Journal: PLoS ONE

Article Title: Simple mapping-based quantification of a mock microbial community using total RNA-seq data

doi: 10.1371/journal.pone.0254556

Figure Lengend Snippet: Flow chart of analysis process of mapping-based RNA-seq analysis to determine microbial community structure. Box indicates branching points in analysis conditions.

Article Snippet: Obtained total RNA from the mock microbial community was used to construct a total RNA-seq sequencing library with a SMARTer stranded RNA-seq kit (Clonetech) following the manufacturer’s instruction.

Techniques: RNA Sequencing Assay

Journal: mSystems

Article Title: Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies

doi: 10.1128/mSystems.00750-21

Figure Lengend Snippet: Impact of eating and drinking on the buccal microbiome. (a) Experimental design. Four healthy nonvegetarian volunteers followed the protocol for 2 days. (b) Unweighted UniFrac distance ordinated with principal coordinate analysis showing the beta diversity at species level. Squares display the buccal swabs in the morning before eating (baseline), circles are the samples after eating (5 min, 30 min, and 240 min), whereas stars represent samples after drinking (5 min, 30 min, and 240 min). Samples were rarefied to 9,000 reads/sample.

Article Snippet: As a positive control, a gut mock community was purchased from ZymoBIOMICS gut microbiome standard (Zymo Research), extracted, and sequenced alongside swab samples.

Techniques:

Journal: bioRxiv

Article Title: Evaluation of established methods for DNA extraction and primer pairs targeting 16S rRNA gene for bacterial microbiome profiling of olive xylem sap

doi: 10.1101/2020.12.11.420356

Figure Lengend Snippet: Boxplots of Richness and Shannon alpha-diversity indices of olive xylem bacterial communities at OTU taxonomic level determined by different DNA extraction kits and after taxonomic assignments with the Greengenes_13-8 and Silva_132 databases. Boxes represent the interquartile range while the black dots inside the box defines the median and whiskers represent the lowest and highest values. P -value was calculated using Kruskal-Wallis test at P < 0.05.

Article Snippet: In this study, we used a mock microbial community standard to determine if a selected DNA extraction kit (the PowerPlant from Qiagen) within Group 4 (the one providing the highest values of alpha diversity) provides an accurate representation of the identified microbial communities and if this can be affected by the PCR protocol and the reference database used for taxonomic assignation (Greengenes 13-8 and Silva 132).

Techniques: DNA Extraction

Journal: bioRxiv

Article Title: Evaluation of established methods for DNA extraction and primer pairs targeting 16S rRNA gene for bacterial microbiome profiling of olive xylem sap

doi: 10.1101/2020.12.11.420356

Figure Lengend Snippet: Hierarchical clustering dendrogram analysis using Ward method and Bray-Curtis distance (A) and principal coordinates analysis (PCoA) of weighted UniFrac and Bray-Curtis distances (B) of olive xylem bacterial communities obtained by using different DNA extraction kits and after taxonomic assignments with the Greengenes_13-8 and Silva_132 databases. Colored dots represent the four clusters obtained in the hierarchical clustering analysis. PERMANOVA (999 permutations; P < 0.05) was performed to test significant differences according to DNA extraction kits.

Article Snippet: In this study, we used a mock microbial community standard to determine if a selected DNA extraction kit (the PowerPlant from Qiagen) within Group 4 (the one providing the highest values of alpha diversity) provides an accurate representation of the identified microbial communities and if this can be affected by the PCR protocol and the reference database used for taxonomic assignation (Greengenes 13-8 and Silva 132).

Techniques: DNA Extraction

Journal: bioRxiv

Article Title: Evaluation of established methods for DNA extraction and primer pairs targeting 16S rRNA gene for bacterial microbiome profiling of olive xylem sap

doi: 10.1101/2020.12.11.420356

Figure Lengend Snippet: Taxonomic bubble plot of olive xylem bacteria relative abundance at phylum, class and family level present in four groups of DNA extraction kits and after taxonomic assignments with the Greengenes_13-8 and Silva_132 databases. Circle sizes represent the relative abundance and colors indicate DNA extraction kits groups shown in . Only abundances greater than 1% are shown.

Article Snippet: In this study, we used a mock microbial community standard to determine if a selected DNA extraction kit (the PowerPlant from Qiagen) within Group 4 (the one providing the highest values of alpha diversity) provides an accurate representation of the identified microbial communities and if this can be affected by the PCR protocol and the reference database used for taxonomic assignation (Greengenes 13-8 and Silva 132).

Techniques: DNA Extraction