Contribution of omics to biopreservation: Toward food microbiome engineering

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.

Serial cultures in invert emulsion and monophase systems for microbial community shaping and propagation

“…This includes fine-tuning of the emulsion parameters such as droplet size, stability and compatibility with different microbial strains to ensure efficient propagation [ 19 ]. Multi-omics approaches may help to understand how invert emulsion culture affects microbial physiology [ 8 ]. This technology could also benefit from predictive modeling to anticipate outcomes in terms of community structure and functionality [ 59 ].…”

“…These advances have fueled strong interest in microbiome engineering in order to improve the biotechnological potential of microbial communities. It is nowadays well recognized that microbial communities represent an opportunity for applications covering numerous domains such as biocontrol of crop cultures [ 6 ], anaerobic digestion [ 7 ] or biopreservation of food matrices [ 8 ]. Engineering microbiomes requires rational approaches in order to obtain the desired properties.…”

OMICS and Other Advanced Technologies in Mycological Applications

“…Metabolomics can identify the key compounds that are essential for antifungal activity. This approach has been successfully applied against Penicillium commune and Mucor racemosus , resulting in the development of new protective strains [ 203 ]. Additionally, meta-transcriptomics (RNA-Seq of complex community microbial samples) has led to insights into the role of fungal microflora such as Geotrichum candidum and Penicillium camemberti in the cheese ripening process [ 204 ].…”

Application of bio-preservation to enhance food safety: A review

“…In addition, bio-preservation can lower the amount Korean J Food Preserv, 30(2) (2023) of salt, sugar, and chemicals in foods by utilizing microorganisms or their metabolic by-products (Borges et al, 2022). Extending the shelf life of foods by using controlled or natural microbiota or antimicrobials is known as bio-preservation (Singh, 2018).…”

“…One of the main obstacles to the widespread application of bio-preservation is the complexity and diversity of food microbial populations and food matrices (Borges et al, 2022). The aim of this review was to narrow the knowledge gap concerning how food preservation techniques can improve food safety and reduce risk of food borne illnesses.…”