bar-coded 16s rrna gene amplicons  (Pyrosequencing Inc)

Journal: PLoS ONE

Article Title: Evolution of Bacterial Consortia in Spontaneously Started Rye Sourdoughs during Two Months of Daily Propagation

doi: 10.1371/journal.pone.0095449

Figure Lengend Snippet: Three sourdoughs were fermented at 20°C (20-I, 20-II, 20-III) and three sourdoughs fermented at 30°C (30-I, 30-II, 30-III). Sourdoughs were sampled at days 1, 3, 5, 7, 21, 56. The relative abundance at the species level based on partial 16S rRNA gene sequences is given. Species forming less than 5% of the population were grouped together and are shown as ‘Others (<5%)’. (a) and (b) stand for two different sequencing runs.

Article Snippet: Pyrosequencing of bar-coded 16S rRNA gene amplicons was applied to overcome limitation of DGGE analysis and study in-depth the establishment of microbial consortia in spontaneously started rye sourdoughs.

Techniques: Sequencing

Journal: PLoS ONE

Article Title: Evolution of Bacterial Consortia in Spontaneously Started Rye Sourdoughs during Two Months of Daily Propagation

doi: 10.1371/journal.pone.0095449

Figure Lengend Snippet: Ratio of species in the sourdoughs fermented at 20°C (20-I, 20-II, 20-III) or 30°C (30-I, 30-II, 30-III) after 56 backslopping cycles determined by plating on MRS and SDB media or by pyrosequencing of 16S rRNA gene amplicons.

Article Snippet: Pyrosequencing of bar-coded 16S rRNA gene amplicons was applied to overcome limitation of DGGE analysis and study in-depth the establishment of microbial consortia in spontaneously started rye sourdoughs.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: The Complex Interplay between Vaginal Microbiota, HPV Infection, and Immunological Microenvironment in Cervical Intraepithelial Neoplasia: A Literature Review

doi: 10.3390/ijms23137174

Figure Lengend Snippet: Characteristics of studies exploring the association of HPV infection and cervical preinvasive disease to the vaginal microbiome.

Article Snippet: Mengying Wu et al., 2020 [ ] , Shanghai, China; Obstetrics and Gynecology Hospital of Fudan University , 69 premenopausal, non-pregnant patients, prospective case–control study , Scraping from posterior vaginal fornix Deep sequencing of bar-coded 16S rRNA gene fragments (V3–4) using Illumina MiSeq , 31 normal, 22 LSIL, 16 HSIL , − CST II has lower level of Lactobacillus spp. and higher level of strictly anaerobic organisms ( Gardnerella , Atopobium , and Prevotella ) − Prevotella and Streptococcus are increased in HSIL detection − CIN converts the vaginal bacterial community structure from CSTs IV to II − Microbiota diversity is more marked in CST types II and IV ( p < 0.001), above all in type II − Enrichment in the Delftia genus is found in the LSIL and HSIL groups.

Techniques: Infection, Sampling, Microscopy, Immunocytochemistry, Sequencing, DNA Extraction, Hybridization, Marker, Amplification

Journal: Microbiome

Article Title: Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

doi: 10.1186/s40168-016-0172-3

Figure Lengend Snippet: Quantitative PCR analysis of 16S rRNA gene copy numbers. 16S rRNA gene copies per reaction were quantified in the six study subjects using ( a ) PSP extraction method and ( b ) MO BIO extraction method. Fetal side ( FS ), maternal side ( MS ). c , d Comparison of mean cycle threshold values for 16S rRNA gene qPCR. Limit of detection is 38.29 (PSP) and 34.04 (MO BIO). All data sets were analyzed by Kruskal-Wallis with Dunn’s post test. Comparison of any pair of placental samples to controls yielded p > 0.05

Article Snippet: DNA samples were PCR amplified using bar-coded primers flanking the V1V2 region of the 16S rRNA gene, and samples were sequenced using the Illumina method (Fig. , ).

Techniques: Real-time Polymerase Chain Reaction, Extraction, Comparison