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PDQeX prepGEM Bacteria

Suitable for extracting DNA from Gram-positive bacteria, Gram-negative bacteria, protozoa, archaea, colonies and liquid cultures, biofilm and mucosal samples, swabs, and metagenomic DNA including soil, stool, and water.

Double-stranded DNA extracts suitable for PCR, qPCR, targeted amplicon sequencing from metagenomic samples and whole genome sequencing.

Each kit contains PDQeX prepGEM, lysozyme, enhancer, GREEN+ buffer, wash, and extractor tubes.

For processing larger samples, we recommend the PDQeX prepGEM Bacteria HC kits. These kits have the traditional advantages that come with using the PDQeX Nucleic Acid Extractor but also include the new HC extraction cartridges.

These new HC extraction cartridges allow for more sample to be loaded into the cartridge before the purification matrix becomes overloaded. This results in a higher final yield of extracted DNA, meaning the PDQeX prepGEM Bacteria HC kits are better suited for sequencing workflows where a higher yield of DNA is encouraged.

info Product Codes and Prices
# of Reactions Product Code Price
50 XBA0050 $230.00
100 XBA0100 $440.00
500 XBA0500 $2,100.00
1000 XBA1000 $3,970.00
50 HC XBH0050 $230.00
100 HC XBH0100 $440.00
500 HC XBH0500 $2,100.00
1000 HC XBH1000 $3,970.00

Image shows 100, 500 and 1000 reaction kits

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https://microgembio.com/wp-content/uploads/2019/03/C0091-XBH-QSC-RevA.pdfMicroGEM’s PDQeX prepGEM Bacteria Kit provides a simple automated approach to studying a wide range of microbial cultures. Using MicroGEM’s PDQeX Nucleic Acid Extractor, purified double-stranded DNA is generated, making it the perfect solution when working with inhibitory samples (for example soil and stool).

Every aspect of the MicroGEM method ensures the samples are processed quickly and gently. Minimal sample prep, closed tube processing, and gentle lysis ensure that cross contamination and DNA fragmentation are drastically reduced, making MicroGEM’s extraction process streamlined while preserving the integrity of low abundance species.

  • Novel temperature controlled enzymatic lysis using a thermophilic proteinase in combination with mesophilic Lysozyme
  • Rapid workflow- 1/4th the time taken by other methods
  • Easily automated for high throughput
  • Closed system- no cross contamination and protection against pathogens
  • Gentle lysis with no transfer steps- preserves DNA and improves community representation in metagenomic samples
  • Minimal handling and pipetting of samples- DNA is exceptionally intact and high molecular weight.
  • Can be easily adapted to different sample types and workflows


PDQeX handbook (pdf)

Quick Start Card: PDQeX prepGEM Bacteria (pdf)
Quick Start Card: PDQeX prepGEM Bacteria (HC) (pdf)

Safety Data Sheet: PDQeX prepGEM Bacteria (pdf)
Safety Data Sheet: PDQeX prepGEM Bacteria (HC) (pdf)

On-demand webinar: Rapid single-tube preparation of DNA from bacteria for NGS workflows (register)
Hear researchers Jo Stanton and David Saul discuss their recent study showing the sequence quality obtained from DNA extracted using the rapid PDQeX protocol and how it compares to existing methodologies.

Tree Lab: Portable genomics for early detection of plant viruses and pests in sub-saharan Africa. Genes. 10: 632. 2019. (pdf)
This study demonstrated a technical breakthrough in the ability to conduct genomic analysis in the field. The PDQeX was used with the collaborator’s sequencing technologies to conduct real-time identification of viral pathogens on actual samples collected from cassava plants in Tanzania, Uganda, and Kenya.

Rapid extraction of DNA suitable for NGS workflows from bacterial cultures using the PDQeX. BioTechniques. Vol.66, No. 5. 2019. (pdf)
This study compared a conventional column purification method with the PDQeX Nucleic Acid Extractor for purifying DNA for whole genome sequencing. Based on six bacterial suspensions, the PDQeX performed much more rapidly – in under 30 minutes – while producing comparable high-quality extractions.

Inner Workings: Portable DNA sequencer helps farmers stymie devastating viruses. Proceedings of the National Academy of Sciences,116(9), 3351-3353. 2019. (pdf)
This study described the ability to screen Cassava crops for Cassava Mosaic Virus (CMV) using MicroGEM’s PDQeX for rapid DNA extraction. The PDQeX was used as the enabling technology to complement DNA sequencing being conducted in the field in real-time.




WGS – Bacteria

Whole genome sequencing of microbes is a powerful tool for genomic studies comparison, mapping studies, microbial identification, and building reference genomes. High-resolution sequencing data is vital for:

  • Microbial systematics, building reference genomes, and mapping novel genomes.
  • Understanding the temporal and spatial dynamics of epidemics, pathogenesis, co-evolution of host and pathogens.
  • Horizontal gene transfer and antibiotic resistance transmission in a population.
  • Mutational studies using directed evolution of recombinants.
  • Understanding physiology and metabolic pathways of organisms.

Currently available methods of DNA extraction from bacteria are long and laborious and are susceptible to cross-contamination. The PDQeX Bacteria kit enables rapid, hands-free extraction of DNA from bacterial samples. Protocols take a fraction of the time of existing methods without the risk of cross-contamination. The prepared DNA can be used directly in whole genome sequencing workflows without any further purification.

Figure: PDQeX Bacteria produces WGS- ready DNA from bacterial cultures in a fraction of the time needed for other popular methods.

Rapid extraction of DNA suitable for NGS workflows from bacterial cultures using the PDQeX. BioTechniques. Vol.66, No. 5. 2019.” (pdf)

A recent collaborative study by scientists from MicroGEM and the University of Otago compared DNA extracted using the PDQeX Bacteria kit to a competitor’s bacterial DNA extraction protocol. DNA was extracted from thermophilic aerobes with varying cell morphologies and growth optima. The PDQeX extraction, from pre-wash to WGS-ready DNA, took under 30 minutes while the competitor’s protocol, including two incubations and several pipetting, transfer and centrifugation steps, took 2 hours. The DNA extracted from these samples from both methods were sequenced using the Ion Torrent platform (Ion PGM). On all performance measures (DNA yield, quality and sequencing parameters), DNA extracted using the PDQeX method was comparable to that produced by the competitor’s protocol (see Figure below). This study has shown that the PDQeX method rapidly produces high quality DNA suitable for whole genome sequencing.

Figure: Mapping of bacterial reads to reference genomes using the Ion Torrent Coverage Analysis Plug-in software tools comparing PDQeX and Competitor Q’s silica column- based extraction methods. X-axis corresponds to genome position; Y-axis is Base Read Depth.