When ingested in sufficient numbers, probiotics are expected to confer one or more proven health benefits on the consumer. Theoretically, the effectiveness of a probiotic food product is the sum of its microbial quality and its functional potential. Whereas the latter may vary much with the body (target) site, delivery mode, human target population, and health benefit envisaged microbial assessment of the probiotic product quality is more straightforward. The range of stakeholders that need to be informed on probiotic quality assessments is extremely broad, including academics, food and biotherapeutic industries, healthcare professionals, competent authorities, consumers, and professional press. In view of the rapidly expanding knowledge on this subject, the Belgian Superior Health Council installed Working Group “8651 Probiotics” to review the state of knowledge regarding the methodologies that make it possible to characterize strains and products with purported probiotic activity. This advisory report covers three main steps in the microbial quality assessment process, i.e. (i) correct species identification and strain‐specific typing of bacterial and yeast strains used in probiotic applications, (ii) safety assessment of probiotic strains used for human consumption, and (iii) quality of the final probiotic product in terms of its microbial composition, concentration, stability, authenticity, and labeling.

Summary: Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale‐up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory‐scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology. For that purpose, a full scale‐up/down computational framework is already available. This framework links computational fluid dynamics ( CFD ), metabolic flux analysis and agent‐based modelling ( ABM ) for a better understanding of the cell lifelines in a heterogeneous environment. Ultimately, this framework can be used for the design of scale‐down simulators and/or metabolically engineered cells able to cope with environmental fluctuations typically found in large‐scale bioreactors. However, this framework still needs some refinements, such as a better integration of gas–liquid flows in CFD , and taking into account intrinsic biological noise in ABM .