PreBiomics S.r.l, based in Trento, Italy, was founded in 2017 and initially focused on developing its flagship microbiome-based kit, the PreBiomics Implant Test. This innovative assay supports dental professionals in the prevention, early diagnosis and personalized treatment of oral peri-implant diseases. The company also provides metagenomic and metatranscriptomic microbiome analysis, NGS services and bioinformatic data analysis to a range of research centers, primarily within the areas of nutrition, healthcare and academia. Nelli Groff, Senior Biotechnologist at PreBiomics, outlined the team’s offering: “Our services use advanced sequencing technologies and bioinformatics tools to identify and characterize the bacteria, viruses, fungi and other microorganisms present in a human fecal sample, and to understand their potential impact on health. These studies are vital for informing us how we can capitalize on the power of gene expression to provide tailored and highly effective treatments for numerous diseases, including cancers.”

The company opened a new high throughput NGS laboratory in 2023, equipped with 12 ASSIST PLUS pipetting robots to introduce automation into daily liquid handling tasks and build in flexibility for its diversifying and growing workload. PreBiomics’ proprietary test system enables the team thanks to process up to 5000 samples per week, from DNA extraction and library preparation all the way to sequencing, which results in around 100 full sequencing runs every year. Chiara Galeaz, Senior Biotechnologist at PreBiomics, explained why the lab opted to partner with INTEGRA: “It was important for us in designing our lab space that we would have the technology and adaptability to explore new metagenomics services and keep optimizing our day-to-day tasks for maximum efficiency. We were interested in the ASSIST PLUS pipetting robot from INTEGRA because we saw an opportunity to scale up our throughput and reduce hands-on time and manual errors through automation. Nelli and I had used the technology in our previous workplace and had seen firsthand the benefits it could bring in terms of productivity and flexibility. These factors, along with the accessible price point, made the ASSIST PLUS an obvious choice for us when equipping our new facility."

Enhancing sequencing quality and efficiency with INTEGRA’s novel solutions

Figure 1 below illustrates the organization of the PreBiomics NGS workflow. 2 ASSIST PLUS platforms are dedicated to the reformatting of samples from tubes to 96 well plates, and another is used solely to dilute extracted DNA for library preparation. The lab then uses 3 ASSIST PLUS instruments in pre-amplification and a further 2 in library clean-up. Automated pipetting steps are performed with the ASSIST PLUS before using external devices, such as a PCR machine for amplification and an external reader for quantification reactions. Another 2 ASSIST PLUS platforms, each equipped with a D-ONE single channel pipetting module, are then used to carry out the normalization and pooling of the NGS libraries (Figure 1). The remaining 2 systems are left available as backup. 

We recently launched MAGFLO NGS magnetic beads, and PreBiomics completed beta testing trials to evaluate their performance in comparison to the industry gold standard magnetic beads. The lab used MAGFLO beads for size selection and library clean-up, and carried out the liquid handling for the beta testing trial with an ASSIST PLUS mounted with a 12 channel VIAFLO electronic pipette. The magnetic separation steps of the workflow were performed twice, once using a standard magnetic plate and once using a MAG module, for side-by-side comparison.

The new MAG offers powerful magnets that automatically move up and down, removing the need to manually move plates to and from the magnet. It also collects magnetic beads in a single spot, minimizing bead carry-over for more reproducible pipetting and results. This is a major advantage over standard magnetic plate bead pellets, which are collected in a ring shape and require highly precise pipette tip positioning for accurate pipetting. Nelli continued: “We were keen to try out INTEGRA’s novel beads and modules for magnetic separation to improve the reproducibility and quality of our sequencing results. We also knew that automating certain time-consuming components of NGS library preparation would give staff more walk-away time and greatly speed up our repetitive liquid handling tasks, ultimately helping to enhance our sample processing capacity.” 

Optimizing size selection and minimizing variability with MAGFLO NGS beads and MAG 

The combination of MAGFLO NGS magnetic beads with the MAG module for magnetic separation achieved the tightest size selection with the least variation in size of all the options trialed, including the lab’s own gold standard. In addition, the fragments produced were on average the closest to the target size of 750 bp out of all the set-ups tested (Figure 2). The workflow also produced the highest library concentration and the least variation in concentration values of all trialed combinations, demonstrating its reproducibility (Figure 3). 

The group then went on to normalize and pool the size-selected fragments with an ASSIST PLUS equipped with a D-ONE single channel pipetting module, before performing NGS. Sequencing results showed that the set-up using MAGFLO NGS beads and the MAG module produced more reads and less variation between read values than the lab’s existing method (Figure 4). The results were also more reproducible and less variable than when performing NGS library preparation and size selection purely by hand. 

A versatile workflow for automated magnetic bead separation  

The PreBiomics team found the combination of ASSIST PLUS, MAG module and MAGFLO NGS magnetic beads for automated magnetic bead separation to be extremely versatile, as it could be applied across numerous labware formats. It was also easy to adjust and optimize the workflow without extensive programming skills, thanks to the tools’ intuitive user interfaces and VIALAB pipette automation software. “We would definitely recommend the MAG module and MAGFLO NGS beads to others because they provided us with highly reproducible results, which are vital for reliable sequencing outcomes. We also appreciated the ease with which we could modify the programming scripts in VIALAB to quickly adjust experimental parameters whenever needed,” added Chiara. Nelli concluded: “Our ASSIST PLUS robots will be a great help to us in meeting the increasing and varied testing demands we are sure to encounter in the near future. They will also be a valuable asset as we expand our research and services offerings, continue our trailblazing work and advance the field of personalized medicine.”