artistic rendition of a microbe

MicroSEQ Microbial Identification System—achieve right-the-first-time microbial identification

Used in top pharmaceutical companies worldwide, the Applied Biosystems MicroSEQ Rapid Microbial Identification System is ideal for environmental monitoring, contamination investigation, root cause analysis, raw materials testing, and microbial identification in small-molecule and biopharmaceutical manufacturing, and service laboratories. The MicroSEQ System combines the benefits of PCR and DNA sequencing technologies to enable highly accurate results.

Next-generation, high-throughput, comparative DNA sequencing system for identification of bacteria and fungi

The MicroSEQ Rapid Microbial Identification System uses a highly accurate phylogenetic approach for microbial identification based on the sequencing of the 16S rRNA gene for bacteria or the D2 region of the large subunit ribosomal DNA for fungi. The resulting sequences of microbial samples are compared to sequences in our curated and validated collection. Our genotypic microbial identification solution is based on molecular, sequence-based analyses of ribosomal genes in bacteria and fungi and complies with approaches recommended by regulatory agencies for accurate contamination identification.

Designed to support regulatory guidelines

The FDA guidance is intended to help manufacturers meet the requirements in the Agency's current good manufacturing practice (cGMP) regulations (2l CFR parts 210 and 211) when manufacturing sterile drug and biological products using aseptic processing. In the guidance document “Sterile Drug Products Produced by Aseptic Processing – Current Good Manufacturing Practice” October 2004, the FDA clearly identifies genotypic methods of microbial identification to be more accurate and precise than traditional biochemical and phenotypical techniques, so why settle for less?

“Genotypic methods have been shown to be more accurate and precise than traditional biochemical and phenotypic techniques. These methods are especially valuable for investigations into failures (e.g., sterility test; media fill contamination).” (FDA (2004), Sterile Drug Products Produced by Aseptic Processing – Current Good Manufacturing Practice, p. 35)

MicroSEQ ID System is designed to support the recommended qualification guidelines from:

  • International Conference on Harmonization (ICH)
  • United States Pharmacopeia (USP)
  • European Pharmacopoeia (EUP)
  • Japanese Pharmacopoeia (JP)

Generate actionable results in less than 5 hours

With the MicroSEQ Rapid Microbial ID System, bacteria and fungi can be identified in under five hours, using a logical workflow that requires minimum hands-on time. A single, standardized procedure is used for identifying both bacterial and fungal isolates.

colony screeningDNAeppendorf tubeinformaticssearch

Grow culture

Extract DNA

Perform PCR

Sequence the DNA

Identify the organism

  • Growth in solid and liquid medium (pure culture)
  • Lyses cell wall to expose and extract DNA
  • Amplify DNA via PCR
  • 30-minute process
  • Sequence DNA by breaking into segments
  • 60-minute process
  • Perform electrophoresis to pull tagged segments through system
  • Compare sequence to library for identification
How to video for Microbial identification genotypic method using MicroSEQ ID

Watch our how-to video that provides step-by-step instruction from sample preparation to data analysis. It takes you through the streamlined protocol for same-day microbial identification.

Not all databases are created equal

The key to accurate microbial identification is a powerful database. We don't just collect data from other sources. We validate our own findings and confirm accuracy of all entries. Trust the largest validated and curated in silico database which includes over 12,000 strain types that have been confirmed by our scientists and collaborators.

MicroSEQ ID databases provide the largest, most comprehensive, validated libraries for bacteria and fungi




MicroSEQ ID 16S rDNA 500 Microbial Library, v2019



MicroSEQ ID 16S rDNA 500 Supplemental Library, v2019



MicroSEQ ID 16S rDNA Full Gene Library, v2.0



MicroSEQ ID Fungal Gene Library, v2018



The MicroSEQ ID System is a powerful database because it is built on meticulously curated collections and validated using multiple techniques to enable accurate identification.

Scanning electron micrograph of bacteria


Thermo Fisher conducts a rigorous validation process for accurate taxonomic information of new and existing bacterial and fungal species. From sequence information entry, genus and species level validation, to revalidation of existing MicroSEQ library entries–all done by trained personnel–you are offered the most comprehensive, accurate, reliable libraries available for your Pharma QC testing. 

Scanning electron micrograph of rod-shaped microbes


We closely evaluate our libraries and curate for what really matters to our pharma QC customers–quality and accuracy.  We have increased the number of Candida, Cladosproium, Aspergillus, and added species for 223 new genuses for fungal database. We partner with the Westerdijk Fungal Biodiversity Institute, part of the Royal Netherlands Academy of Arts and Sciences, for the latest and reliable sequence information for mycological identification and classification.

Scanning electron micrograph of spiral shaped microbe


Increasing the power of this database, Thermo Fisher Scientific regularly updates the MicroSEQ ID Software Library. This helps ensure that your MicroSEQ ID database is always up to date by providing periodic updates of quality checked and validated bacterial and fungal sequences.

Webinar Image

Webinar: Microbial Identification via DNA-Sequencing Methods to Support Risk Mitigation Strategies

The utilization of microorganism identification through DNA sequencing provides an in-depth and comprehensive view of the variety of organisms that may pose a risk to controlled environments or final product. Discussion of standards requiring characterization, identification, and techniques of a genotypic microbial identification method will be covered.

In this webinar we will:

  • Review current methods of microbial monitoring
  • Discuss when it's appropriate to identify organisms to help with risk mitigation
  • Evaluate methods of microbial characterization
  • Go over examples of difficult sample types and how we managed the analysis

Watch webinar now ›

Proven technology

Accurate identification of environmental isolates is required to support active environmental monitoring programs within pharmaceutical manufacturing environments and to implement accurate Corrective and Preventive Actions (CAPAs) for products and processes to reduce the risk of contamination. The comparative gene sequence analysis of ribosomal DNA (rDNA) has been shown to have the highest accuracy of microbial identification system technologies and has been considered the gold standard for microbial identification for over a decade. The MicroSEQ ID microbial identification system, based on comparative rDNA sequencing of the 16S region (for bacteria) or the LSU D2 region (for fungi), is a proven method for rapid and accurate microbial identification.


The target for bacterial identification is the 16S ribosomal RNA (rRNA) gene sequence. The 16S rRNA is ubiquitous and can therefore be used to study phylogenetic relationships among all bacteria. With the MicroSEQ ID method, users have the option of choosing to sequence the first 500 bp of the 16S rDNA gene or the full 1,500 bp. Kits and the supporting validated library databases are available for both options. The first 500 bp are sufficient for a routine identification that encompasses 3 of the 9 hypervariable regions of the 16S gene (Figure 1). In some cases the 500 bp region is not sufficient to discriminate among very closely related bacteria and therefore requires a more informative full-gene read (Figure 2). Furthermore, sequencing of the entire 1,500 bp sequence is required when describing a new species.

Fungi and yeast

Comparative sequence analyses of both the expansion region D2 of the larger rRNA molecule in the large subunit of the eukaryotic ribosome (LSU-D2) and ITS regions have been successfully used for identification and classification of fungi down to the species level. The ITS region exhibits more variability, which can give rise to many more “sequence types” than the D2 region when used for sequence-based fungal identification. Fungal genomes may contain more than 100 copies of the rDNA cluster; it therefore is critical to understand and differentiate between simple sequence variability and sequence variability that reflects actual relatedness. The MicroSEQ ID fungal database is derived from sequences from LSU-D2 rDNA, which helps deliver highly reliable fungal identification and classification in routine identification tests.

Graphical depiction of hypervariable regions within the 16S rNA gene

Figure 1. Hypervariable regions within the 16S rRNA gene. There are 9 hypervariable regions within the bacterial 16S gene, indicated in green. The conserved regions are indicated in blue.

Figure 2. Sequence data taken from the first 500 bp (lower tree) are not sufficient to differentiate Mycobacterium abscessus (ATCC 19977) and Mycobacterium chelonae chelonae (ATCC 35752). Extending the sequence to the full 1,500 bp allows for differentiation of these two species (upper tree). Similarly, the differences between Mycobacterium farcinogenes (ATCC 35753) and Mycobacterium senegalense (ATCC 35796) as well as Mycobacterium africanum (ATCC 25420) and Mycobacterium microti (ATCC 19422) become more apparent when analyzed using the full 1,500 bp sequence.

Integrated software solution for microbial identification

MicroSEQ ID Microbial Identification Software is part of the integrated workflow for the identification and classification of bacterial and fungal sequences for scientists working in QC microbiology laboratory setting. MicroSEQ ID Software v3.1 for Applied Biosystems 3500 Series Genetic Analyzers (for high-throughput sample analysis) and the MicroSEQ ID Software for Applied Biosystems SeqStudio Genetic Analyzer v1.0 (for low-throughput sample analysis).

Regardless of the platform, the MicroSEQ ID Software provides essential data analysis to confidently identify and classify your bacterial or fungal sequence.

MicroSEQ ID software for microbial identification


  • Identify sequences of interest using a library of over 12,000 validated microbial and fungal sequences
  • Fully integrated set-up on the 3500 Genetic Analyzer series and SeqStudio Genetic Analyzer
  • Supported and fully tested for Windows™ 10 operating system
  • Includes security, audit, and e-signature features to help enable 21 CFR Part 11 compliance

MicroSEQ ID Software - Plate layout. Visual plate layout allows for easy setup with minimal chance of error.

MicroSEQ ID software for microbial identification

MicroSEQ ID Software - Analysis QC Report. Comprehensive view of results identifying top species match with drill-down options to view detailed sequence matching.

MicroSEQ ID software for microbial identification

A platform to meet all needs

In-house microbial identification allows you to quickly identify contaminants and develop a plan for correction. We have expanded our platform offering to allow access of the MicroSEQ ID system, regardless of your throughput needs. For same-day low microbial identification that allows you to keep control of your samples, we recommend the SeqStudio Genetic Analyzer that offers low throughput, smaller footprint, and economical price. For the large sample throughput needs, we recommend the high throughput, established 3500 Genetic Analyzer series.

We believe internal microbial identification is possible for all our customers, regardless of their size or needs.

PlatformSeqStudio35003500 XL
SeqStudio genetic analyzer3500 genetic analyzer3500 XL
Number of capillaries4824
Injection speed45 min/injection130 min/injection130 min/injection
IDs / 8 hrs*10622
IDs / 24 hrs*463494**
Software platformMicroSEQ ID SWMicroSEQ ID SWMicroSEQ ID SW
Supports 21 CFR Part 11YesYesYes
Library databaseBacteria, FungalBacteria, FungalBacteria, Fungal
Ease of useEasyMediumMedium

* includes sample preparation time of 6 hours


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