NCIMB's skilled microbiologists have extensive experience of identifying unknown bacterial and fungal isolates.

They can confirm the presence of microorganisms within products, quantify groups of organisms within a sample and undertake microbial community analysis.

Identification of unknown isolates

Our microbial identification service undertakes identification of unknown bacterial and fungal isolates from manufacturing environments, and can carry out strain to strain comparison to help trace the source of contaminants and tackle spoilage issues.

Of course, microorganisms aren’t always an unwanted presence.  They play a vital role in the production of many products and we can also confirm the presence or absence of specific bacterial strains in products such as silage inoculants and probiotic animal feed.

We provide fast confidential and accurate identification of bacteria, yeasts and moulds to Good Manufacturing Practice (GMP) standards. Our well established quality management system is certified to ISO 9001:2015.

We offer our customers:

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

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. 

Sequenced data is examined against the validated MicroSEQ® database. When this 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.

Strain to strain comparison and differentiation

Comparison of isolates at the strain level can be valuable when tracing the source of spoilage in manufacturing environments is it also important with respect to the patented use of bacteria, and for the production of probiotic products and silage inoculants. 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 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.
  • MLST via NGS - this approach uses whole genome sequencing data to perform MLST on a genome wide scale.

Fungal identification – yeasts and moulds

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. 

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

Metagenomics - microbial community analysis

NCIMB can undertake microbial community analysis to help customers assess soil health or identify the different populations of microorganisms present during processes such as silage production.

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

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, 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.