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International Journal of Systematic and... May 2024Two rod-shaped, obligate anaerobic, Gram-stain-positive bacteria isolated from the pig faeces were designated YH-ols2216 and YH-ols2217. Analysis of 16S rRNA gene...
Two rod-shaped, obligate anaerobic, Gram-stain-positive bacteria isolated from the pig faeces were designated YH-ols2216 and YH-ols2217. Analysis of 16S rRNA gene sequences revealed that these isolates were most related to the members of the family , within the order , and KCTC 25474 with 92.0 and 92.5% similarities, respectively. The 16S rRNA gene sequence similarity within isolates was 99.9 %; and those between isolates YH-ols2216 and YH-ols2217, and DSM 20586, the type species of the type genus within the family , were 88.5 and 88.7 %, respectively. Those between isolates and PW2, the type species of the type genus within the family , were 88.7 and 89.1 %, respectively. The multi-locus sequence tree revealed that the isolates, alongside the genera and , formed a distinct cluster between the families and . The average nucleotide identities and digital DNA-DNA hybridization values for the isolates and their most closely related strains ranged from 67.7 to 76.2 % and from 18.4 to 23.3 %, respectively. The main cellular fatty acids of the isolates were C DMA, C 9, C 12OH, C, and C. The cell wall contained the peptidoglycan -diaminopimelic acid. Lactate was the main end-product of the isolates. The major polar lipids of isolate YH-ols2217 were aminophospholipid, aminolipids, and lipids. Menaquinones were not identified in the cells of the isolates. The DNA G+C contents of isolates YH-ols2216 and YH-ols2217 were 67.5 and 67.6 mol%, respectively. Considering these chemotaxonomic, phenotypic, and phylogenetic properties, fam. nov. is proposed within the order . YH-ols2216 (=KCTC 25708=NBRC 116429) and YH-ols2217 (=KCTC 25709=NBRC 116430) represent a novel taxon within this new family and the name gen. nov., sp. nov. is proposed. In addition, the genera and are transferred to the family fam. nov.
Topics: RNA, Ribosomal, 16S; Phylogeny; Fatty Acids; DNA, Bacterial; Animals; Bacterial Typing Techniques; Sequence Analysis, DNA; Base Composition; Feces; Swine; Nucleic Acid Hybridization; Actinobacteria; Peptidoglycan
PubMed: 38728210
DOI: 10.1099/ijsem.0.006382 -
International Journal of Systematic and... Sep 2014A Gram-stain-positive, obligately anaerobic, short rod, designated strain HHRM1715(T), was isolated from the blood of a patient with Fournier's gangrene, complicated by...
A Gram-stain-positive, obligately anaerobic, short rod, designated strain HHRM1715(T), was isolated from the blood of a patient with Fournier's gangrene, complicated by sepsis. On the basis of 16S rRNA gene sequence analysis, strain HHRM1715(T) was shown to belong to the genus Atopobium and was most closely related to Atopobium minutum (95 % similarity). The results of 16S rRNA-gene-based phylogenetic analysis, cellular fatty acid analysis and differential biochemical tests, showed that strain HHRM1715(T) represented a novel species of the genus Atopobium. We therefore describe Atopobium deltae sp. nov. with HHRM1715(T) ( = LMG 27987(T) = CCUG 65171(T)) as the type strain and propose an emended description of the genus Atopobium with regard to the DNA G+C content.
Topics: Actinobacteria; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Fournier Gangrene; Humans; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 24944340
DOI: 10.1099/ijs.0.065243-0 -
BMC Research Notes Mar 2012Atopobium vaginae and Gardnerella vaginalis are major markers for bacterial vaginosis. We aimed to determine the MIC and MBC range of the broad-spectrum anti-infective...
BACKGROUND
Atopobium vaginae and Gardnerella vaginalis are major markers for bacterial vaginosis. We aimed to determine the MIC and MBC range of the broad-spectrum anti-infective and antiseptic dequalinium chloride for 28 strains, belonging to 4 species of the genus Atopobium, i.e. A. vaginae, A. minutum, A. rimae and A. parvulum.
METHODS
The MIC was determined with a broth microdilution assay.
RESULTS
The MIC and MBC for Atopobium spp. for dequalinium chloride ranged between < 0.0625 and 2 μg/ml.
CONCLUSIONS
This study demonstrated that dequalinium chloride inhibits and kills clinical isolates of A. vaginae at concentrations similar to those of clindamycin and lower than those of metronidazole.
Topics: Actinobacteria; Anti-Bacterial Agents; Bacteroides fragilis; Clindamycin; Culture Media; Dequalinium; Female; Humans; Metronidazole; Microbial Sensitivity Tests; Vagina; Vaginosis, Bacterial
PubMed: 22429611
DOI: 10.1186/1756-0500-5-151 -
Journal of Clinical Microbiology Sep 2011Acquired vancomycin resistance in Gram-positive anaerobes has been reported only in Australia and Canada from rare vanB-positive stool samples in the absence of...
Acquired vancomycin resistance in Gram-positive anaerobes has been reported only in Australia and Canada from rare vanB-positive stool samples in the absence of vancomycin-resistant enterococci (VRE). We report the emergence of VanB-type resistance in Clostridium clostridioforme and Atopobium minutum involved in human infections in France.
Topics: Actinobacteria; Clostridium; DNA, Bacterial; France; Genes, Bacterial; Gram-Positive Bacterial Infections; Humans; Male; Middle Aged; Molecular Sequence Data; Sequence Analysis, DNA; Vancomycin Resistance
PubMed: 21775552
DOI: 10.1128/JCM.00308-11 -
International Journal of Systematic and... Apr 2011Strain 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...
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, lac15, lac16 and lac31(T) formed a genetically coherent group (100 % interstrain sequence similarity) within the bigeneric Olsenella-Atopobium branch of the family Coriobacteriaceae, class Actinobacteria. This group was most closely related to the type strains of the two recognized Olsenella species, namely Olsenella uli (sequence similarity of 96.85 %) and Olsenella profusa (sequence similarity of 97.20 %). The sequence similarity to the type strain of Atopobium minutum, the type species of the genus Atopobium, was 92.33 %. Unlike those of O. uli and O. profusa, outgrown colonies of strains A2, lac15, lac16 and lac31(T) were opaque and greyish-white with an umbonate elevation on solid culture media. The four novel strains were characterized as being well-adapted and presumably indigenous to the gastrointestinal tract of homoeothermic vertebrates: they were mesophilic, microaerotolerant, neutrophilic and acidotolerant, bile-resistant, mucin-utilizing and markedly peptidolytic lactic acid bacteria. The results of DNA-DNA hybridizations, cellular fatty acid analysis and other differential phenotypic (physiological and biochemical) tests confirmed that strains A2, lac15, lac16 and lac31(T) represent a novel species of the genus Olsenella. On the basis of the genotypic and phenotypic results, we therefore describe Olsenella umbonata sp. nov., with lac31(T) ( = CCUG 58604(T) = DSM 22620(T) = JCM 16156(T)) as the type strain and A2 ( = CCUG 58212 = DSM 22619 = JCM 16157) as an additionally available reference strain. Also, based on our data, we propose emended descriptions of the genus Olsenella and the species Olsenella uli and Olsenella profusa.
Topics: Actinobacteria; Anaerobiosis; Animals; Bacterial Typing Techniques; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Jejunum; Lactic Acid; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Rumen; Sequence Analysis, DNA; Sheep; Swine
PubMed: 20435744
DOI: 10.1099/ijs.0.022954-0 -
International Journal of Food... Feb 2010The induction of apoptosis in mammalian cells by bacteria is well reported. This process may assist infection by pathogens whereas for non-pathogens apoptosis induction...
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 cancer cell line, Caco-2. The results show a major apoptotic effect for the pathogens, mild effects for the probiotic strains and A. minutum, but no effect for commensal E. coli. The mild apoptotic effects observed are consistent with the beneficial roles of probotics in protection against colon cancer and suggest, for the first time, that A. minutum possesses similar advantageous, anti-cancerous activity. Although bacterial infection increased Caco-2 membrane FAS levels, caspase-8 was not activated indicating that apoptosis is FAS independent. Instead, in all cases, apoptosis was induced through the mitochondrial pathway as indicated by BAX translocation, cytochrome c release, and caspase-9 and -3 cleavage. This suggests that an intracellular stimulus initiates the observed apoptosis responses.
Topics: Apoptosis; Bacteria; Caco-2 Cells; Caspase 3; Caspase 8; Caspase 9; Cell Membrane; Cytochromes c; Humans; bcl-2-Associated X Protein; fas Receptor
PubMed: 20036023
DOI: 10.1016/j.ijfoodmicro.2009.11.015 -
Journal of Clinical Microbiology Feb 2007Four 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...
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 and sepsis (strain CA2). While the first three patients survived, the last patient died 2 weeks after the episode of bacteremia. All four isolates are strictly anaerobic, nonsporulating, gram-positive coccobacilli that were unidentified by conventional phenotypic tests and commercial identification systems. They grow on sheep blood agar as nonhemolytic pinpoint colonies after 48 h of incubation at 37 degrees C in an anaerobic environment. All are catalase positive and motile, with flagella. They produce acid from arabinose, glucose, mannose, and xylose. They do not produce indole or reduce nitrate. They are sensitive to penicillin, vancomycin, and metronidazole but resistant to cefotaxime. 16S rRNA gene sequence analysis showed 16.0%, 16.8%, and 21.0% base differences from Clostridium propionicum, Clostridium neopropionicum, and Atopobium minutum, respectively. The G+C content of strain HKU16T is 40.2% +/- 2.2%. Based on their phylogenetic affiliation, unique G+C content, and phenotypic characteristics, we propose a new genus and species, Catabacter hongkongensis gen. nov., sp. nov., to describe the bacterium, for which HKU16 is the type strain, and suggest that it be assigned to a new family, Catabacteriaceae. The gastrointestinal tract was probably the source of the bacterium for at least three of the four patients. The isolation of a catalase-positive, motile, nonsporulating, anaerobic gram-positive bacillus in clinical laboratories should raise the possibility of C. hongkongensis. Further studies should be performed to ascertain the epidemiology and other disease associations of this bacterium.
Topics: Adult; Aged; Anaerobiosis; Bacteremia; Bacterial Typing Techniques; Base Composition; Blood; Canada; Culture Media; Female; Gram-Positive Bacteria; Gram-Positive Bacterial Infections; Hong Kong; Humans; Male; Middle Aged; Molecular Sequence Data; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 17122022
DOI: 10.1128/JCM.01831-06 -
Applied and Environmental Microbiology Oct 2002Excessive 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...
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) depending on the substrate, its concentration, and the method used. Monensin (5 micro M) inhibited NH(3) production from proteins, peptides, and amino acids by an average of 28% with substrate at 2 mg/ml, compared to 48% with substrate at 20 mg/ml (P = 0.011). Of the total bacterial population, 1.4% grew on Trypticase alone, of which 93% was eliminated by 5 micro M monensin. Many fewer bacteria (0.002% of the total) grew on amino acids alone. Nineteen isolates capable of growth on Trypticase were obtained from four sheep. 16S ribosomal DNA and traditional identification methods indicated the bacteria fell into six groups. All were sensitive to monensin, and all except one group (group III, similar to Atopobium minutum), produced NH(3) at >250 nmol min(-1) mg of protein(-1), depending on the medium, as determined by a batch culture method. All isolates had exopeptidase activity, but only group III had an apparent dipeptidyl peptidase I activity. Groups I, II, and IV were most closely related to asaccharolytic ruminal and oral Clostridium and Eubacterium spp. Group V comprised one isolate, similar to Desulfomonas piger (formerly Desulfovibrio pigra). Group VI was 95% similar to Acidaminococcus fermentans. Growth of the Atopobium- and Desulfomonas-like isolates was enhanced by sugars, while growth of groups I, II, and V was significantly depressed by sugars. This study therefore demonstrates that different methodologies and different substrate concentrations provide an explanation for different apparent rates of ruminal NH(3) production reported in different studies and identifies a diverse range of hyper-ammonia-producing bacteria in the rumen of sheep.
Topics: Animals; Bacteria; Fermentation; In Vitro Techniques; Monensin; Peptides; RNA, Ribosomal, 16S; Rumen; Sheep
PubMed: 12324340
DOI: 10.1128/AEM.68.10.4925-4931.2002 -
Clinical Infectious Diseases : An... Sep 1997A new method of identifying bacteria, phylogenetic 16S rRNA sequencing, has led to major reorganizations among most genera of anaerobic bacteria. The pigmented... (Review)
Review
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 includes 11 pigmented species and one nonpigmented species, P. catoniae; P. levii-like and P. endodontalis-like organisms are candidates for the genus. Fusobacterium nucleatum currently has five subspecies, and F. varium includes the former F. pseudonecrophorum. Former Wolinella recta and Wolinella curva now are Campylobacter rectus and Campylobacter curvus; Campylobacter showae is a new species. Isolates included in the bile-sensitive former Bacteroides gracilis now are Campylobacter gracilis; the bile-resistant B. gracilis isolates were transferred to a new genus, Sutterella, as S. wadsworthensis. The new Actinomyces species include two subspecies of the A. neuii and the A. radingae-A. turicensis complex. The genus Eubacterium sensu stricto is represented by E. limosum, and the former E. alactolyticum was reclassified in a new genus, Pseudoramibacter, as P. alactolyticus. Recent entries include E. saphenum, E. minutum, E. exiguum, E. infirmum, and E. tardum. A new genus, Atopobium houses some former lactobacilli and streptococci. The genus Peptostreptococcus also have four new species; P. hydrogenalis, P. lacrimalis, P. lactolyticus, and P. vaginalis.
Topics: Bacteria, Anaerobic; Gram-Negative Anaerobic Bacteria; Gram-Positive Bacteria; Humans
PubMed: 9310640
DOI: 10.1086/516227