Description:

////Technical specification:

////Short description:
Digital PCR is for absolute quantification, nucleic acid detection, and rare mutation detection using microfluidic array plate (MAP) technology technology and TaqMan® chemistry.

////Keywords:
Digital PCR, Quantification of microorganisms, DNA

Description:

The SHIME® (Simulator of the Human Intestinal Microbial Ecosystem) model is currently the most representative in vitro technology to comprehensively simulate the properties of the digestive tract. The SHIME® model can reproduce a wide range of physiological and microbial parameters in vivo, including body temperature, intestinal volume, enzyme concentrations, feeding cycles, pH, and microbial diversity in different parts of the colon. In addition to the physically separated colonic reactors, SHIME® can be upgraded with a mucosal 'compartment' (M-SHIME®) that mimics the microenvironment of the intestinal wall. This enhancement allows the specific role of mucosal and luminal niches in the microbial community to be investigated. These compartments are colonised by specific and differentiated microbial communities due to differences in physiological conditions. This makes SHIME® an excellent model for assessing not only when a digested sample will affect the microbiota, but also the location of the impact.

Description:

"Ion GeneStudio S5, together with the Ion Chef automated library and template preparation system, enables a streamlined next-generation sequencing (NGS) workflow for targeted sequencing that is flexible and adaptable. Genomic DNA (10–100 ng) isolated from the sample is converted to a sequencing library by selective amplification of regions of interest using the Ion AmpliSeq protocol that enables highly multiplexed PCR amplification of up to 20,000 targets in a single tube. Eliminating primerdimers a fraction of the targets pecific Ion AmpliSeq primers are digested away from the amplified product, followed by a ligation step to add adapter sequences to the amplicons.

////Technical specification:

The sequencing is carried out on a semiconductor detector by direct recording of the H produced in the sequencing reaction.

Up to 100 different genomes can be analysed simultaneously and up to 130 million reads can be performed in a single reaction.

////Short description:
Extracting DNA from a sample and preparing the library for sequencing; Genetic identification of micro-organisms; 16S metagenomics studies; Multi-genome analysis and mutation searching; de novo sequencing.

////Keywords:
Sequencing of DNA, Ion Torrent, library preparation, 16S RNA