Bacterial Identification

Our standard service for bacterial identification is based on the well-known MicroSEQ microbial identification system. This highly accurate and trusted method takes a phylogenetic approach that involves sequencing a section of ribosomal DNA. For bacterial identification, the 16S rRNA gene is sequenced with full gene or 500bp options available. The sequence data is then compared to sequences in the validated MicroSEQ database to obtain a match.

We use a DNA sequencing approach to identification of bacteria because it has the potential to offer an unambiguous result - ultimately it is the DNA that defines the species. Other benefits are that because no growth is required, it can be used to quickly identify both viable and non-viable organisms, those with complex growth requirements, Gram-variable isolates, and slow growing strains.

By their nature, environmental isolates can be very diverse, and no commercially available validated identification methods (of any kind) are exhaustive in their coverage. Therefore we sometimes find that the validated database we use returns a genus rather than a species level match. In these cases we use the the sequenced data to search other published (but non-validated) sources in order to obtain a species level match. We can also compare the sequence to the client's own historic data, or use it to search the NCIMB reference collection.

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. We believe this approach ensures our customers can obtain the best available identification for their isolates.

Our standard bacterial 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. Please get in touch to discuss your requirements and the options available.

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. There are two approaches we use:

• 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.
• We undertake whole genome sequencing for strain to strain comparison. Various analyses can be run to compare the sequences and indicate if two genomes are the same species or strain. We also run analyses that look for genes that are shared between the genomes, and highlight those that are not, and we can look for small nucleotide variations between genomes.

Pure cultures can be sent to us for identification as plates, slopes or broths that have been incubated to produce sufficient growth.   Please get in touch before shipping samples, complete a sequencing request form and send with the 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.