Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies

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.

Microbiome-based solutions to address new and existing threats to food security, nutrition, health and agrifood systems' sustainability

“…Inoculants consisting mostly of individual strains are used for bioaugmentation and as biofertilizers to colonize the plant environment (e.g., rhizosphere or endosphere) (Beed et al, 2011;Uzoh and Babalola, 2018). Although limitations/hurdles remain (e.g., efficacy in various field conditions), which require knowledge advances (Compant et al, 2019), impressive success already exists, e.g., the application of N 2 -fixing rhizobia as inoculants for soybean in Brazil saved ∼US$ 10.2 billion in N fertilizers (Olmo et al, 2022). Also, a recent metastudy highlighted the potential of microbial inoculants as biofertilizer and to improve stress resilience (Li et al, 2022).…”

The need for an integrated multi‐OMICs approach in microbiome science in the food system

“…From 2011 when ‐omics started to be used routinely in foods studies (De Filippis et al., 2018), an impressive number of papers reported the application of these technologies to allow thorough characterization of the microbiome in agro‐food systems (Olmo et al., 2022). Amplicon sequencing remains the main approach for such studies (Parente et al., 2020) and is used mainly for observational studies with an ecological purpose.…”

Food systems microbiome‐related educational needs

“…The importance of multidisciplinary applied sciences in food systems microbiome R&D, hands‐on training and collaboration between universities and industry must be highlighted. Nowadays, microbiome science is an interdisciplinary research field connected to diverse areas, for example, agriculture, food science, biotechnology, bioeconomy, mathematics (informatics, statistics and modelling), plant pathology and human/veterinary medicine (Olmo et al, 2022 ). Bioinformatics plays an increasing role in predicting and assessing the desired and undesired effects of microorganisms on food systems (Garrigues et al, 2013 ).…”

“…The impact of academia on industrial success is undeniably high as many of the products in the market and start‐up companies originated from academic leads (Olmo et al, 2022 ; Rasmussen & Wright, 2015 ). Universities and other public research institutions serve as major sources for trained research employees, novel scientific hypotheses, modes of action and early‐stage technologies.…”

“…The citizen's perception of microorganisms is generally negative, due to their association with disease and food spoilage (Simard, 2021 ). However, the vast majority of the planet's microorganisms are not pathogenic (Balloux & van Dorp, 2017 ), and in many cases, we rely on their ability to break down a wide range of substrates to maintain the cycling of elements, disposal of sewage, remediation of toxic materials, composting, producing fermented food and more (Hou et al, 2020 ; Insam & de Bertoldi, 2007 ; Nascimento et al, 2018 ; Olmo et al, 2022 ; Parvez et al, 2006 ). Timmis et al ( 2019 ) consider that there is an urgent need for microbiology literacy in our society, because microbial activities affect everyone in diverse ways and are key for sustainable and economic development (Callens et al, 2022 ; D'Hondt et al, 2021 ).…”