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 directly from the DNA of complex faecal or skin samples.