The MxQ group has three Biosafety Type II laboratories devoted to the microbiological analysis of food, soil and water, including irrigation water, process water and reclaimed water. The microbiological analyses of food are performed in the main Biosafety Lab. Water analyses are executed in the second Biosafety Lab located in a separate building next to CEBAS-CSIC main building, while the third Biosafety lab is placed in the pilot plant, used to perform challenge tests mimicking industrial processing practices. These facilities are equipped with all the tools needed for detecting and quantifying microorganisms following classical and molecular methods.
This unit is equipped with advanced devices needed for genome analysis in food, water and soil samples. The MxQ group uses a broad set of genome protocols that allow the quantitative and qualitative analyses of nucleic acids (DNA and RNA) up to genome-wide gene expression and genotyping studies using different platforms including:
- DNA and RNA thermocyclers (BIO RAD)
- Real-time PCR (Applied Biosystems QuantStudio 5)
- RT Multiplex Thermocycler (GeneDisc, Pall)
The QX ONE Droplet Digital PCR (ddPCR) System (BIO RAD) is a highly precise system for the sensitive and reproducible nucleic acid detection and quantification primarily because measurements are performed by dividing the sample into partitions. Each partition is analyzed after end-point PCR cycling for the presence (positive reaction) or absence (negative reaction) of a fluorescent signal, and the absolute number of molecules present in the sample is calculated. It does not rely on a standard curve for sample target quantification, reducing errors and improving precision.
The Genomic unit is also equipped with versatile tools for assessing the quantity and quality of the extracted DNA and RNA, allowing the evaluation of integrity, concentration and purity, such as 4150 TapeStation System for Sample Quality Control, Gel Image Capture System and Nanodrop for ARN/ADN extraction purity device.
METAGENOMIC SEQUENCING UNIT
The MxQ group can study the genetic material recovered directly from food and environmental samples through metagenomic sequencing, which allows the comprehensive analysis of all genes present in a complex sample. Microbiome analysis is performed using a Real-time, long read sequencers (MinION Mk1C CapEx, Oxford Nanopore Technologies), which allows identification, classification and quantitation of microbes within a complex biological sample. The long-read metagenomic sequencing is an effective, culture-free method to study microbial communities with considerable accuracy.
This facility is devoted to the characterization and quantification of volatile and non-volatile secondary metabolites and small molecules of various metabolic pathways. The MxQ group is able to perform qualitative or quantitative analysis by detecting the spectra of a series of samples and combining them with chemical pattern recognition methods. These advanced tools used by the unit include: Gas chromatography-mass spectrometry (GS-MS 7890 Agilent) with solid-phase microextraction, treatment and derivatization of samples.
- Headspace GC-MS (Agilent GC model 7890A equipped with an Agilent MS detector model 5975C).
- UPLC-ESI-MS Triple Quadrupole for directed metabolomics analysis (Agilent UPLC model 1290 infinity and Triple Quadrupole Mass Spectrometer model 6460).
- UPLC-ESI-QTOF-MS for untargeted metabolomics analysis (Agilent UPLC model 1290 infinity and Accurate-Mass Quadrupole time-of-flight model 6550).
- HPLC-DAD-ESI-MSn for identification by fragmentation (Agilent HPLC model 1200 series and Bruker ion trap spectrometer model HCT 122 Ultra).
- HPLC-DAD-ESI-MS for identification and quantification (Agilent HPLC model 1200 series and Single Quadrupole Mass Spectrometer model 6120).
- UPLC-UV-QToF-MS-SPE-NMR ‘On-line’ for undirected metabolomics, isolation of non-identified metabolites and structural analysis by NMR (Bruker UPLC model maXis Impact and Bruker RMN model AVANCE III HD 500 MHz CryoProbe Prodigy BBO).