Microbiology

Our skilled microbiologists undertake identification of unknown isolates, and can perform strain to strain comparison of as well as providing microbial community analysis.

We can work with clients to problem solve microbial issues with waste streams and monitor efficacy of remedial action.

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

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^® database. 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 NCIMB reference collection and the client’s own historic data 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 microbial issues in manufacturing environments and comparing them to previous events. There are some different approaches to strain to strain comparison and differentiation:

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

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, if it is required. 

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 undesirable organisms, enabling remedial action to be taken and modified in response to results as necessary.

We can develop customised qPCR assays for specific organisms of interest to individual clients, or undertake assays for a range of commonly requested organisms.

This technique, which has revolutionised understanding of environmental microbiology, uses sequencing information to analyse the whole microbial population from a single sample. It identifies the groups of microorganisms present to give a comprehensive picture of the microbial ecosystem.  NCIMB can undertake microbial community analysis to help customers assess soil health or identify the different populations of microorganisms present during bioremediation processes.

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, raw materials or contaminated products, but please contact us 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 know 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 Microbiology Services.