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1.Study on high throughput sequencing identification of Fructus Arctii and five counterfeit species mix power.

Yan-Ping XING ; Si-You CHEN ; Liang XU ; Yong-Man LIANG ; Jia-Hao WANG ; Bing WANG ; Tao LIU ; Ting-Guo KANG

China Journal of Chinese Materia Medica 2018;43(19):3862-3866

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

2.First Case Report of Bacteremia Due to Catabacter hongkongensis in a Korean Patient.

Yong Jun CHOI ; Eun Jeong WON ; Soo Hyun KIM ; Myung Geun SHIN ; Jong Hee SHIN ; Soon Pal SUH

Annals of Laboratory Medicine 2017;37(1):84-87

3.Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis.

Ki Ho HONG ; Sung Kuk HONG ; Sung Im CHO ; Eunkyung RA ; Kyung Hee HAN ; Soon Beom KANG ; Eui Chong KIM ; Sung Sup PARK ; Moon Woo SEONG

Annals of Laboratory Medicine 2016;36(5):441-449

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

1.Study on high throughput sequencing identification of Fructus Arctii and five counterfeit species mix power.

2.First Case Report of Bacteremia Due to Catabacter hongkongensis in a Korean Patient.

3.Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis.

4.Fusobacterium Isolates Recovered From Colonic Biopsies of Inflammatory Bowel Disease Patients in Korea.

5.Identification of Pasteurella canis in a Soft Tissue Infection Caused by a Dog Bite: The First Report in Korea.

6.Flavobacterium ceti From Blood Samples of a Korean Patient With Alcoholic Liver Cirrhosis.

7.First Case of Pulmonary Mycobacterium parascrofulaceum Infection in a Patient With Bronchiectasis in Korea.

8.Ancient Mitochondrial DNA Analyses of Ascaris Eggs Discovered in Coprolites from Joseon Tomb.

9.The First Case of Concurrent Infective Endocarditis and Spondylitis Caused by Streptococcus tigurinus.

10.Combined hearing and deafness gene mutation screening of 11,046 Chinese newborns.

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