Microbial Identification

At NCIMB we have extensive experience of providing fast, confidential and accurate identification of bacteria and fungi to Good Manufacturing Practice (GMP) standards. 

Our microbial ID service supports pharmaceutical, cosmetic and personal care companies in their routine environmental monitoring programmes and we can help problem solve specific contamination issues in manufacturing environments. 

We offer our customers:

  • A validated and auditable service.
  • Same day, next day, three day and ten day turnaround options.
  • Clear, easy to understand reporting,  tailored to your requirements.
  • Easy sample submission.

Validated and auditable

  • NCIMB’s microbial identification services follow auditable procedures using validated equipment and are undertaken to GMP standards. 
  • We operate a well-established quality management system certified to ISO 9001:2015.   
  • Our clients include major pharmaceutical companies based in the UK and overseas, and we are regularly audited by them, ensuring we meet their high standards.

Responsive service

We offer a responsive service and have introduced a range of sample turnaround times to help our customers prioritise identification of their most important isolates and optimise use of budgets.   We can deliver same day and next day results for samples received before 10am, as well as providing three day and ten day services, with options available for reporting. 

Bacterial identification

We undertake rapid genotypic identification of bacterial isolates, including mycoplasma, by sequencing the 16S ribosomal DNA gene with full gene or 500bp options available.  This technique can rapidly identify both viable and non-viable organisms, those with complex growth requirements and Gram variable isolates, as well as slow growing and/or non-fermenters.

Sequenced data is examined against the validated MicroSEQ® database in the first instance. When MicroSEQ doesn’t provide a high enough species level match we can also use the more comprehensive, non-validated, European Nucleotide Archive (ENA) database from EMBL-EBI, the client’s own historic data collection and the NCIMB reference collection to match sequences to published data.

As custodians of the UK’s National Collection of Industrial, Food and Marine Bacteria, we have immediate access to this unique source of authentic reference material. We also have access to a number of private collections, ensuring a comprehensive coverage of genera and species.

Customer reports can be tailored to your requirements and include top sequence matches and phylogenetic trees.

Strain to strain comparison and differentiation

NCIMB offers comparison of isolates at strain level.  This can be valuable when tracing the source of objectionable organisms in manufacturing environments and comparing them to previous contaminants. It can also be very important with respect to the use of bacteria in patented processes and for the production of probiotic products. We can use three different approaches:

  • 16S rDNA sequencing can be used for basic strain comparison when the full 16s (1500bp) is sequenced. Alignment of sequences highlights major differences, but does not always distinguish between closely related strains.
  • Multilocus sequence typing (MLST) is a highly reproducible DNA sequencing-based technique. Sequences of internal fragments of (typically) seven essential house-keeping genes, i.e. those essential for cells to function, are used to characterise isolates.
  • MLST via NGS - this approach uses whole genome sequencing data to perform MLST on a genome wide scale.

Fungal identification – yeasts and moulds

Fungi can cause serious problems for pharmaceutical manufacturers, and species level identification gives valuable information that can be used when investigating contamination issues or excursions from normal populations.

There are two distinct approaches to genotypic identification of fungi: sequencing of the D2 region of the large subunit ribosomal DNA (D2 LSU), and sequencing of either one or both of the internal transcribed spacer regions between the small and large subunit ribosomal RNA genes (ITS). At NCIMB we combine these techniques to offer a comprehensive service that gives our customers the most reliable species level identification available.

For D2 LSU identification, sequences are analysed against the validated MicroSEQ database.  In some cases, however, this only gives a genus level identification. When this occurs we often find a species level identification can be obtained by using the ITS method.

Next generation sequencing

We offer next generation sequencing for microbial community analysis and whole genome sequencing. Whole genome sequencing is the ultimage in organism characterisation. It is a valuable technique for microbiome studies, the discovery of useful properties, searching for antibiotic resistance genes, identifying virulence factors and strain comparison.

Quantitative polymerase chain reaction (qPCR)

NCIMB offers a qPCR service. Quantitative polymerase chain reaction is a valuable means of determining the presence or absence of an organism or group of organisms in a sample, whilst also providing very rapid quantitative information. For example, it can be used to monitor the presence of objectionable organisms, enabling remedial action to be taken and modified in response to results as necessary.

Sample submission

Pure cultures can be sent to us for identification as plates, slopes or broths that have been incubated to produce sufficient growth.   Please complete a sequencing request form and send with isolates to be identified.

We can also accept mixed cultures and other sample formats, such as samples of water, swabs, slimes or contaminated products, but please contact us to discuss the options available prior to submitting them for identification. Same and next day services may not be available for these sample types.

NCIMB does not accept active cultures of dangerous human pathogens or organisms isolated from clinical or diseased plant materials for identification.   We cannot accept isolates known to be greater than ACDP category 2 and ACGM class 1.

Take care to package samples appropriately.

For customers shipping from outside of the UK, see our Identification request form for advice on paperwork for customs. Detailed advice on the packaging of isolates is available on request - contact us for more information.