dead target cells in environmental waters. The result revealed that the detection of the Bacteroides–Prevotella 16S rRNA genetic markers in environmental waters mainly reflected the presence of ‘viable but non-culturable’ Bacteroides–Prevotella cells. These findings indicate that seasonal and geographical variations in persistence of these host-specific Bacteroides–Prevotella 16S rRNA genetic markers must be considered when we use them as alternative fecal indicators in environmental waters.
