Microbial Identification

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

Our microbial ID service undertakes genotypic identification of unknown isolates for food and drinks manufacturers, and can carry out strain to strain comparison of isolates to help trace the source of contaminants and tackle spoilage issues.

Of course, microorganisms aren’t always an unwanted presence in foodstuffs, and play a vital role in the production of many products.  Our identification service can be used to confirm the presence or absence of specific bacterial strains in products such as probiotic foods.

We offer our customers:

• Validated and auditable identification of isolates using the latest DNA sequencing-based techniques.
• A range of turn around options including same and next day interim reporting.
• Clear, easy to understand reporting, tailored to your requirements.
• Easy sample submission.

• 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.

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. 

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 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^®. 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.

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 two different approaches:

• 16S rDNA sequencing can be used for basic strain comparison when the full 16s (1500bp) is sequenced. An 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.

Fungi can cause significant spoilage issues for food manufacturers, and species level identification can give valuable additional information that can be used when it comes to investigating excursions from normal populations or contamination issues.   

The development of genotypic techniques has been a great step forward in this regards and two distinct approaches have emerged: 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 that if a species level identification is required, it can be obtained by using the ITS method.

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 unwanted organisms, enabling remedial action to be taken and modified in response to results as necessary, or to confirm the presence of a probiotic strain.

We can develop customised qPCR assays for specific organisms of interest to individual clients, or undertake assays for a range or organisms that are commonly requested within the food and drink industry.

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, slimes or contaminated products, but please contact us to discuss prior to submitting them for identification.

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. Detailed advice on the packaging of isolates is available on request.

Please contact us to find out more about our Bacterial and Fungal Identification Services.