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Review
. 2022 Jul 4:13:834622.
doi: 10.3389/fmicb.2022.834622. eCollection 2022.

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

Rocío Olmo  1   2 , Stefanie Urimare Wetzels  1   2 , Jaderson Silveira Leite Armanhi  3   4 , Paulo Arruda  4   5   6 , Gabriele Berg  7   8   9 , Tomislav Cernava  7 , Paul D Cotter  10   11 , Solon Cordeiro Araujo  12   13 , Rafael Soares Correa de Souza  3   5 , Ilario Ferrocino  14 , Jens C Frisvad  15 , Marina Georgalaki  16 , Hanne Helene Hansen  17 , Maria Kazou  16 , George Seghal Kiran  18 , Tanja Kostic  19 , Susanne Krauss-Etschmann  20   21 , Aicha Kriaa  22 , Lene Lange  23 , Emmanuelle Maguin  22 , Birgit Mitter  19 , Mette Olaf Nielsen  24 , Marta Olivares  25 , Narciso Martín Quijada  1   2 , Marina Romaní-Pérez  25 , Yolanda Sanz  25 , Michael Schloter  26 , Philippe Schmitt-Kopplin  27 , Sarah Craven Seaton  28 , Joseph Selvin  18 , Angela Sessitsch  19 , Mengcen Wang  29 , Benjamin Zwirzitz  30 , Evelyne Selberherr  2 , Martin Wagner  1   2
Affiliations
Review

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

Rocío Olmo et al. Front Microbiol. .

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.

Keywords: agrifood system; food microbiome; microbiome-based applications; multi-omics analyses; success case studies.

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Conflict of interest statement

At the time of writing, SS was employed by Indigo Ag. RdS and JA was employed by Symbiomics Microbiome Solutions. YS had a patent on a Bifidobacterium strain for obesity licensed (WO2012/076739A1). AS and BM had a patent on the plant-endophyte combinations and uses therefor (US9364005B2). The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The handling editor BM declared a shared affiliation with the authors MO, MR-P, and YS at the time of review.

Figures

Figure 1
Figure 1
Schematic workflow of the integrative approach that led to the discovery of the first seed-endophytic bacterium that confers holistic disease resistance to rice plants. Its discovery was facilitated by large-scale microbiome analyses that were complemented with a series of cultivation-dependent and-independent experiments. The approach led to the discovery of Sphingomonas melonis ZJ26 that shapes a disease-resistant rice phenotype.
Figure 2
Figure 2
Soybean microbial inoculation and co-inoculation in Brazil. (A–C) Individual state contributions to soybean production (A), adoption by states (% of area) of Bradyrhizobium-based inoculants (B) and adoption by states (% of area) of Azospirillum-based inoculants (C) for co-inoculation in Brazil in the 2019/2020 soybean crop season. (D) Total number of inoculant doses for BNF, Bradyrhizobium-based inoculant applied to soybean and Azospirillum-based inoculant for grasses, sold in Brazil over several years. A partial number of doses are shown in the 2019/2020 crop season due to incomplete data collection (Source: ANPII/Spark). Data from the 2019/2020 crop season were based on 3,551 interviewed farmers covering an extrapolated soybean planted area of 98% with a 95% confidence level and a 1.6% margin of error.
Figure 3
Figure 3
Flowchart describing the development of the products for the improvement of drought-stress tolerance based on the microbial strain. The activities and main outputs of key academic and industrial partners are shown.
Figure 4
Figure 4
Flowchart for production of the new feed additive EP199. Rapeseed meal and brown seaweed biomass are co-fermented by lactic acid bacteria (LAB).
Figure 5
Figure 5
Schematic workflow describing microbial source tracking in slaughter facilities based on 16S rRNA gene amplicon HTS. The left box illustrates a schematic map of a meat processing plant with sampling areas marked in red. The right box shows the final result, a heatmap with the predicted relative contribution of specific genera from the sampled source environments. The figure was modified from Zwirzitz et al. (2020) published under http://creativecommons.org/licenses/by/4.0/.
Figure 6
Figure 6
Schematic representation of the process followed to identify and assess the probiotic potential of Bifidobacterium pseudocatenulatum CECT 77.
See this image and copyright information in PMC

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