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.
Strain to strain comparison and differentiation
Next generation sequencing
We offer next generation sequencing for microbial community analysis and whole genome sequencing. Whole genome sequencing is the ultimage in organism characterisation. It is a valuable technique for microbiome studies, the discovery of useful properties, searching for antibiotic resistance genes, identifying virulence factors and strain comparison.
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 different approaches:
- 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.
- 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.
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, 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.
Detailed advice on the packaging of isolates is available on request - contact us for more information.