INDfood LAB woman working with the device

Personalised nutrition for disease prevention - INDfood Lab

The main activity of the lab’s researchers is the design and development of biotransformation technologies to enhance the functional potential of various materials (commercialisation). The focus of the lab’s researchers is on the development and characterisation of innovative products for the modification of the human microbiota ecosystem.

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INDfood LAB

The research will use one of the most representative in vitro technologies, the SHIME (Simulator of the Human Intestinal Microbial Ecosystem) model, to simulate the complex physiological, chemical and microbiological properties of the digestive tract. SHIME® can be considered as an in vitro clinical trial that can provide knowledge and evidence on the mechanism of action of a specific treatment and additional data for in vivo studies. The biomaterial functionality studies will use state-of-the-art molecular techniques using the available next generation sequencing tools ION5 Sequencing and QuantStudio Absolute Q Digital-PCR-System.

Services

Digestive tests with the Twin SHIME system.
Long-term in vitro digestion studies simulating real human gut conditions: different pH levels in different parts of the simulated gut, temperature and anaerobic conditions. Samples are taken from different parts of the simulated digestive system to investigate: changes in the microbiota (possibly in the lumen itself and/or in the mucin layer), short fatty acids, amino acids, nutrient release. Duration of the study 6-12 weeks.

Digestive studies Triple SHIME system.
Long-term in vitro digestive studies simulating realistic conditions in the human intestine: different pH levels in different parts of the simulated intestine, temperature and anaerobic conditions. Samples are taken from different parts of the simulated digestive system to investigate: microbiota changes, short fatty acids, amino acids, nutrient release. Duration of the study: 24-72 hours.

DNA or RNA sequencing (number of samples from 20 to 90).
Sequencing is performed with the new generation Ion GeneStudio S5 sequencer. Sequencing from 200 to 600 bp with 2M to 80M reads is possible. Sequencing is performed using Ion 510 &520 &530 reagent kits and Ion 520, 520,530 or 540 chips.

Preparation of the sample library for the NGS 16S sequencing run.
DNA extraction and concentration of the sample. For amplification, the variable 16S rRNA regions are amplified and assigned a commercial number (Ion Xpress Barcode adapters kits are used). DNA sequencing libraries are prepared using the Ion 16S Metagenomic and Ion Plus Fragment Library kits. Pooling of samples for sequencing analysis (if necessary).

Determination of the number of micro-organisms (or other cellular DNA) by digital PCR.
Determination of micro-organism DNA copy number by Quant Studio Absolute digital PCR. Primers and probes are currently available for the DNA copy number determination of the following genera of micro-organisms: Lactobacillus, Bacteroides, Clostridium, Prevotella, Bifidobacterium and Enterobacter.

Isolation of the DNA of micro-organisms.
DNA is extracted from the available sample using the PureLink Microbiome DNA Purification kit.