Accurate and rapid bacterial and fungal identification using validated MicroSEQ® sequencing workflows and curated reference database.
BaseClear provides microbial identification services using the MicroSEQ® system, a fully validated platform for DNA based identification of bacteria and fungi. By combining targeted PCR amplification with Sanger sequencing and curated reference databases, this service delivers highly reliable species level identification. The workflow is standardized end-to-end, ensuring reproducibility and consistent data quality across projects.
This service is designed for clients in pharmaceutical, food, environmental, and industrial microbiology who require accurate identification of microbial isolates. It is particularly valuable in quality control, contamination investigations, and regulatory environments where validated methodologies and traceable results are essential. The approach addresses common challenges such as ambiguous phenotypic identification and inconsistent results from non-standardized sequencing methods.
The MicroSEQ® workflow is based on targeted sequencing of taxonomically informative regions of ribosomal DNA genes. For bacterial identification, a conserved region of the 16S rDNA gene is amplified, after which approximately the first 500 base pairs are sequenced. This region includes multiple hypervariable domains that provide sufficient discriminatory power for species-level identification in most cases. For fungal identification, sequencing focuses on the D2 region of the large subunit (LSU) rDNA gene, generating consensus sequences of approximately 200–300 base pairs.
Primers are designed to anneal to conserved flanking regions, ensuring broad applicability across taxa, while the intervening variable regions capture sequence diversity. The resulting sequences are processed using the MicroSEQ® analysis pipeline and compared against curated and validated reference libraries containing over 2200 bacterial and 1600 fungal species. Because both the wet-lab workflow and the database are validated as a single system, variability in identification outcomes is minimized compared to open or non-curated databases.
Clients receive a report including the processed sequence data, quality metrics, and results of the homology search against the validated MicroSEQ® database. The report provides the closest matching species, similarity scores, and interpretation guidance. Standard turnaround times are 2–5 working days for bacterial samples or for fungal samples, with expedited options delivering results within one working day after sample receipt.
Upon request, this service can be performed under GMP-compliant conditions. In this case, additional documentation, traceability, and quality assurance measures are applied in accordance with GMP requirements.
You submit your samples through our online order portal, including the required sample information.
Upon arrival, samples are logged, checked for completeness and condition, and prepared for analysis according to standardized MicroSEQ® workflows.
Target regions of the 16S rDNA gene (bacteria) or D2-LSU region (fungi) are amplified and sequenced using validated MicroSEQ® protocols.
Sequences are analyzed against het validated MicroSEQ® database, and a detailed identification report is released and uploaded to the order portal within the agreed turnaround time.
Bacterial species in validated database
Fungal species in validated database
Working day for fast track turnaround available
End-to-end MicroSEQ® workflow
Sequencing approximately 500 base pairs of the 16S rRNA gene provides sufficient taxonomic resolution for most bacterial identifications. This region contains multiple hypervariable domains that differentiate species while maintaining high amplification success rates. It also ensures compatibility with validated MicroSEQ® protocols and databases.
MicroSEQ® differs by offering a fully validated workflow including reagents, protocols, and curated databases. This integration reduces variability and increases reproducibility compared to open workflows that rely on non-standardized methods and public databases.
Species level identification is typically achieved for many bacteria and fungi using this method. However, closely related species with highly similar ribosomal sequences may require additional loci or whole genome sequencing for full resolution.
The D2 region of the LSU rRNA gene provides a robust balance between conservation and variability for fungal identification. It allows reliable amplification across diverse taxa while offering sufficient discriminatory power for many species.
This method may not resolve very closely related species with nearly identical ribosomal sequences. In such cases, additional genetic markers or higher-resolution approaches may be recommended.
Database matches are highly reliable because the MicroSEQ® libraries are curated and validated. Each identification is based on sequence similarity scoring combined with quality-controlled reference data.
A mixed culture cannot be reliably identified to species level using this method. The MicroSEQ® workflow is based on Sanger sequencing of a single dominant DNA template, which requires a pure culture to generate a clear and interpretable sequence. In mixed cultures, overlapping sequence signals are produced, preventing accurate identification. For mixed samples, isolation of single colonies prior to analysis or the use of alternative approaches such as metagenomic sequencing may be recommended.
This service can be performed under GMP-compliant conditions upon request. In such cases, the workflow is executed with enhanced documentation, traceability, and quality controls aligned with GMP requirements. This includes controlled procedures, audit-ready reporting, and full sample and data traceability.
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