Custom Microbial DNA qPCR Arrays

For real-time PCR-based, customized microbial identification or profiling


  • Enables profiling of a customized panel of microbial genes or species
  • Contains highly sensitive and specific Microbial DNA qPCR Assays
  • A variety of plate layouts available to suit your research needs


Product Details

The Custom Microbial DNA qPCR Array contains user-defined assays for detection of microbial species or microbial genes.

To order a Custom Microbial DNA qPCR Array, please use this excel file.


Linearity and dynamic range
Microbial DNA qPCR Assays display linear amplification across a dynamic range from 10 to 106 copies of DNA template (see figure,  Linearity and sensitivity of Microbial DNA qPCR Assays).

Lower limit of quantification (LLOQ)
The LLOQ is the lowest concentration of template that still falls into the linear range of the standard curve (see figure,  Limit of detection versus lower limit of quantification). Across all Microbial DNA qPCR Assays, 93% have an LLOQ of <100 gene copies (see figure,  The LLOQ for all Microbial DNA qPCR Assays reveals high sensitivity). 92% of microbial identification assays meet this LLOQ, as do 95% of virulence gene assays and 97% of antibiotic resistance gene assays (see figures,  The LLOQ for microbial identification Microbial DNA qPCR Assays reveals high sensitivity The LLOQ for virulence factor gene detection Microbial DNA qPCR Assays reveals high sensitivity, and  The LLOQ for antibiotic resistance gene detection Microbial DNA qPCR Assays reveals high sensitivity).

Each Microbial DNA qPCR Assay is stringently tested to ensure that it detects only one target species or gene (see figure,  Microbial DNA qPCR Assays are highly specific). For assays that do detect more than one target, a list of detected targets and in silico predictions is included on the product sheet.

This specificity is maintained even when samples have high species complexity, such as in stool, sputum, and plaque (see figure,  Microbial DNA qPCR Assays display high sensitivity even in complex metagenomic samples), and is verifiable by sequencing methods (see figure,  Specificity of the Antibiotic Resistance Genes Microbial DNA qPCR Array is confirmed by pyrosequencing). 

Microbial DNA qPCR Assays are highly reproducible, both in intra- and inter-individual variability tests (see figure,  Microbial DNA qPCR Arrays generate reliably reproducible results).
See figures


Microbial DNA qPCR Assays are designed to detect bacterial 16S rRNA gene and fungal ribosomal rRNA gene sequences for species identification, as well as detecting virulence factor genes and antibiotic resistance genes using PCR amplification primers and hydrolysis-probe detection.

Custom Microbial DNA qPCR Arrays are 96- or 384-well plates with assays defined by the customer, arranged according to your needs; for example, one can order a 96-well plate with 48 assays to be used with 2 samples, or with 12 assays to be tested with 8 samples. Controls are integrated on each plate to test for the presence of fungal DNA, bacterial DNA, host genomic DNA, and success of the PCR reaction, ensuring confidence in the results.


The Microbial DNA qPCR Array procedure is simple and can be carried out in any laboratory with a real-time PCR instrument. DNA is isolated using the QIAamp kit that is suited for the sample type, and then mixed with the appropriate Microbial qPCR Mastermix. The mixture is aliquotted across the array plate, and real-time PCR is performed to obtain the raw CT values for each assay. The complimentary data analysis software is then used to profile genes or species in the sample.


Custom Microbial DNA qPCR Arrays are highly suited for the rapid and accurate profiling of a custom panel of microbial species, virulence factor genes, or antibiotic resistance genes. For example, a microbial species identification panel assembled by our experts was used to explore the underlying causes of bacterial vaginosis (see figures,  The Vaginal Flora Microbial DNA qPCR Array provides accurate profiling for cervical swab samples and  Vaginal samples positive for Gardnerella vaginalis also show changes in commensal and bacterial vaginosis-related microbes compared to healthy samples), while a panel for antibiotic resistance genes identified these genes in samples from the gut or from sewage (see figures,  The Microbial DNA qPCR Array screens gut microbiota for the presence of antibiotic resistance genes and  The Antibiotic Resistance Genes Microbial DNA qPCR Array identified antibiotic resistance genes in sewage samples).
See figures

Supporting data and figures


Analysis Software (1)
Brochures & Guides (2)
Microbial product configurator guide
For application-specific microbial identification and profiling by real-time PCR
Safety Data Sheets (1)
Download Safety Data Sheets for QIAGEN product components.
Kit Handbooks (1)
For real-time PCR-based profiling/detection of microbial species, antibiotic resistance genes or virulence factor genes