Fructus Arctii is a traditional Chinese medicine. The main counterfeit species are the seeds of Arctium tomentosum, Onopordum acanthium, Silybum marianum, Saussurea costus, Amorpha fruticosa. Traditional identification methods or molecular barcoding techniques can identify Fructus Arctii and its counterfeit species. However, the identification of the mixture of it and its spurious species is rarely reported. In this paper, we sequenced the ITS2 sequences of Fructus Arctii and 5 kinds of spurious species mix powder by high-throughput sequencing to identify the mixed powder species and providing new ideas for the identification of Fructus Arctii mix powder. The total DNA in mixed powder was extracted, and the ITS2 sequences in total DNA was amplified. Paired-end sequencing was performed on the DNA fragment of the community using the Illumina MiSeq platform. The sequence was analyzed by the software FLASH, QIIME and GraPhlAn etc. The results showed that the high quality ITS2 sequences of 39910 mix samples were obtained from the mixed samples, of which the total ITS2 sequence of the samples genus was 34 935. Phylogenetic analysis showed that the samples contained Fructus Arctii, A. tomentosum, O. acanthium, S. marianum, S. costus and A. fruticosa. Using ITS2 sequences as DNA barcodes, high-throughput sequencing technology can be used to detect the Fructus Arctii and its spurious specie in mixed powder, which can provide reference for the quality control, safe use of medicinal materials of Fructus Arctii and the identification of mixed powder of traditional Chinese medicine.
Arctium ; chemistry ; classification ; DNA Barcoding, Taxonomic ; DNA, Plant ; genetics ; DNA, Ribosomal Spacer ; genetics ; Drug Contamination ; Drugs, Chinese Herbal ; standards ; Fabaceae ; Fruit ; High-Throughput Nucleotide Sequencing ; Milk Thistle ; Onopordum ; Phylogeny ; Saussurea

No abstract available.
Aged ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Cefotaxime/analogs & derivatives/therapeutic use ; Cholangiopancreatography, Endoscopic Retrograde ; Gallstones/surgery ; Gram-Negative Anaerobic Bacteria/drug effects/genetics/*isolation & purification ; Gram-Negative Bacterial Infections/*diagnosis/drug therapy/microbiology ; Humans ; Male ; Metronidazole/therapeutic use ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; Tomography, X-Ray Computed

No abstract available.
Animals ; Anti-Bacterial Agents/pharmacology ; Bites and Stings ; Disk Diffusion Antimicrobial Tests ; Dogs ; Female ; Humans ; Middle Aged ; Pasteurella/drug effects/genetics/*isolation & purification ; Pasteurella Infections/*diagnosis/microbiology ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Republic of Korea ; Sequence Analysis, DNA ; Soft Tissue Infections/*diagnosis/microbiology

BACKGROUND: Next-generation sequencing (NGS) can detect many more microorganisms of a microbiome than traditional methods. This study aimed to analyze the vaginal microbiomes of Korean women by using NGS that included bacteria and other microorganisms. The NGS results were compared with the results of other assays, and NGS was evaluated for its feasibility for predicting vaginitis. METHODS: In total, 89 vaginal swab specimens were collected. Microscopic examinations of Gram staining and microbiological cultures were conducted on 67 specimens. NGS was performed with GS junior system on all of the vaginal specimens for the 16S rRNA, internal transcribed spacer (ITS), and Tvk genes to detect bacteria, fungi, and Trichomonas vaginalis. In addition, DNA probe assays of the Candida spp., Gardnerella vaginalis, and Trichomonas vaginalis were performed. Various predictors of diversity that were obtained from the NGS data were analyzed to predict vaginitis. RESULTS: ITS sequences were obtained in most of the specimens (56.2%). The compositions of the intermediate and vaginitis Nugent score groups were similar to each other but differed from the composition of the normal score group. The fraction of the Lactobacillus spp. showed the highest area under the curve value (0.8559) in ROC curve analysis. The NGS and DNA probe assay results showed good agreement (range, 86.2-89.7%). CONCLUSIONS: Fungi as well as bacteria should be considered for the investigation of vaginal microbiome. The intermediate and vaginitis Nugent score groups were indistinguishable in NGS. NGS is a promising diagnostic tool of the vaginal microbiome and vaginitis, although some problems need to be resolved.
Area Under Curve ; Bacteria/*genetics/isolation & purification ; Bacterial Proteins/genetics ; Candida/*genetics/isolation & purification ; Female ; Fungal Proteins/genetics ; Gardnerella vaginalis/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; ROC Curve ; Sequence Analysis, DNA ; Trichomonas vaginalis/genetics/isolation & purification ; Vagina/*microbiology ; Vaginitis/*diagnosis/microbiology

No abstract available.
Adult ; Aged ; Biopsy ; Colon/*microbiology/pathology ; Fusobacterium/genetics/*isolation & purification ; Humans ; Inflammatory Bowel Diseases/microbiology/*pathology ; Male ; Middle Aged ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Republic of Korea ; Sequence Analysis, DNA ; Young Adult

No abstract available.
Aged ; Asian Continental Ancestry Group ; Enterobacteriaceae/classification/*genetics/isolation & purification ; Humans ; Male ; Phylogeny ; Pneumonia/*diagnosis/microbiology ; Pulmonary Disease, Chronic Obstructive/*diagnosis ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Republic of Korea ; Sequence Analysis, DNA

Coagulase-negative staphylococci (CoNS) are reported to be the leading cause of nosocomial bloodstream infections. Staphylococcus pettenkoferi is a novel member of CoNS that was first isolated from the human blood and bursitis wound in 2002. We have reported cases of 6 S. pettenkoferi strains isolated from blood specimens, including one pathogen and 5 contaminants and catheter colonizers. Brucker Biotyper (Brucker Daltonics, Bremen, Germany) and molecular typing with 16S rRNA gene sequencing confirmed the 6 isolates as S. pettenkoferi. The conventional phenotypic identification of these isolates is not reliable owing to their inconsistent biochemical characteristics. Five of the 6 isolates were found to be resistant to oxacillin, and all isolates showed susceptibility to vancomycin and linezolid. For accurate identification of this novel species, advanced methods by using Brucker Biotyper or molecular methods such as 16S rRNA gene sequencing are required.
Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology/therapeutic use ; DNA, Bacterial/chemistry/metabolism ; Drug Resistance, Bacterial/drug effects ; Female ; Humans ; Linezolid/pharmacology ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Oxacillin/pharmacology ; Phenotype ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; Staphylococcal Infections/drug therapy/*microbiology/pathology ; Staphylococcus/drug effects/*genetics/isolation & purification ; Vancomycin/pharmacology

No abstract available.
Acupuncture Therapy ; Aged ; DNA/chemistry/genetics/metabolism ; Echocardiography ; Endocarditis/*diagnosis/microbiology ; Humans ; Magnetic Resonance Imaging ; Male ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; Spondylitis/*diagnosis/microbiology ; Streptococcus/*genetics/isolation & purification

Astragalus membranaceus var. mongholicus and Hedysarum polybotrys belong to different genera, but have similar drug efficacy in traditional Chinese medicine theory, and H. polybotrys was used as the legal A. membranaceus var. mongholicus previously. In this study, similarities and differences between them were analyzed via their ITS/ITS2 fragments information. The ITS (internal transcribed spacer) regions were amplified using polymerase chain reaction and then sequenced in two-way. The alignment lengths of ITS regions were 616 bp, in which 508 loci were consistent, and 103 loci were different, accounting for 82.47% and 16.72% of the total ITS nucleotides in length, respectively. As genotype determines phenotype, 1HNMR-based metabolomic approach was further used to reveal the chemical similarities and differences between them. Thirty-four metabolites were identified in the 1H NMR spectra, and twenty-seven metabolites were the common components. Amino acids, carbohydrates and other primary metabolites were similar, while a large difference existed in the flavonoids and astragalosides. This study suggests that A. membranaceus var. mongholicus and H. polybotrys show similarities and differences from molecular and chemical perspectives, which has laid a foundation for elucidating the effective material basis of drug with similar efficacy and resources utilization.
Astragalus membranaceus ; chemistry ; genetics ; DNA, Plant ; genetics ; DNA, Ribosomal Spacer ; genetics ; Drugs, Chinese Herbal ; chemistry ; Fabaceae ; chemistry ; genetics ; Flavonoids ; chemistry ; Metabolome ; Metabolomics

OBJECTIVETo evaluate the efficacy of combined newborn hearing screening and deafness-related mutation screening.

METHODSEleven thousand and forty-six newborn babies were screened with otoacoustic emission, automatic auditory brainstem response and genetic testing using a standard protocol. Common mutations of three deafness-related genes have included GJB2 (c.235delC, c.299-300delAT), mtDNA 12srRNA (c.1494C>T, c.1555A>G) and SLC26A4 (c.2168A>G, c.IVS7-2A>G).

RESULTSThe detection rate for hearing loss in the first-step screening was 0.81% (90/11,046). 513 individuals were found to carry one or two mutant alleles, which gave a carrier rate of 4.64% (513/11,046). Five hundred and eighty-four newborns were positive for hearing screening and genetic screening. Among these, 19 have failed both tests, 71 have failed hearing screening, and 494 have failed genetic screening. The combined hearing and genetic screening has given a positive rate of 5.29%.

CONCLUSIONNeither hearing screening nor genetic screening is sufficient to identify individuals susceptible to auditory disorders. Combined used of these methods can improve the rate of detection.

Asian Continental Ancestry Group ; genetics ; China ; Connexin 26 ; Connexins ; genetics ; DNA Mutational Analysis ; DNA, Mitochondrial ; chemistry ; genetics ; Deafness ; diagnosis ; ethnology ; genetics ; Gene Frequency ; Genetic Predisposition to Disease ; ethnology ; genetics ; Genetic Testing ; methods ; Genotype ; Hearing ; genetics ; Hearing Tests ; Humans ; Infant, Newborn ; Membrane Transport Proteins ; genetics ; Mutation ; Neonatal Screening ; methods ; Polymerase Chain Reaction ; RNA, Ribosomal ; genetics ; Reproducibility of Results ; Sensitivity and Specificity