Agradecimentos: The authors would like to thank Jens Legarth (CEO of FermentationExpert & European Protein companies) for Figure 3. We also greatly thank Cameron Strachan for proofreading the manuscript. The COMET-K1 competence centre FFoQSI is funded by the Austrian federal ministries BMK, BMDW and the Austrian provinces Niederoesterreich, Upper Austria and Vienna within the scope of COMET—Competence Centers for Excellent Technologies. The programme COMET is handled by the Austrian Research Promotion Agency FFG. This work was supported by the European Union’s Horizon 2020 R&I programme under grant agreement No. 818116 (MicrobiomeSupport) Ver menos

Abstract: Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard Ver menos