Microbial identification

BaseClear offers all-inclusive services for fast and reliable identification of bacteria and fungi. We specialize in rapid microbial identification, root cause analysis of environmental contamination, and pathogen detection using advanced molecular techniques such as (q)-PCR, DNA sequencing, and MALDI-TOF. The accurate data provided by our fungal and bacterial identification services are suitable for Quality Assurance and Quality Control laboratories in the food, water, pharmaceutical, and public health industries.

Identification methods


BaseClear offers microbial identification services using the revolutionary MicroSEQ® system from Applied Biosystems. The MicroSEQ® system is recommended by various agencies around the world, including the US and European Pharmacopoeia. The MicroSEQ® system is validated and results are blasted against a commercially validated database. The system is based on PCR and DNA sequencing, without the need for time-consuming growth. It is suitable for quick microbial screening (1 working day for our fast service!) of even the most difficult samples.


In addition BaseClear offers microbial identification services using the VITEK® MS from BioMérieux. At this moment this technology can only be used for bacterial and yeast samples. This proteotypic technology is 30-40% more accurate compared to existing phenotypic methods. Main advantages of this system are the fast turnaround time (possible within a couple of hours!) and the low pricing compared to other identification methods.


For fungi we also offer fungal identification services based on in-house developed protocols. With this service identification of fungal samples is achieved by PCR and DNA sequencing of the ITS (internal transcribed spacer) gene. This gene is approximately 1400 base pairs long. For reporting a public (non-validated) database is used.


  • Complete package of molecular methods for bacterial and fungal identifications available
  • Our specialists can advise which option best fits your needs
  • Faster and more reliable than conventional microbial identification methods
  • Fast turnaround time – possible within 24 hours
  • BaseClear is an independent and certified service laboratory working with GMP and ISO compliant methods and standards
  • We also offer GMP identifications through our GMP brand ProBase Pharma (visit www.probasepharma.com/services/microbial-identification).

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