Microbial Identification, Sequencing and qPCR Services

NCIMB offers accurate identification of bacteria and fungal isolates, strain to strain comparison, community analysis of mixed samples and quantification of organisms or groups of organisms in a sample.

In addition to some of the world's biggest pharmaceutical manufacturers, our customers include household names in food, drink and energy production. We also work with small companies and start-ups. Our UK-based microbial sequencing and identification labs support customers in their routine environmental monitoring programmes, and we can help problem solve specific contamination issues in manufacturing environments.

Our microbial identification service  is undertaken to GMP standards. We operate a well-established quality management system certified to ISO 9001:2015 and are regularly audited by customers, ensuring that we meet their high standards.

We offer a responsive, customer-focussed 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.

NCIMB uses a genotypic approach to the identification of isolates. We use this method because it has the potential to offer an unambiguous result. Ultimately, it is the DNA sequence that defines the species.

One of the things our customers tell us they value about our service is the help and advice that they get from our laboratory staff. We are always happy to help you choose the right service to meet your needs.

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.

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. However, species level identification of fungi can be challenging, particularly when relying on phenotypic methods.

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.

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 approaches:

• Full gene 16S rDNA sequencing:  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.
• Multi Locus Sequence Typing (MLST).  MLST uses the sequences of internal fragments of seven essential housekeeping genes to characterise isolates, by comparing profiles with previously published data.
• Whole genome sequencing: Whole genome sequencing provides more data for comparison of isolates and has a number of other benefits. The whole genomes can be compared and various analyses can be run to determine how closely related strain are. We can also look for genes that are shared between genomes, highlight those that are not, and look for small nucleotide variations.

Our standard identification service is for pure isolates. We can also accept mixed cultures and other sample types such as waters, slimes and contaminated products. We can plate these out and identify isolates obtained, or our next generation sequencing lab can analyse by 16S metagenomics - this can be a useful method for mixed or complex samples as there is no requirement for growth. Turnaround times are usually 3 - 10 days.

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.

We can develop customised assays for organisms or functional genes of interest as well as undertaking commonly requested tests.

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.

If sending mixed cultures or other sample formats, such as water, swabs, slimes or contaminated products, please contact us to discuss the options available prior to shipping. 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.

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