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Review
. 2022 Aug 2:13:951182.
doi: 10.3389/fmicb.2022.951182. eCollection 2022.

Contribution of omics to biopreservation: Toward food microbiome engineering

Frédéric Borges  1 , Romain Briandet  2 , Cécile Callon  3 , Marie-Christine Champomier-Vergès  2 , Souad Christieans  4 , Sarah Chuzeville  5 , Catherine Denis  6 , Nathalie Desmasures  7 , Marie-Hélène Desmonts  8 , Carole Feurer  9 , Françoise Leroi  10 , Sabine Leroy  11 , Jérôme Mounier  12 , Delphine Passerini  10 , Marie-France Pilet  13 , Margot Schlusselhuber  7 , Valérie Stahl  8 , Caroline Strub  14 , Régine Talon  11 , Monique Zagorec  13
Affiliations
Review

Contribution of omics to biopreservation: Toward food microbiome engineering

Frédéric Borges et al. Front Microbiol. .

Abstract

Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.

Keywords: biopreservation; fermentation; food; microbiome; pathogen; safety; shelf life; spoilage.

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Conflict of interest statement

The 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.

Figures

FIGURE 1
FIGURE 1
Major advances in the field of biopreservation thanks to omics approaches. The objective of biopreservation is to induce growth cessation or decay of pathogens and spoilers. Omics approaches have shown that in response to biopreservation, target microorganisms modulate the expression of genes involved in cell metabolism, stress tolerance and virulence. In addition, omics revealed that biopreservation can decrease the diversity of food microbiota. Conversely, depending on its structure, the food microbiota can either improve or reduce the effectiveness of biopreservation agents. Food microbiota can also have intrinsic protective properties and thus inhibit unwanted microorganisms.
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