fecal bacterial 16s rdna v4-v6 region-targeted  (Pyrosequencing Inc)

Journal: Preventive Nutrition and Food Science

Article Title: The Efficacy of Probiotics Supplementation on the Quality of Life of Patients with Gastrointestinal Disease: A Systematic Review of Clinical Studies

doi: 10.3746/pnf.2024.29.3.237

Figure Lengend Snippet: Notable outcomes of selected RCT studies assessing the effects of probiotics on GI diseases

Article Snippet: , Japan , ·Purified DNA was used as a template for the following two-step polymerase chain reaction. ·Fecal microbiota was measured using fecal bacterial 16S rDNA V4-V6 region-targeted pyrosequencing. , CP2305 favorably changed the fecal characteristics compared with placebo among patients with IBS with either diarrhea or constipation subtypes.

Techniques: Probiotics, Bacteria, Derivative Assay, Sequencing, Extraction, Polymerase Chain Reaction, Amplification, Real-time Polymerase Chain Reaction, Purification

Journal: Microbial Ecology

Article Title: How Communities of Marine Stramenopiles Varied with Environmental and Biological Variables in the Subtropical Northwestern Pacific Ocean

doi: 10.1007/s00248-021-01788-7

Figure Lengend Snippet: Heatmap showing co-occurrences between the taxonomic groups of MAST and prokaryotic communities based on a sPLS function using relative correlations (mixOmics). The heatmap colors indicate the correlation coefficients. Missing data for one sample for the prokaryotic community (Or2057St01) was due to PCR failure

Article Snippet: The PCR conditions for 18S were an initial denaturation at 95 °C for 3 min; 30 cycles at 94 °C for 30 s, 47 °C for 45 s, 72 °C for 30 s, and a final extension at 72 °C for 2 min. PCR primers for 16S rDNA V5-V6 region used prokaryotic universal primers set 787F (5’-[illumina adaptor]- ATTAGATACCCNGGTAG-3’) and 1046R (5’-[illumina adaptor]- CGACAGCCATGCANCACCT-3’) [ ].

Techniques:

Journal: Seminars in immunology

Article Title: Microbiota Dysbiosis in Select Human Cancers: Evidence of Association and Causality

doi: 10.1016/j.smim.2017.08.001

Figure Lengend Snippet: Oral microbiota profiling in human head and neck cancers.

Article Snippet: 16S rDNA (V3, V6) amplicon Illumina sequencing on salivary DNA. qPCR validation targeting bacterial candidates discovered by sequencing.

Techniques: DNA-DNA Hybridization, Bacteria, PCR Cloning, Sequencing, Isolation, Amplification, Cloning, In Situ, Biomarker Discovery, Illumina Sequencing

Journal: Seminars in immunology

Article Title: Microbiota Dysbiosis in Select Human Cancers: Evidence of Association and Causality

doi: 10.1016/j.smim.2017.08.001

Figure Lengend Snippet: Microbiota profiling in human pancreatic cancer and lung cancer.

Article Snippet: 16S rDNA (V3, V6) amplicon Illumina sequencing on salivary DNA. qPCR validation targeting bacterial candidates discovered by sequencing.

Techniques: Biomarker Discovery, Hybridization, Microarray, Amplification, Illumina Sequencing, Sampling, Bacteria, Sequencing, Derivative Assay, Control

Journal: Seminars in immunology

Article Title: Microbiota Dysbiosis in Select Human Cancers: Evidence of Association and Causality

doi: 10.1016/j.smim.2017.08.001

Figure Lengend Snippet: Oral microbiota profiling in human head and neck cancers.

Article Snippet: Cross sectional study. Discovery cohort: Lung SCC (10), AC (10); healthy controls (10). Validation cohort: Lung SCC (13), AC (28); healthy controls (15). China 2015 (99). , 16S rDNA (V3, V6) amplicon Illumina sequencing on salivary DNA. qPCR validation targeting bacterial candidates discovered by sequencing. , Increased abundance of salivary Capnocytophaga and Veillonella may discriminate SCC and AC from healthy controls. The abundance of Neisseria was decreased in SCC and AC compared with healthy controls. , Patient details were not provided. Antibiotic treatment was not stated..

Techniques: DNA-DNA Hybridization, Bacteria, PCR Cloning, Sequencing, Isolation, Amplification, Cloning, In Situ, Biomarker Discovery, Illumina Sequencing

Journal: Seminars in immunology

Article Title: Microbiota Dysbiosis in Select Human Cancers: Evidence of Association and Causality

doi: 10.1016/j.smim.2017.08.001

Figure Lengend Snippet: Microbiota profiling in human pancreatic cancer and lung cancer.

Article Snippet: Cross sectional study. Discovery cohort: Lung SCC (10), AC (10); healthy controls (10). Validation cohort: Lung SCC (13), AC (28); healthy controls (15). China 2015 (99). , 16S rDNA (V3, V6) amplicon Illumina sequencing on salivary DNA. qPCR validation targeting bacterial candidates discovered by sequencing. , Increased abundance of salivary Capnocytophaga and Veillonella may discriminate SCC and AC from healthy controls. The abundance of Neisseria was decreased in SCC and AC compared with healthy controls. , Patient details were not provided. Antibiotic treatment was not stated..

Techniques: Biomarker Discovery, Hybridization, Microarray, Amplification, Illumina Sequencing, Sampling, Bacteria, Sequencing, Derivative Assay, Control

Journal: Nature Communications

Article Title: Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn's disease

doi: 10.1038/ncomms13419

Figure Lengend Snippet: ( a ) Interaction network of differentially abundant OTUs; each node represents an OTU and are sized according to their number of interactions; each edge denotes a significant co-exclusion (red) or co-occurence (grey) relationship between OTUs. Nodes are coloured by their number of significant co-exclusions. ( b ) The qPCR quantification of A. parvulum in control and CD microbiota as a function of disease severity. ΔCt was calculated by subtracting average Ct values of universal 16S rDNA from average Ct values of A. parvulum specific primers ( n =18 for controls, nine for mild CD and seven for moderate and severe CD). ** P <0.01 estimated using Kruskal–Wallis followed by Dunn's post hoc test. Crosses indicate the mean while horizontal lines indicate the median. ( c ) Principal component analysis of the differentially expressed proteins among controls and CD patients categorized as a function of disease severity. ( d ) Functional annotation (cellular component) analysis of the differentially expressed proteins; the 10 most significantly enriched functional groups (GO terms) are shown (Fisher's exact test P <10 − 13 ). The illustrated P values are for classifications that were significantly enriched compared to the whole proteomic data set.

Article Snippet: 16S rDNA-V6 libraries for all the samples were constructed, with triplicate libraries constructed for the re-extract samples and sent for Illumina sequencing as described above.

Techniques: Control, Functional Assay

Journal: Nature Communications

Article Title: Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn's disease

doi: 10.1038/ncomms13419

Figure Lengend Snippet: ( a ) Interaction network of differentially abundant OTUs; each node represents an OTU and are sized according to their number of interactions; each edge denotes a significant co-exclusion (red) or co-occurence (grey) relationship between OTUs. Nodes are coloured by their number of significant co-exclusions. ( b ) The qPCR quantification of A. parvulum in control and CD microbiota as a function of disease severity. ΔCt was calculated by subtracting average Ct values of universal 16S rDNA from average Ct values of A. parvulum specific primers ( n =18 for controls, nine for mild CD and seven for moderate and severe CD). ** P <0.01 estimated using Kruskal–Wallis followed by Dunn's post hoc test. Crosses indicate the mean while horizontal lines indicate the median. ( c ) Principal component analysis of the differentially expressed proteins among controls and CD patients categorized as a function of disease severity. ( d ) Functional annotation (cellular component) analysis of the differentially expressed proteins; the 10 most significantly enriched functional groups (GO terms) are shown (Fisher's exact test P <10 − 13 ). The illustrated P values are for classifications that were significantly enriched compared to the whole proteomic data set.

Article Snippet: Note that the conserved V6 sequence used for the Ion Torrent sequencing is identical to those used in the 16S rDNA-V6 Illumina library construction described above.

Techniques: Control, Functional Assay