Probiotics are specific microbial strains that have a beneficial effect on the health of the host and are defined as “Live microorganisms that, when administered in adequate amounts, confer a health benefit on the host”. In 2002, a joint FAO/WHO Expert Consultation on Evaluation of Health and Nutritional Properties of Probiotics in Food proposed the first guideline for the evaluation of probiotics in food. One of the points was to use accurate taxonomy of the microorganism and identify it at the strain level. Strain identification is expected to be done using a reproducible genetic method or a unique phenotypic trait. Various typing methods with different technical features, costs and feasibilities are available for this purpose. While Whole Genome Sequencing (WGS) is progressively replacing Pulsed Field Gel Electrophoresis (PFGE) as the gold standard of strain identification in research as well as the clinical, pharmaceutical, food, feed and industrial fields, it is not yet fully accessible to all laboratories with respect to the cost and/or technical expertise required. Depending on the purpose of identification, WGS is not always needed. For example, routine analysis for quality control of probiotic food products requires high throughput techniques within a short time frame. This Bulletin is an update of the Bulletin of the IDF N°462/2013 which presents and compares different available typing methods for probiotic strains in terms of their capacity and limits of use for identification at the strain level.
