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      New Genomic Techniques applied to food cultures: a powerful contribution to innovative, safe, and sustainable food products

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          Abstract

          Nontransgenic New Genomic Techniques (NGTs) have emerged as a promising tool for food industries, allowing food cultures to contribute to an innovative, safe, and more sustainable food system. NGTs have the potential to be applied to microorganisms, delivering on challenging performance traits like texture, flavour, and an increase of nutritional value. This paper brings insights on how nontransgenic NGTs applied to food cultures could be beneficial to the sector, enabling food industries to generate innovative, safe, and sustainable products for European consumers. Microorganisms derived from NGTs have the potentials of becoming an important contribution to achieve the ambitious targets set by the European ‘Green Deal’ and ‘Farm to Fork’ policies. To encourage the development of NGT-derived microorganisms, the current EU regulatory framework should be adapted. These technologies allow the introduction of a precise, minimal DNA modification in microbial genomes resulting in optimized products carrying features that could also be achieved by spontaneous natural genetic evolution. The possibility to use NGTs as a tool to improve food safety, sustainability, and quality is the bottleneck in food culture developments, as it currently relies on lengthy natural evolution strategies or on untargeted random mutagenesis.

          Abstract

          Nontransgenic New Genomic Techniques offer a promising path for the food industry to create innovative, safe, and sustainable microbial products, but EU regulations need adjustment to fully harness their potential.

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          Most cited references29

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          Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

          Current genome-editing technologies introduce double-stranded (ds) DNA breaks at a target locus as the first step to gene correction. 1,2 Although most genetic diseases arise from point mutations, current approaches to point mutation correction are inefficient and typically induce an abundance of random insertions and deletions (indels) at the target locus from the cellular response to dsDNA breaks. 1,2 Here we report the development of base editing, a new approach to genome editing that enables the direct, irreversible conversion of one target DNA base into another in a programmable manner, without requiring dsDNA backbone cleavage or a donor template. We engineered fusions of CRISPR/Cas9 and a cytidine deaminase enzyme that retain the ability to be programmed with a guide RNA, do not induce dsDNA breaks, and mediate the direct conversion of cytidine to uridine, thereby effecting a C→T (or G→A) substitution. The resulting “base editors” convert cytidines within a window of approximately five nucleotides (nt), and can efficiently correct a variety of point mutations relevant to human disease. In four transformed human and murine cell lines, second- and third-generation base editors that fuse uracil glycosylase inhibitor (UGI), and that use a Cas9 nickase targeting the non-edited strand, manipulate the cellular DNA repair response to favor desired base-editing outcomes, resulting in permanent correction of ∼15-75% of total cellular DNA with minimal (typically ≤ 1%) indel formation. Base editing expands the scope and efficiency of genome editing of point mutations.
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            CRISPR provides acquired resistance against viruses in prokaryotes.

            Clustered regularly interspaced short palindromic repeats (CRISPR) are a distinctive feature of the genomes of most Bacteria and Archaea and are thought to be involved in resistance to bacteriophages. We found that, after viral challenge, bacteria integrated new spacers derived from phage genomic sequences. Removal or addition of particular spacers modified the phage-resistance phenotype of the cell. Thus, CRISPR, together with associated cas genes, provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity.
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              Lactic acid properties, applications and production: A review

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                Author and article information

                Contributors
                Journal
                FEMS Microbiol Lett
                FEMS Microbiol Lett
                femsle
                FEMS Microbiology Letters
                Oxford University Press
                0378-1097
                1574-6968
                2024
                06 February 2024
                06 February 2024
                : 371
                : fnae010
                Affiliations
                Sacco , via Manzoni 29/A, 22071 Cadorago, Italy
                Lesaffre , 101 rue de Menin, 59706 Marcq-en-Baroeul, France
                Lallemand SAS , 19 rue des Briquetiers, 31700 Blagnac, France
                Novonesis , Gammel Venlighedsvej 14, 2970 Hoersholm, Denmark
                Novonesis , Gammel Venlighedsvej 14, 2970 Hoersholm, Denmark
                Sacco , via Manzoni 29/A, 22071 Cadorago, Italy
                IFF , 925 Page Mill Road, Palo Alto, CA 94304, United States
                DSM-Firmenich , Alexander Fleminglaan 1, 2613 AX, Delft, the Netherlands
                Lesaffre , 101 rue de Menin, 59706 Marcq-en-Baroeul, France
                Sacco , via Manzoni 29/A, 22071 Cadorago, Italy
                Lallemand SAS , 19 rue des Briquetiers, 31700 Blagnac, France
                EFFCA - European Food and Fermentation Cultures Association, c/o Kellen, 188 Avenue de Tervueren, Brussels, Postbox 4, 1150 Brussels, Belgium
                Author notes
                Corresponding author. EFFCA - European Food and Fermentation Cultures Association, c/o Kellen, 188 Avenue de Tervueren, Brussels, Postbox 4, 1150 Brussels, Belgium. E-mail: jrusek@ 123456kellencompany.com
                Author information
                https://orcid.org/0009-0002-3946-4067
                https://orcid.org/0009-0009-5412-0722
                Article
                fnae010
                10.1093/femsle/fnae010
                10890814
                38323486
                959120d7-0cfe-44d4-9807-d0477e0f551d
                © The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 02 November 2023
                : 11 January 2024
                : 05 February 2024
                : 23 February 2024
                Page count
                Pages: 7
                Categories
                Minireview
                Food Microbiology
                AcademicSubjects/SCI01150

                Microbiology & Virology
                new genomic techniques,genome editing,gm regulatory framework,sustainability,nontransgenic,food cultures

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