Contribution of Omics to Biopreservation: Toward Food Microbiome Engineering

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2022 Aug 19

PMID 35983334

Authors

Frederic Borges

Romain Briandet

Cecile Callon

Marie-Christine Champomier-Verges

Souad Christieans

Sarah Chuzeville

Catherine Denis

Nathalie Desmasures

Marie-Helene Desmonts

Carole Feurer

Francoise Leroi

Sabine Leroy

Jerome Mounier

Delphine Passerini

Marie-France Pilet

Margot Schlusselhuber

Valerie Stahl

Caroline Strub

Regine Talon

Monique Zagorec

Affiliations

Soon will be listed here.

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.

Citing Articles

Ultra-processed plant-based analogs: Addressing the challenging journey toward health and safety.

Martin-Miguelez J, Martin I, Gonzalez-Mohino A, Olegario L, Peromingo B, Delgado J J Food Sci. 2024; 89(12):10344-10362.

PMID: 39656797 PMC: 11673454. DOI: 10.1111/1750-3841.17588.

The dual role of microbes in food safety and human health: from pathogens to probiotics.

Onyeaka H, Odeyemi O Future Microbiol. 2024; 20(2):99-101.

PMID: 39632688 PMC: 11792840. DOI: 10.1080/17460913.2024.2437273.

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

Dijamentiuk A, Mangavel C, Gapp C, Elfassy A, Revol-Junelles A, Borges F Microb Cell Fact. 2024; 23(1):50.

PMID: 38355580 PMC: 10865683. DOI: 10.1186/s12934-024-02322-3.

Minimal Processing Technologies for Production and Preservation of Tailor-Made Foods.

Berdejo D, Garcia-Gonzalo D, Oulahal N, Denkova-Kostova R, Shopska V, Kostov G Food Technol Biotechnol. 2023; 61(3):357-377.

PMID: 38022877 PMC: 10666941. DOI: 10.17113/ftb.61.03.23.8013.

OMICS and Other Advanced Technologies in Mycological Applications.

Wijayawardene N, Boonyuen N, Ranaweera C, de Zoysa H, Padmathilake R, Nifla F J Fungi (Basel). 2023; 9(6).

PMID: 37367624 PMC: 10302638. DOI: 10.3390/jof9060688.

References

Connell J, Ritschdorff E, Whiteley M, Shear J . 3D printing of microscopic bacterial communities. Proc Natl Acad Sci U S A. 2013; 110(46):18380-5. PMC: 3832025. DOI: 10.1073/pnas.1309729110. View

Garnier L, Penland M, Thierry A, Maillard M, Jardin J, Coton M . Antifungal activity of fermented dairy ingredients: Identification of antifungal compounds. Int J Food Microbiol. 2020; 322:108574. DOI: 10.1016/j.ijfoodmicro.2020.108574. View

Pinilla C, Stincone P, Brandelli A . Proteomic analysis reveals differential responses of Listeria monocytogenes to free and nanoencapsulated nisin. Int J Food Microbiol. 2021; 346:109170. DOI: 10.1016/j.ijfoodmicro.2021.109170. View

Saint Martin C, Darsonval M, Gregoire M, Caccia N, Midoux L, Berland S . Spatial organisation of Listeria monocytogenes and Escherichia coli O157:H7 cultivated in gel matrices. Food Microbiol. 2022; 103:103965. DOI: 10.1016/j.fm.2021.103965. View

Ellegaard K, Engel P . Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota. Front Microbiol. 2016; 7:1475. PMC: 5030217. DOI: 10.3389/fmicb.2016.01475. View

Li J, Yang X, Shi G, Chang J, Liu Z, Zeng M . Cooperation of lactic acid bacteria regulated by the AI-2/LuxS system involve in the biopreservation of refrigerated shrimp. Food Res Int. 2019; 120:679-687. DOI: 10.1016/j.foodres.2018.11.025. View

Nouaille S, Even S, Charlier C, Le Loir Y, Cocaign-Bousquet M, Loubiere P . Transcriptomic response of Lactococcus lactis in mixed culture with Staphylococcus aureus. Appl Environ Microbiol. 2009; 75(13):4473-82. PMC: 2704839. DOI: 10.1128/AEM.02653-08. View

Lenz A, Williamson K, Pitts B, Stewart P, Franklin M . Localized gene expression in Pseudomonas aeruginosa biofilms. Appl Environ Microbiol. 2008; 74(14):4463-71. PMC: 2493172. DOI: 10.1128/AEM.00710-08. View

Lin X, Lohans C, Duar R, Zheng J, Vederas J, Walter J . Genetic determinants of reutericyclin biosynthesis in Lactobacillus reuteri. Appl Environ Microbiol. 2015; 81(6):2032-41. PMC: 4345372. DOI: 10.1128/AEM.03691-14. View

10.

Laursen M, Bahl M, Licht T, Gram L, Knudsen G . A single exposure to a sublethal pediocin concentration initiates a resistance-associated temporal cell envelope and general stress response in Listeria monocytogenes. Environ Microbiol. 2014; 17(4):1134-51. DOI: 10.1111/1462-2920.12534. View

11.

Warnecke T, Gill R . Organic acid toxicity, tolerance, and production in Escherichia coli biorefining applications. Microb Cell Fact. 2005; 4:25. PMC: 1208944. DOI: 10.1186/1475-2859-4-25. View

12.

Guillier L, Stahl V, Hezard B, Notz E, Briandet R . Modelling the competitive growth between Listeria monocytogenes and biofilm microflora of smear cheese wooden shelves. Int J Food Microbiol. 2008; 128(1):51-7. DOI: 10.1016/j.ijfoodmicro.2008.06.028. View

13.

Ferrier R, Hezard B, Lintz A, Stahl V, Augustin J . Combining individual-based modeling and food microenvironment descriptions to predict the growth of Listeria monocytogenes on smear soft cheese. Appl Environ Microbiol. 2013; 79(19):5870-81. PMC: 3811370. DOI: 10.1128/AEM.01311-13. View

14.

Rimaux T, Vrancken G, Vuylsteke B, De Vuyst L, Leroy F . The pentose moiety of adenosine and inosine is an important energy source for the fermented-meat starter culture Lactobacillus sakei CTC 494. Appl Environ Microbiol. 2011; 77(18):6539-50. PMC: 3187176. DOI: 10.1128/AEM.00498-11. View

15.

Meola M, Rifa E, Shani N, Delbes C, Berthoud H, Chassard C . DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products. BMC Genomics. 2019; 20(1):560. PMC: 6615214. DOI: 10.1186/s12864-019-5914-8. View

16.

Stiles M . Biopreservation by lactic acid bacteria. Antonie Van Leeuwenhoek. 1996; 70(2-4):331-45. DOI: 10.1007/BF00395940. View

17.

Delpech P, Rifa E, Ball G, Nidelet S, Dubois E, Gagne G . New Insights into the Anti-pathogenic Potential of against Based on RNA Sequencing Profiling. Front Microbiol. 2017; 8:359. PMC: 5340753. DOI: 10.3389/fmicb.2017.00359. View

18.

Wang X, Wang S, Zhao H . Unraveling microbial community diversity and succession of Chinese Sichuan sausages during spontaneous fermentation by high-throughput sequencing. J Food Sci Technol. 2019; 56(7):3254-3263. PMC: 6582033. DOI: 10.1007/s13197-019-03781-y. View

19.

Kumar R, Meiller-Legrand T, Alcinesio A, Gonzalez D, Mavridou D, Meacock O . Droplet printing reveals the importance of micron-scale structure for bacterial ecology. Nat Commun. 2021; 12(1):857. PMC: 7870943. DOI: 10.1038/s41467-021-20996-w. View

20.

McNair L, Siedler S, Vinther J, Hansen A, Neves A, Garrigues C . Identification and characterization of a new antifungal peptide in fermented milk product containing bioprotective Lactobacillus cultures. FEMS Yeast Res. 2018; 18(8). DOI: 10.1093/femsyr/foy094. View