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International Journal of Systematic and... Mar 2010We isolated several strains from various clinical samples (five samples of blood, four of intra-abdominal pus and one of infected soft tissue) that were anaerobic,...
Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.
We isolated several strains from various clinical samples (five samples of blood, four of intra-abdominal pus and one of infected soft tissue) that were anaerobic, motile or non-motile and Gram-positive rods. Some of the strains formed spores. Phylogenetic analysis of the 16S rRNA gene sequence showed that these organisms could be placed within clostridial cluster IV as defined by Collins et al. [(1994). Int J Syst Bacteriol 44, 812-826] and shared more than 99 % sequence similarity with Clostridium orbiscindens DSM 6740(T) and Eubacterium plautii DSM 4000(T). Together, they formed a distinct cluster, with Bacteroides capillosus ATCC 29799(T) branching off from this line of descent with sequence similarities of 97.1-97.4 %. The next nearest neighbours of these organisms were Clostridium viride, Oscillibacter valericigenes, Papillibacter cinnamivorans and Sporobacter termitidis, with sequence similarities to the respective type strains of 93.1-93.4, 91.2-91.4, 89.8-90 and 88.7-89.3 %. On the basis of biochemical properties, phylogenetic position, DNA G+C content and DNA-DNA hybridization, it is proposed to unify Clostridium orbiscindens and Eubacterium plautii in a new genus as Flavonifractor plautii gen. nov., comb. nov., with the type strain Prévot S1(T) (=ATCC 29863(T) =VPI 0310(T) =DSM 4000(T)), and to reassign Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov., with the type strain CCUG 15402A(T) (=ATCC 29799(T) =VPI R2-29-1(T)).
Topics: Bacterial Infections; Bacterial Typing Techniques; Bacteroides; Base Composition; Clostridium; DNA, Bacterial; DNA, Ribosomal; Eubacterium; Humans; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S
PubMed: 19654357
DOI: 10.1099/ijs.0.016725-0 -
Phytomedicine : International Journal... Oct 2020Cyclocarya paliurus polysaccharide (CCPP), a primary active component in the leaves of Cyclocarya paliurus (Batal.) Iljinsk (C. paliurus), has the ability to treat type...
BACKGROUND
Cyclocarya paliurus polysaccharide (CCPP), a primary active component in the leaves of Cyclocarya paliurus (Batal.) Iljinsk (C. paliurus), has the ability to treat type 2 diabetes mellitus (T2DM), but cannot be digested by our digestive system. Therefore, mechanisms of regulating the gut microbiota and intestinal metabolites might exist.
PURPOSE
To reveal the potential mechanism of CCPP treatment, this study aimed to investigate the alterations of the gut microbiota and intestinal metabolites especially short chain fatty acids (SCFAs) in type 2 diabetic rats.
STUDY DESIGN AND METHODS
Type 2 diabetic rat models were developed, and the therapeutic effects of CCPP were evaluated. Metagenomics analysis was utilized to analyze the alterations to the gut microbiota, and UHPLC-QTOF/MS-based untargeted metabolomics analysis of colon contents was used to identify the differential intestinal metabolites. GC/MS was used to measure the SCFAs in rat's colon contents and human fecal inoculums. Furthermore, the expression of SCFA receptors including GPR41, GPR43 and GPR109a was verified by qRT-PCR and the concentration of glucagon-like peptide-1(GLP-1) and peptide tyrosinetyrosine (PYY) was measured by Elisa.
RESULTS
Inhibition of the blood glucose levels and improvements in glucose tolerance and serum lipid parameters were observed after CCPP treatment. Eleven SCFA-producing species including Ruminococcus_bromii, Anaerotruncus_colihominis, Clostridium_methylpentosum, Roseburia_intestinalis, Roseburia_hominis, Clostridium_asparagiforme, Pseudoflavonifractor_capillosus, Intestinimonas_butyriciproducens, Intestinimonas_sp._GD2, Oscillibacter_valericigenes and Oscillibacter_ruminantium were clearly increased in the CCPP group. Furthermore, our study indicated that CCPP increases the production of SCFAs both in vivo and in vitro, and the gut microbiota are the key factor of this process. The SCFA receptors including GPR41, GPR43 and GPR109a, were significantly stimulated in the CCPP treated rats, which was accompanied by the upregulated expression of GLP-1 and PYY.
CONCLUSION
These results demonstrated that CCPP could alleviate type 2 diabetic symptoms by increasing the SCFA-producing bacteria, promoting the production of SCFAs and upregulating SCFA-GLP1/PYY associated sensory mediators.
Topics: Adult; Animals; Diabetes Mellitus, Experimental; Diabetes Mellitus, Type 2; Fatty Acids, Volatile; Feces; Female; Gastrointestinal Microbiome; Glucagon-Like Peptide 1; Humans; Hypoglycemic Agents; Juglandaceae; Male; Metabolomics; Metagenome; Plant Leaves; Plants, Medicinal; Polysaccharides; Rats, Sprague-Dawley
PubMed: 32663709
DOI: 10.1016/j.phymed.2020.153268 -
International Journal of Systematic and... Dec 2013A Gram-positive, spore-forming, non-motile, strictly anaerobic rod-shaped bacterium was isolated from the caecal content of a TNF(deltaARE) mouse. The isolate, referred...
A Gram-positive, spore-forming, non-motile, strictly anaerobic rod-shaped bacterium was isolated from the caecal content of a TNF(deltaARE) mouse. The isolate, referred to as strain SRB-521-5-I(T), was originally cultured on a reduced agar medium containing yeast extract, rumen fluid and lactic acid as main energy and carbon sources. Phylogenetic analysis of partial 16S rRNA genes revealed that the species most closely related to strain SRB-521-5-I(T) were Flavonifractor plautii and Pseudoflavonifractor capillosus (<95 % sequence similarity; 1436 bp). In contrast to F. plautii and P. capillosus, strain SRB-521-5-I(T) contained a substantial amount of C18 : 0 dimethylacetal. Additional major fatty acids were C14 : 0 methyl ester, C16 : 0 dimethylacetal and C18 : 0 aldehyde. Strain SRB-521-5-I(T) differed in its enzyme profile from F. plautii and P. capillosus by being positive for dextrin, maltotriose, turanose, dl-lactic acid and d-lactic acid methyl ester but negative for d-fructose. In reduced Wilkins-Chalgren-Anaerobe broth, strain SRB-521-5-I(T) produced approximately 8 mM butyrate and 4 mM acetate. In contrast to F. plautii, the strain did not metabolize flavonoids. It showed intermediate resistance towards the antibiotics ciprofloxacin, colistin and tetracycline. Based on genotypic and phenotypic characteristics, we propose the name Intestinimonas butyriciproducens gen. nov., sp. nov. to accommodate strain SRB-521-5-I(T) ( = DSM 26588(T) = CCUG 63529(T)) as the type strain.
Topics: Animals; Bacteria, Anaerobic; Bacterial Typing Techniques; Base Composition; Butyrates; DNA, Bacterial; Female; Gram-Positive Endospore-Forming Rods; Intestines; Mice; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 23918795
DOI: 10.1099/ijs.0.051441-0 -
International Journal of Systematic and... Jun 2018An obligately anaerobic, Gram-positive, non-spore-forming, straight rod-shaped bacterium, designated strain 3BBH22, was isolated from a faecal sample of a healthy...
An obligately anaerobic, Gram-positive, non-spore-forming, straight rod-shaped bacterium, designated strain 3BBH22, was isolated from a faecal sample of a healthy Japanese woman. The 16S rRNA gene sequence analysis showed that strain 3BBH22 formed a monophyletic cluster with species in the genera Pseudoflavonifractor and Flavonifractor within the family Ruminococcaceae and had highest similarity to Pseudoflavonifractor capillosus ATCC 29799 (96.7 % sequence similarity), followed by Flavonifractor plautii ATCC 29863 (96.4 %). Acetate and butyrate were produced by strain 3BBH22 as metabolic end-products. The major cellular fatty acids were C14 : 0, C16 : 0, C18 : 1ω9c, C16 : 0 dimethyl acetal, C18 : 0 and C18 : 2ω6,9c. No respiratory quinones were detected. In contrast to F. plautii JCM 32125, strain 3BBH22 did not degrade quercetin, one of the flavonoids. P. capillosus JCM 32126 also did not. Strain 3BBH22 was differentiated from P. capillosus JCM 32126 by its inability to hydrolyse aesculin. The G+C content of the genomic DNA was 61.2±1.0 mol%. On the basis of these data and the phylogenetic tree based on 89 proteins, strain 3BBH22 represents a novel species in a novel genus of the family Ruminococcaceae, for which the name Lawsonibacter asaccharolyticus gen. nov., sp. nov. is proposed. The type strain of L. asaccharolyticus is 3BBH22 (=JCM 32166=DSM 106493).
Topics: Adult; Bacterial Typing Techniques; Base Composition; Butyrates; Clostridiales; DNA, Bacterial; Fatty Acids; Feces; Female; Humans; Japan; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 29745868
DOI: 10.1099/ijsem.0.002800 -
Microbial Drug Resistance (Larchmont,... Oct 2014Multidrug resistance in Bacteroides spp. and related genera is uncommon and has not been described in Latin America until now. We studied phenotypically and...
Multidrug resistance in Bacteroides spp. and related genera is uncommon and has not been described in Latin America until now. We studied phenotypically and genotypically the multidrug resistance of 10 clinical strains of Bacteroides, two of Parabacteroides distasonis, and one of Pseudoflavonifractor capillosus recovered in a national hospital between 2006 and 2010. To this end, we determined minimum inhibitory concentrations (MICs) of amoxicillin, amoxicillin-clavulanic acid, cefotaxime, imipenem, clindamycin, ciprofloxacin, tetracycline, and metronidazole using E-tests, evaluated the isolates for β-lactamases with nitrocefin hydrolysis tests, performed a polymerase chain reaction (PCR)-based screening of erm, tet, and nim genes, obtained partial gyrA sequences, and studied the effect of tazobactam and efflux pump inhibitors (EPI) on the MIC of cefotaxime, clindamycin, and ciprofloxacin. Three isolates were resistant to four different classes of antibiotics and 10 were resistant to three. β-lactam resistance was in most cases due to β-lactamases susceptible of partial inhibition by tazobactam. Ten isolates were cfxA-positive and two isolates had cepA. Twelve isolates were highly resistant to clindamycin and nine were highly resistant to ciprofloxacin. However, these phenotypes were not linked to ermA, ermB, ermF, and ermG or mutations in gyrA. Addition of EPI lowered the MICs of clindamycin and ciprofloxacin of one and four isolates, respectively. Twelve isolates had tetQ and four were positive for tetM. In both cases, genes of the two-component system RteAB accompanied tet genes. Although metronidazole susceptibility was universal, nim genes were not present. To our knowledge, this is the first report of multidrug resistance due to less commonly identified or alternative mechanisms in strains of Bacteroides and related species from a developing country.
Topics: Anti-Bacterial Agents; Bacteroides; Bacteroides Infections; Clindamycin; Clostridium; Clostridium Infections; Costa Rica; Drug Resistance, Multiple, Bacterial; Genes, Bacterial; Genotype; Humans; Metronidazole; Mutation; Phenotype; beta-Lactamases; beta-Lactams
PubMed: 24606061
DOI: 10.1089/mdr.2013.0180 -
Alimentary Pharmacology & Therapeutics May 2016Proton pump inhibitor (PPI) use is associated with an increased risk of Clostridium difficile infection (CDI), though the mechanism is unclear. PPI induced alterations...
BACKGROUND
Proton pump inhibitor (PPI) use is associated with an increased risk of Clostridium difficile infection (CDI), though the mechanism is unclear. PPI induced alterations to the gut microbiome may facilitate the emergence of CDI, though the effects of PPIs on gut microbiota are not well characterised. [Correction added on 10 March 2016, after first online publication: microflora has been changed to microbiota throughout the article.]
AIM
To compare the faecal microbiomes of long-term PPI users to those with no history of PPI use.
METHODS
We used a population-based database to identify individuals with ≥5 years of continuous PPI use along with non-PPI using controls. Stool samples were subjected to microbiological analysis, with hierarchical clustering at genus level, along with alpha and beta diversity measures comparing the two groups. Metadata was accounted for using quantile regression to eliminate potential confounding variables in taxonomic abundance comparisons.
RESULTS
Sixty-one subjects (32 PPI, 29 controls) were analysed. While no significant differences in alpha diversity were found between the PPI users and controls, a moderate shift of the PPI users away from the non-PPI user cluster in the beta diversity was observed. After controlling for pertinent confounders, we discovered a decrease in Bacteroidetes and an increase in Firmicutes at the phylum level. We also performed species classifications and found Holdemania filiformis and Pseudoflavonifractor capillosus to be increased and decreased in the PPI cohort, respectively.
CONCLUSIONS
Long-term PPIs use has an effect on the gut microbiome. The alteration in the ratio of Firmicutes to Bacteroidetes may pre-dispose to the development of CDI.
Topics: Aged; Bacteroidetes; Clostridium Infections; Feces; Female; Firmicutes; Gastrointestinal Microbiome; Humans; Male; Middle Aged; Proton Pump Inhibitors; Risk Factors
PubMed: 26923470
DOI: 10.1111/apt.13568