Streamlining microbiome analysis with magnetic bead solutions

Italian start-up PreBiomics Srl has automated key liquid handling steps in its high-throughput NGS microbiome analysis workflows by implementing 12 ASSIST PLUS pipetting robots from Integra Biosciences. The lab has also tested Integra’s MAG module and the new MAGFLO™ NGS magnetic beads for library preparation during NGS size selection, resulting in highly reproducible sequencing outcomes.

PreBiomics' proprietary assay, the PreBiomics Implant Test, aids dental professionals in preventing, diagnosing, and personalising treatments for oral peri-implant diseases. The company offers metagenomic and metatranscriptomic microbiome analysis, NGS services, and bioinformatic data analysis to various research centres focused on nutrition, healthcare, and academia. Its advanced microbiome analysis system can process up to 5,000 samples weekly, covering everything from DNA extraction and library preparation to sequencing, with approximately 100 sequencing runs completed each year.

To enhance automation and flexibility for its expanding workload, PreBiomics opened a new high-throughput NGS lab in 2023, equipped with 12 ASSIST PLUS pipetting robots. Chiara Galeaz, Senior Biotechnologist at PreBiomics, explained the decision to partner with Integra: “We selected ASSIST PLUS robots to provide the flexibility needed for diverse client requests and to manage our growing workload. These platforms have significantly increased our throughput while reducing hands-on time and minimising manual errors.”

The company has recently completed beta testing of magnetic bead and magnetic separation solutions from various providers, including Integra’s MAGFLO NGS magnetic beads and MAG module. The MAG module features powerful magnets that automatically move up and down, eliminating the need to manually transfer plates. During the beta trial, liquid transfers were performed using an ASSIST PLUS with a 12-channel VIAFLO electronic pipette. The combination of MAG and MAGFLO NGS achieved the tightest size selection and highest library concentration compared to other options, including the lab’s own gold standard, with fragment sizes closely matching the target. Additionally, the MAG module and MAGFLO NGS produced more reads and less variability between read values than the lab’s existing methods.

Nelli Groff, Senior Biotechnologist at PreBiomics, stated: “We were eager to explore Integra’s magnetic bead separation solutions to enhance our sequencing data quality. MAG and MAGFLO NGS provided highly reproducible results, essential for reliable sequencing outcomes. We also appreciated the ease of modifying programming scripts in the VIALAB pipette automation software, allowing us to adjust experimental parameters as needed.” She concluded, “Our ASSIST PLUS robots will be invaluable as we continue to advance personalised medicine.”

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