-
International Journal of Systematic and... Aug 2020A strain of an obligately anaerobic, Gram-stain-negative rod-shaped bacterium is described by phenotypical, biochemical and genotypical characterization. This strain...
A strain of an obligately anaerobic, Gram-stain-negative rod-shaped bacterium is described by phenotypical, biochemical and genotypical characterization. This strain A2879 was isolated from an abscess swab of a patient sampled during routine care at hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequence) revealed the strain to belong to the genus , but to be distant from recognized species, with the closest relationship to . Unambiguous identification also proved possible by MALDI-TOF MS. The genomic DNA G+C content was 41.5 mol%. Strain A2879 was moderately saccharolytic and proteolytic. The most abundant cellular long-chain fatty acids were anteiso-C and iso-C. In view of these data, strain A2879 is considered to represent a novel species within the genus , for which the name sp. nov. is proposed. The type strain is A2879 (=DSM 108027=CCOS 1233=CCUG72808). As this strain has been isolated from a clinical sample, it is considered relevant for human medicine and health in general, and in particular for the fields of clinical microbiology and infectious diseases. This description will enable routine and research laboratories alike to easily identify the novel taxon, allowing its role in the context of human health and disease or microbiota to be further elucidated.
Topics: Abscess; Adult; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Germany; Humans; Male; Phylogeny; Prevotella; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 32735207
DOI: 10.1099/ijsem.0.004316 -
PloS One 2014Molecular techniques have uncovered vast numbers of organisms in the cystic fibrosis (CF) airways, the clinical significance of which is yet to be determined. The aim of...
BACKGROUND
Molecular techniques have uncovered vast numbers of organisms in the cystic fibrosis (CF) airways, the clinical significance of which is yet to be determined. The aim of this study was to describe and compare the microbial communities of the lower airway of clinically stable children with CF and children without CF.
METHODS
Bronchoalveolar lavage (BAL) fluid and paired oropharyngeal swabs from clinically stable children with CF (n = 13) and BAL from children without CF (n = 9) were collected. DNA was isolated, the 16S rRNA regions amplified, fragmented, biotinylated and hybridised to a 16S rRNA microarray. Patient medical and demographic information was recorded and standard microbiological culture was performed.
RESULTS
A diverse bacterial community was detected in the lower airways of children with CF and children without CF. The airway microbiome of clinically stable children with CF and children without CF were significantly different as measured by Shannon's Diversity Indices (p = 0.001; t test) and Principle coordinate analysis (p = 0.01; Adonis test). Overall the CF airway microbial community was more variable and had a less even distribution than the microbial community in the airways of children without CF. We highlighted several bacteria of interest, particularly Prevotella veroralis, CW040 and a Corynebacterium, which were of significantly differential abundance between the CF and non-CF lower airways. Both Pseudomonas aeruginosa and Streptococcus pneumoniae culture abundance were found to be associated with CF airway microbial community structure. The CF upper and lower airways were found to have a broadly similar microbial milieu.
CONCLUSION
The microbial communities in the lower airways of stable children with CF and children without CF show significant differences in overall diversity. These discrepancies indicate a disruption of the airway microflora occurring early in life in children with CF.
Topics: Bronchoalveolar Lavage Fluid; Child; Child, Preschool; Corynebacterium; Cystic Fibrosis; Female; Humans; Infant; Male; Microbiota; Prevotella; Pseudomonas aeruginosa; Respiratory Mucosa; Streptococcus pneumoniae
PubMed: 25526264
DOI: 10.1371/journal.pone.0109798 -
BMC Microbiology Jul 2013Sika deer (Cervus nippon) have different dietary preferences to other ruminants and are tolerant to tannin-rich plants. Because the rumen bacteria in domestic Sika deer...
BACKGROUND
Sika deer (Cervus nippon) have different dietary preferences to other ruminants and are tolerant to tannin-rich plants. Because the rumen bacteria in domestic Sika deer have not been comprehensively studied, it is important to investigate its rumen bacterial population in order to understand its gut health and to improve the productivity of domestic Sika deer.
RESULTS
The rumen bacterial diversity in domestic Sika deer (Cervus nippon) fed oak leaves- (OL group) and corn stalks-based diets (CS group) were elucidated using 16S rRNA gene libraries and denaturing gradient gel electrophoresis (DGGE). Overall, 239 sequences were examined from the two groups, 139 clones from the OL group were assigned to 57 operational taxonomic units (OTUs) and 100 sequences from the CS group were divided into 50 OTUs. Prevotella-like sequences belonging to the phylum Bacteroidetes were the dominant bacteria in both groups (97.2% OL and 77% CS), and sequences related to Prevotella brevis were present in both groups. However, Prevotella shahii-like, Prevotella veroralis-like, Prevotella albensis-like, and Prevotella salivae-like sequences were abundant in the OL group compared to those in the CS group, while Succinivibrio dextrinosolvens-like and Prevotella ruminicola-like sequences were prevalent in the CS group. PCR-DGGE showed that bacterial communities clustered with respect to diets and the genus Prevotella was the dominant bacteria in the rumen of domestic Sika deer. However, the distribution of genus Prevotella from two groups was apparent. In addition, other fibrolytic bacteria, such as Clostridium populeti and Eubacterium cellulosolvens were found in the rumen of domestic Sika deer.
CONCLUSIONS
The rumen of domestic Sika deer harbored unique bacteria which may represent novel species. The bacterial composition appeared to be affected by diet, and sequences related to Prevotella spp. may represent new species that may be related to the degradation of fiber biomass or tannins. Moreover, the mechanism and biological functions of Prevotella spp. in the rumen ecosystem, and synergistic interactions with other microorganisms should be noticed.
Topics: Animals; Bacteria; Biota; China; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Diet; Dietary Fiber; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Rumen; Ruminants; Sequence Analysis, DNA; Tannins
PubMed: 23834656
DOI: 10.1186/1471-2180-13-151 -
International Journal of Systematic and... Aug 2008Three strains of anaerobic, variably pigmenting, Gram-negative bacilli isolated from human oral mucosal tissue were subjected to a comprehensive range of phenotypic and...
Three strains of anaerobic, variably pigmenting, Gram-negative bacilli isolated from human oral mucosal tissue were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. 16S rRNA gene sequence analysis and DNA-DNA hybridization revealed that the strains constituted a novel group within the genus Prevotella, being most closely related to Prevotella melaninogenica and Prevotella veroralis. A novel species, Prevotella histicola sp. nov., is proposed to accommodate these strains. Prevotella histicola is saccharolytic and produces acetic acid and succinic acid as major end products of fermentation and trace to minor amounts of isovaleric acid and lactic acid. The G+C content of the DNA of the type strain is 43 mol%. The type strain of Prevotella histicola is T05-04T (=DSM 19854T=CCUG 55407T).
Topics: Acetic Acid; Bacterial Typing Techniques; Base Composition; Carcinoma, Squamous Cell; DNA, Bacterial; DNA, Ribosomal; Genes, rRNA; Genotype; Humans; Molecular Sequence Data; Mouth Mucosa; Mouth Neoplasms; Nucleic Acid Hybridization; Phenotype; Phylogeny; Prevotella; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Species Specificity; Succinic Acid
PubMed: 18676457
DOI: 10.1099/ijs.0.65656-0 -
Oral Diseases Apr 2008Compare the microbial profiles on the tongue dorsum in patients with halitosis and control subjects in a UK population using culture-independent techniques.
AIM
Compare the microbial profiles on the tongue dorsum in patients with halitosis and control subjects in a UK population using culture-independent techniques.
MATERIALS AND METHODS
Halitosis patients were screened according to our recently developed recruitment protocol. Scrapings from the tongue dorsum were obtained for 12 control subjects and 20 halitosis patients. Bacteria were identified by PCR amplification, cloning and sequencing of 16S rRNA genes.
RESULTS
The predominant species found in the control samples were Lysobacter-type species, Streptococcus salivarius, Veillonella dispar, unidentified oral bacterium, Actinomyces odontolyticus, Atopobium parvulum and Veillonella atypica. In the halitosis samples, Lysobacter-type species, S. salivarius, Prevotella melaninogenica, unidentified oral bacterium, Prevotella veroralis and Prevotella pallens were the most commonly found species. For the control samples, 13-16 (4.7-5.8%) of 276 clones represented uncultured species, whereas in the halitosis samples, this proportion increased to 6.5-9.6% (36-53 of 553 clones). In the control samples, 22 (8.0%) of 276 clones represented potentially novel phylotypes, and in the halitosis samples, this figure was 39 (7.1%) of 553 clones.
CONCLUSIONS
The microflora associated with the tongue dorsum is complex in both the control and halitosis groups, but several key species predominate in both groups.
Topics: Bacterial Typing Techniques; Biofilms; Case-Control Studies; DNA, Bacterial; Gram-Positive Asporogenous Rods; Halitosis; Humans; Liver Transplantation; Polymerase Chain Reaction; Prevotella; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Tongue
PubMed: 18336372
DOI: 10.1111/j.1601-0825.2007.01371.x -
International Journal of Systematic and... Aug 2007Two 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...
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.
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)).
Topics: Anaerobiosis; DNA, Bacterial; DNA, Ribosomal; Molecular Sequence Data; Oryza; Phylogeny; Polysaccharides; Prevotella; RNA, Ribosomal, 16S; Soil Microbiology
PubMed: 17684261
DOI: 10.1099/ijs.0.64914-0 -
International Journal of Systematic and... May 2007Six strains (CB7(T), CB18, CB23, CB26, CB28 and CB35(T)) were isolated from human faeces. Based on phylogenetic analysis, phenotypic characteristics, cellular fatty acid...
Six strains (CB7(T), CB18, CB23, CB26, CB28 and CB35(T)) were isolated from human faeces. Based on phylogenetic analysis, phenotypic characteristics, cellular fatty acid profiles and menaquinone profiles, these strains could be included within the genus Prevotella and made up two clusters. 16S rRNA gene sequence analysis indicated that five strains were most closely related to Prevotella veroralis, sharing about 92 % sequence similarity; the remaining strain was most closely related to Prevotella shahii, sharing about 90 % sequence similarity. All six strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid compositions of the six strains differed significantly from those of other Prevotella species. Five strains (CB7(T), CB18, CB23, CB26 and CB28) contained dimethyl acetals and the major menaquinones of these strains were MK-11, MK-12 and MK-13. The major menaquinones of CB35(T) were MK-12 and MK-13. Based on phenotypic and phylogenetic findings, two novel species, Prevotella copri sp. nov. and Prevotella stercorea sp. nov., are proposed, representing the two different strain clusters. The DNA G+C contents of strains CB7(T) and CB35(T) were 45.3 and 48.2 mol%, respectively. The type strains of P. copri and P. stercorea are CB7(T) (=JCM 13464(T)=DSM 18205(T)) and CB35(T) (=JCM 13469(T)=DSM 18206(T)), respectively.
Topics: Anaerobiosis; Bacterial Typing Techniques; Bacteroidaceae Infections; Base Composition; Carbohydrate Metabolism; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Enzymes; Fatty Acids; Feces; Genes, rRNA; Humans; Molecular Sequence Data; Movement; Phylogeny; Pigments, Biological; Prevotella; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; Spores, Bacterial; Vitamin K 2
PubMed: 17473237
DOI: 10.1099/ijs.0.64778-0 -
Oral Microbiology and Immunology Dec 1998Strains resembling Prevotella melaninogenica were isolated from healthy subjects and patients with periodontal disease and were identified using: a 5-test phenotypic...
Strains resembling Prevotella melaninogenica were isolated from healthy subjects and patients with periodontal disease and were identified using: a 5-test phenotypic screen; commercial identification kits; and a 16S rRNA-based polymerase chain reaction (PCR) method. Eleven clinical isolates closely resembling P. melaninogenica, and all from patients with periodontitis, were able to agglutinate erythrocytes. In the electron microscope, hemagglutinating isolates showed fimbria-like structures, that were not seen on non-hemagglutinating isolates. Some strains were further classified with PCR-restriction fragment-length polymorphism (RFLP) of 16S rRNA genes. Amplified 16S rDNA was digested using five different endonucleases, separated with agarose gel electrophoresis, stained and photographed. Photographs were then scanned, digitized and a distance matrix calculated using Dice coefficient, where the presence or absence of a band was used as a character. The distance matrix was plotted as a phenogram. At 70% similarity six clusters were seen. Type strains of separate Prevotella species did not fall into any cluster. Hemagglutinating isolates fell into three clusters: four clustered with the type strains of P. melaninogenica and Prevotella veroralis; four with other P. melaninogenica isolates and two hemagglutinating isolates clustered together Prevotella loescheii. The PCR-RFLP results showed that the hemagglutinating strains did not form a homogenous group inside the Prevotella genus.
Topics: Adult; Bacterial Typing Techniques; Fimbriae, Bacterial; Hemagglutination; Humans; Mouth; Periodontal Diseases; Polymerase Chain Reaction; Prevotella melaninogenica
PubMed: 9872112
DOI: 10.1111/j.1399-302x.1998.tb00692.x -
Oral Microbiology and Immunology Aug 1994Twenty-two tetracycline-resistant (tetr) anaerobic and facultative anaerobic bacteria isolated from periodontal pockets of 12 patients with refractory periodontitis were...
Twenty-two tetracycline-resistant (tetr) anaerobic and facultative anaerobic bacteria isolated from periodontal pockets of 12 patients with refractory periodontitis were examined for the presence of the Tet Q determinant by DNA-DNA hybridization. Dot blots of bacterial DNA were tested with an intragenic digoxigenin-labelled tet(Q) probe consisting of a 1.45 kb EcoRI/PvuII fragment from plasmid pNFD13-2. Southern blots of chromosomal DNA digested with the restriction enzyme EcoRI were also examined. The tet(Q) probe hybridized with DNA from 8 of the 22 tetr strains, including 2 Prevotella intermedia strains and one strain each of Prevotella nigrescens, Prevotella loescheii, Prevotella veroralis and Prevotella melaninogenica. The tetr strains of Mitsuokella dentalis and Capnocytophaga ochracea also hybridized with the probe. The lack of discernible plasmid DNA in all the probe-positive isolates suggests that these tetracycline-resistance genes were chromosomally encoded. The probe hybridized with a different size fragment in all the isolates. This study extends the number of species that carry the tet(Q) gene to include several outside the genera Prevotella and Bacteroides.
Topics: Anti-Bacterial Agents; Bacteria, Anaerobic; Bacteroides; Blotting, Southern; Capnocytophaga; DNA Probes; DNA, Bacterial; Genes, Bacterial; Humans; Microbial Sensitivity Tests; Nucleic Acid Hybridization; Periodontal Diseases; Plasmids; Prevotella; Prevotella intermedia; Prevotella melaninogenica; R Factors; Restriction Mapping; Sequence Analysis, DNA; Tetracycline; Tetracycline Resistance
PubMed: 7478767
DOI: 10.1111/j.1399-302x.1994.tb00067.x -
Journal of Dentistry Jun 1993The predominant microbial flora associated with adult periodontitis was investigated in 21 patients aged 20-40 years. Microorganisms from samples of subgingival plaque...
The predominant microbial flora associated with adult periodontitis was investigated in 21 patients aged 20-40 years. Microorganisms from samples of subgingival plaque were cultured on selective and non-selective media under aerobic and anaerobic conditions. Ten species or groups out of a total of 31 were found to comprise the predominant cultivable flora: diphtheroids, Porphyromonas asaccharolytica, coagulase-negative staphylococci, 'Streptococcus milleri'-group, Bacteroides ureolyticus, Capnocytophaga ochracea, the Prevotella veroralis/buccalis complex, P. intermedia, P. oralis and unidentified Prevotella spp. Two species previously reported at periodontitis sites, namely P. gingivalis and Fusobacterium nucleatum, were not isolated, whereas Prevotella species accounted for the majority of isolates in this investigation. The large proportion of non-pigmented Prevotella species, P. asaccharolytica and B. ureolyticus that were found have not generally been reported previously. The role of these microorganisms and also coagulase-negative staphylococci, diphtheroids and the 'Streptococcus milleri'-group requires further investigation in adult periodontitis.
Topics: Adult; Bacteria, Anaerobic; Colony Count, Microbial; Dental Plaque; Female; Gram-Negative Bacteria; Gram-Positive Bacteria; Humans; Male; Periodontitis
PubMed: 8315093
DOI: 10.1016/0300-5712(93)90029-p