Journal: Annals of Clinical Microbiology and Antimicrobials

Article Title: Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review

doi: 10.1186/s12941-024-00698-z

Figure Lengend Snippet: Main characteristics of the studies included in this review. NI, No information

Article Snippet: (Wolcott et al., 2009) , USA , Prospective , Ulcer debris , 40 , 16s metagenomics , centrifugation at 14,000 rpm for 30 s and resuspended in 500 µl RLT buffer (Qiagen), 5 mm steel bead (Qiagen), 500 µl sterile 0.1 mm glass beads, TissueLyser (Qiagen), and run at 30 Hz for 5 min. , QIAamp DNA Mini Kit (Qiagen) , No , , tag-encoded FLX and Titanium amplicon pyrosequencing (Roche) , Roche/454 GS FLX Titanium platform , NET and C# analysis pipeline with BLASTn , NCBI Bacterial database..

Techniques: Sample Prep, DNA Extraction, Sequencing, Centrifugation, Sterility, Amplification, Selection, DNA Purification, Software, Incubation, Polymerase Chain Reaction

Journal: Annals of Clinical Microbiology and Antimicrobials

Article Title: Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review

doi: 10.1186/s12941-024-00698-z

Figure Lengend Snippet: Main characteristics of the studies included in this review. NI, No information

Article Snippet: (Wolcott et al., 2009) , USA , Prospective , Ulcer debris , 40 , 16s metagenomics , centrifugation at 14,000 rpm for 30 s and resuspended in 500 µl RLT buffer (Qiagen), 5 mm steel bead (Qiagen), 500 µl sterile 0.1 mm glass beads, TissueLyser (Qiagen), and run at 30 Hz for 5 min. , QIAamp DNA Mini Kit (Qiagen) , No , , tag-encoded FLX and Titanium amplicon pyrosequencing (Roche) , Roche/454 GS FLX Titanium platform , NET and C# analysis pipeline with BLASTn , NCBI Bacterial database..

Techniques: Sample Prep, DNA Extraction, Sequencing, Centrifugation, Sterility, Amplification, Selection, DNA Purification, Software, Incubation, Polymerase Chain Reaction

Journal: Gut Microbes

Article Title: Modulation of gut microbiota in healthy rats after exposure to nutritional supplements

doi: 10.1080/19490976.2020.1779002

Figure Lengend Snippet: Overview of the studies of modulation of rat gut microbiota by different nutritional supplements.

Article Snippet: Fermentable carbohydrates , 24 male BioBreeding rats (28 to 42-d-old) n = 8, cellulose (C: 5% w/w) n = 8, wheat bran (WB: 5% w/w) n = 8, high amylose maize starch (RS: 5% w/w resistant starch) Fecal pellets collected at the end of the feeding trial (d 28). Cecal contents collected during necropsy following completion of the balance phase (d 42). , 6 weeks , Community DNA isolated using Qiagen DNA Stool Isolation Kit Bacterial tag-encoded FLX amplicon sequencing Silva database Phylotypes classified using the Ribosomal Data-base DNA Shotgun metagenomic library construction and sequencing (Roche GS-FLX Titanium sequencing) MEGAN , Cecal communities were dominated by the phylum Firmicutes with higher abundance of Lachnospiraceae compared to feces. In feces the community structure was shifted toward the phylum Bacteroidetes. , .

Techniques: Starch, DNA Extraction, Sequencing, Bacteria, Control, Derivative Assay, Residue, Amplification, Sampling, Spectrophotometry, Real-time Polymerase Chain Reaction, Terminal Restriction Fragment Length Polymorphism, Software, Probiotics, Isolation, Incubation, SYBR Green Assay, Formulation, Activity Assay, Purification, Fluorescence, In Situ Hybridization, Flow Cytometry, Next-Generation Sequencing, Denaturing Gradient Gel Electrophoresis

Journal: Antibiotics

Article Title: The Microbiome of Peri-Implantitis: A Systematic Review of Next-Generation Sequencing Studies

doi: 10.3390/antibiotics12111610

Figure Lengend Snippet: Summary of techniques of DNA extraction, amplification, and sequencing.

Article Snippet: Kumar et al., 2012 [ ] , Qiagen DNA MiniAmp kit, QIAGEN, Venlo, The Netherlands , PCR amplification of 16s rRNA at the V1–V3 and V7–V9 regions , The Titanium platform was used to perform multiplexed bacterial-tag-encoded FLX amplicon pyrosequencing. , Greengenes.

Techniques: DNA Extraction, Amplification, Sequencing, Software, Purification, Concentration Assay, Spectrophotometry, DNA Purification, Plasmid Preparation