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MicroSEQ Microbial Identification System
Used by leading pharmaceutical and biotech manufacturers worldwide, the Applied Biosystems MicroSEQ Rapid Microbial Identification System offers reliable, species-level microbial identification to support environmental monitoring, contamination investigations, raw materials testing, and root cause analysis in regulated QC environments. When product quality, compliance, and manufacturing continuity are at stake, the MicroSEQ system is designed to deliver answers without unnecessary uncertainty, providing confidence on demand and helping laboratories act with clarity and speed. As a strategic investment in laboratory capability, the MicroSEQ system empowers teams to help reduce risk over time, build more predictable programs, and help reduce reliance on costly third-party testing.
Whether implementing microbial ID for the first time or strengthening existing workflows, this solution offers laboratories the accuracy, scalability, and documentation confidence needed to maintain compliance and control.
End-to-end workflow solution for microbial identification
The MicroSEQ Rapid Microbial ID System unifies PCR, sequencing, and data analysis into one integrated workflow that is predictable, scalable, and easy to validate across laboratories and sites. The components are developed and tested together, designed to deliver dependable results that support faster decision-making and reduce operational inefficiencies.
- Reliable accuracy: Targeted sequencing of the 16S rRNA gene for bacteria and the D2 region for fungi delivers high discrimination power and species-level resolution across diverse organisms, reducing ambiguity and unnecessary follow-up testing
- Built for compliance: Designed on principles recommended by ICH, USP, EUP, and JP to support defensible contamination investigations, robust documentation, and audit readiness
- Fast time to answers: Species-level results in about five hours from colony to answer help labs act swiftly and reduce delays that impact downstream manufacturing steps
- Broad organism coverage: Large curated libraries for bacteria and fungi strengthen confidence across environmental monitoring programs
- Standardized for scalability: Common protocols and standardized reagents promote consistent performance across instruments and sites
- Global support: Training, validation services, and experience help reduce risk over time and support long-term operational excellence
This unified solution helps laboratories transition from reactive troubleshooting to proactive oversight, improving microbial ID outcomes and quality programs.
Why sequence-based identification delivers greater confidence
Sequence-based microbial identification evaluates stable genetic markers to produce reliable species-level results that help laboratories deliver answers without unnecessary uncertainty. This molecular approach enhances result clarity, strengthens contamination investigations, and supports root cause identification on demand in ways that reduce repeat testing and accelerate corrective actions.
In many regulated environments, labs balance speed with accuracy. Sequence-based methods enable both rapid insight and deep resolution, helping teams make confident decisions faster. By offering broader, validated coverage and stronger resolution for challenging organisms, sequence-based workflows reinforce confidence in compliance and reduce long-term reliance on third-party services.
Proven genotypic identification for reliable results
Accurate species identification is foundational to strong environmental monitoring and contamination control strategies. Genotypic microbial identification measures stable genetic sequences to help labs achieve high-confidence identification with less variability. This leads to more predictable, reproducible performance, stronger contamination investigations, and better control of risk over time.
Highlights:
- DNA-based results reduce ambiguity that can slow investigations
- High discrimination power supports differentiation between organisms with similar observable characteristics
- Reliable performance contributes to scalability across multi-site operations
The MicroSEQ system uses comparative rDNA sequencing of the 16S region (bacteria) and LSU D2 region (fungi) to generate species-level identification that supports confident decision-making for routine QC and investigation workflows.
“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).”
U.S. Food and Drug Administration. Sterile Drug Products Produced by Aseptic Processing—Current Good Manufacturing Practice U.S. Food and Drug Administration. FDA, October 2004.
Webinar: Microbial identification via DNA‑sequencing method to support risk mitigation
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. This webinar discusses the standards requiring characterization, identification, and techniques of a genotypic microbial identification method.
Go from culture to answer in less than 5 hours
When deviations occur, speed and accuracy are both mission critical. The MicroSEQ system integrates MSID software, sample preparation reagents, application kits, thermal cyclers, and sequencing systems into a tightly harmonized workflow that supports predictable, rapid turnaround.
A single, standardized workflow facilitates species-level identification in under five hours from colony to result. This fast performance supports root cause identification on demand, accelerates investigations, and helps laboratories maintain operational predictability across testing programs.
Standardized workflow for multi-site confidence
A standardized microbial ID workflow supports consistent, predictable outcomes across multiple laboratories, instruments, and teams. By aligning sample preparation, sequencing, and data analysis protocols, this approach simplifies training and validation, strengthens data integrity, and helps global organizations scale microbial identification programs with confidence.
Predictable workflows also reduce variability that can increase risk over time and help laboratories build documented processes that stand up to regulatory scrutiny. For quality teams, standardized practices drive operational efficiency and deeper insights across sites.
Scalable microbial ID for growing demands
Microbial identification needs to support not just current workflows but future growth and expanded operational demands. The MicroSEQ system is designed for scalability so that laboratories of varying sizes can achieve consistent performance and dependable results whether supporting a single site or a global network.
Standardized protocols, shared validated libraries, and harmonized reporting across instruments and facilities help organizations implement microbial identification programs that are consistent, defendable, and efficient. As laboratory workloads increase, the system supports higher throughput while maintaining accuracy and data integrity. This helps reduce rework, lower reliance on external partners, and deliver confidence on demand across many testing environments. With scalable performance built into the workflow, the MicroSEQ system helps quality teams expand microbial identification capabilities while maintaining control, reducing risk over time, and supporting long term operational excellence.
Easy PCR-ready template preparation
The Applied Biosystems PrepMan Ultra Sample Preparation Reagent was developed for the rapid preparation of DNA template from gram-negative pathogens for use in PCR amplification reactions. It has been used to prepare PCR-ready template from a wide variety of different sources, including bacteria, yeast, filamentous fungi, from a plate or from liquid culture, mammalian tissue smears, human cells (buccal swab), and mammalian whole blood. It offers a simple rapid protocol, helping reduce time-to-results.
All-inclusive reagent kits and libraries
Specific and easy-to-use, MicroSEQ kits provide all the reagents needed for robust microbial identification. Complementary PCR and Sequencing kits have been tested and internally validated to meet or exceed regulatory guidelines. There are several kits and corresponding data libraries to choose from—covering more than 12,000 strain types of bacteria and fungi.
Precise PCR control
The Applied Biosystems VeritiPro Thermal Cycler offers proven reliability with advanced temperature control technology and connectivity. Take advantage of next-level PCR optimization with the precision offered by VeriFlex temperature control technology.
Simple, flexible sequencing platforms
The Applied Biosystems SeqStudio Series of genetic analyzers offer the high quality and reliable performance of Sanger sequencing and fragment analysis that scientists need, while leveraging design improvements and technological advances for increased flexibility, easier operation, enhanced connectivity, and remote serviceability.
Fast, accurate data analysis
Unlock the power of precise bacterial and fungal sequence identification with MicroSEQ Identification Software 4.0, tailored for the Applied Biosystems SeqStudio genetic analyzers. Experience advanced analysis, packed with features that elevate your workflow while supporting compliance with 21 CFR Part 11 regulatory standards.
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