MicroSEQ Microbial Identification System—powerful database for accurate 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.

Not all databases are created equal

The key to accurate microbial identification is a powerful database. The MicroSEQ ID System is the most powerful database available because it is built on meticulously curated collections and validated using multiple techniques to enable accurate identification. 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 10,000 strain types that have been validated by our scientists and collaborators.

MicroSEQ Microbial Identification System – key steps to a powerful database

Validated

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. 

Curated

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 geniuses 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.

Updated

Increasing the power of this database, Thermo Fisher Scientific has developed the MicroSEQ ID Software Library Subscription.This unique service 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.

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MicroSEQ ID Software library subscription service
MicroSEQ-System_nobackground-final

The new MicroSEQ ID Software Library Subscription service will deliver scheduled updates of validated and curated D2 fungal and 500 base pair (bp) 16S microbial sequence libraries from 2019 - 2020. This subscription will continue to build on your current MicroSEQ ID Software library system. No more mining, researching, or waiting to get your samples back from an outside company.

Learn more ›

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.

Bacteria

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.

seq-data-hyperVariable-745x150

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.

The 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 researchers working in the QC microbiology laboratory setting.

  • Identify sequences of interest using a library of over 2,300 validated microbial sequences
  • Set up and run plates directly on Applied Biosystems 3500/3500xl instrument platform
  • Analyze data from Applied Biosystems 3730/xl, 3130/xl and 310 analyzers
  • Supported and fully tested for Windows™ 7 operating system
  • Includes security, audit, and e-signature features to help enable 21 CFR Part 11 compliance
Video: Hear about the features introduced in MicroSEQ ID Software version 3.0:

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.

Bacteria

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.

seq-data-hyperVariable-745x150

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.

The 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 researchers working in the QC microbiology laboratory setting.

  • Identify sequences of interest using a library of over 2,300 validated microbial sequences
  • Set up and run plates directly on Applied Biosystems 3500/3500xl instrument platform
  • Analyze data from Applied Biosystems 3730/xl, 3130/xl and 310 analyzers
  • Supported and fully tested for Windows™ 7 operating system
  • Includes security, audit, and e-signature features to help enable 21 CFR Part 11 compliance
Video: Hear about the features introduced in MicroSEQ ID Software version 3.0:
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