Valorisation of the Nestl Culture Collection: from gene to function - PowerPoint PPT Presentation

Valorisation of the Nestlé Culture Collection: from gene to function LABIP Expert Workshop S. Duboux, Nestlé Research Center CONFIDENTIAL CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

The Nestlé Culture Collection The Nestlé central repository of food grade bacteria More than 3000 isolates CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 2 10.05.2017 S. Duboux, NRC

Sequencing of the Nestlé Culture Collection A mixed technology approach 2 nd generation sequencing: Illumina 3r d generation sequencing: Pacific BioSciences 95 isolates Average of 3 Nature Reviews Microbiology 13, 787 – 794 (2015) contigs 2776 isolates Average of 98 contigs 10.05.2017 CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 3 S. Duboux, NRC

Exploring NCC using the «From gene to function» approach Genomic sequences obtained by Illumina & Genome storage, comparison & screening Assembly, gene prediction and functional annotation PacBio Identification using In silico assessment of Functional in silico screening: whole genome data genes & pathways virulence & antibiotic resistance Kanehisa et al. Nucleic Acids Res. 2012 Jan; 40 (Database issue): D109 – D114. Varghese et al. Nucleic Acids Research, 2015, Vol. 43, No. 14 6761 – 6771 Chen at al. Nucleic Acids Res. 2016 January 4; 44(Database issue): D694 – D697 CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 4 10.05.2017 S. Duboux, NRC

«From gene to function» proof of concept activities • 2776 proprietary NCC genomes (> 6 millions of genes) • 7261 public reference microorganisms (pro & eukaryotes) • All integrated in a centralized user friendly web-based software From gene to function Enzymes - Example 1: Novel glucanotransferase Enzymes Fermentation Probiotic converting starch into slowly digestible fibers CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 30.01.2017

A new class of α -glucanotransferase able to synthesize slowly digestible starch derivatives Glucansucrases (GSs) GtfB-like proteins GH70 GtfB Lactic acid bacteria Leemhuis et al. Appl Microbiol Biotechnol (2013) 97:181 – 193. Starch modifying enzymes GH13 Bacteria Archaea Eukaryotes CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 6 10.05.2017 S. Duboux, NRC

Natural GtfB variants in the Nestlé Culture Collection  106 genes encoding GtfB-like enzymes in NCC:  Most of them encoded by L. delbrueckii strains.  GtfB-like proteins were also found in L. fermentum , L. plantarum , L. reuteri, L. helveticus , L. sanfranciscensis and S. thermophilus strains  GtfB-like novel variant found in L. fermentum NCC 2970 Gangoiti et al. 2017, submitted CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 7 10.05.2017 S. Duboux, NRC

NCC 2970 GtfB produces a novel slowly digestible (α1→3) glucan Open questions • In vivo digestibility and impact on glycemic response ? • Applicability in product matrix ? • Impact on microbiome ? Gangoiti et al. Sci Rep. 2017 Jan 6;7:39761 CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 8 10.05.2017 S. Duboux, NRC

«From gene to function» proof of concept activities • 2776 proprietary NCC genomes (> 6 millions of genes) • 7261 public reference microorganisms (pro & eukaryotes) • All integrated in a centralized user friendly web-based software From gene to function Probiotic - Example 2: β -galactosidase producing Enzymes Fermentation Probiotic probiotics for lactose maldigestion CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 30.01.2017

Can probiotics compensate digestive enzyme defficiencies ? Lactase deficiency as a proof of concept Lactose maldigestion Normal lactose digestion (lactase deficiency) Misselwitz et al. United European Gastroenterol J. 2013 Jun;1(3):151-9 CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 10 10.05.2017 S. Duboux, NRC

β -galactosidase producing probiotics S. thermophilus vs B. longum Streptococcus thermophilus Bifidobacterium longum From Donaldson et al. 2016, Nature CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 11 10.05.2017 S. Duboux, NRC

β -galactosidase producing probiotics S. thermophilus significantly improved lactose digestion PoC clinical trial on 37 lactose maldigestor subjects Primary outcome: lactose maldigestion (exhaled hydrogen) Milk 18g lactose + B. longum Milk 18g lactose + S. thermophilus Milk 18g lactose Lactose free milk POS vs B. longum POS vs S. thermophilus POS vs NEG NEG vs B. longum NEG vs S. thermophilus B. longum vs S. thermophilus CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 12

Conclusion & outlook • “ F rom gene to function” approach proven to be powerful to valorize Nestlé Culture Collection for novel concepts around: • Enzymes • Fermentation processes • Probiotics • Further use of this platform to enhance nutritional values, optimize taste and texture, add functional benefits, and/or increase sustainability of our products. CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 13 10.05.2017 S. Duboux, NRC

Acknowledgments Nestlé Intitute of Health Sciences Institute of Materials Science Institute of Nutritional Science Clinical Development Unit Functional Genomics Enzymes Gut Ecosystem Rafael Crabbe Déborah Moine Yvette Fleury-Rey Annick Mercenier Emma Wynn Coralie Fournier Christina Vafeiadi Gabriela Bergonzelli Aude Chevalier Mohamed Kassam Jean-Luc Sauvageat Maurice Beaumont et al. Patrick Descombes Frederik Delodder Peter Sperisen Tech. Microbiology Dominik Grathwohl Aliénor Genevaz Antonio De Castro R&D Konolfingen Institute of Food Safety & Josette Sidoti Tung Nguyen Analytical Sciences Anne Bruttin Fermentation technology Christoph Bolten Biljana Bogicevic Applied Mathematics Guenolée Prioult Andreas Rytz Prototyping group Caroline Barretto Julia Tanguy Catherine Ngom-Bru Audrey Vissières François Rechenmann et al. Pierre-Alain Richon Anne-Catherine Portmann Lubbert Dijkhuisen et al. CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 14 10.05.2017 S. Duboux, NRC

How industry can embrace new technologies to improve genetic diversity of LABs Should industry first evaluate the full potential of natural diversity before/instead of “improving” it ? CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation 15 10.05.2017 S. Duboux, NRC