BaseClear offers strain-specific quantification services based on quantitative real-time PCR (qPCR). With this services we develop strain-specific primers for the detection and quantification of specific microbial strains in complex faecal or skin samples. These strain-specific qPCR assays can be used in microbiome studies, e.g. in clinical trials.

Quantification of strains in clinical samples

In microbiome-based clinical research project it might be crucial to be able to identify a particular strain from all other strains of the same species and to link the strain to the clinical observations found. Regulatory agency guidelines highlight the need for strain‐specific identification in clinical trials. Publications demonstrating inaccurate identification of strains indicate that molecular biological methods should be used in addition to conventional microbiology in species identification.

Not only identification but also quantification of the strains is necessary in most applications. The quest for strain‐specific quantification is demanding, as the strain is usually analysed from a mixed bacterial population. Our qPCR method is rapid and can be performed on the large numbers of samples that are processed in clinical studies. The real‐time PCR technique combines the specificity and speed of conventional PCR with the ability to quantify bacteria without cultivation and is suitable for rapid quantification of bacterial species direct from the DNA of complex faecal or skin samples.

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Meet Tom van den Bogert!

Tom is our metagenomics and microbiome specialist. He is responsible for the development of new and improved metagenomics and microbial profiling services, which are based on Next-Generation sequencing and related technologies. Tom completed his PhD research at the Laboratory for Microbiology at Wageningen University. He studied community and genomic analysis of the human small intestine microbiota in a project funded by TI Food and Nutrition entitled "Complex fermentations."

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