Valorisation of the Nestl Culture Collection: from gene to function - - PowerPoint PPT Presentation
Valorisation of the Nestl Culture Collection: from gene to function LABIP Expert Workshop S. Duboux, Nestl Research Center CONFIDENTIAL CONFIDENTIAL Proprietary information of Nestl S. A., Vevey, Switzerland This document should not
CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation
CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation
The Nestlé central repository of food grade bacteria
More than 3000 isolates
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A mixed technology approach
95 isolates Average of 3 contigs 2776 isolates Average of 98 contigs
2nd generation sequencing: Illumina 3rd generation sequencing: Pacific BioSciences
Nature Reviews Microbiology 13, 787–794 (2015)
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Genomic sequences
PacBio
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Genome storage, comparison & screening Assembly, gene prediction and functional annotation
In silico assessment of virulence & antibiotic resistance
Chen at al. Nucleic Acids Res. 2016 January 4; 44(Database issue): D694–D697
Identification using whole genome data
Varghese et al. Nucleic Acids Research, 2015, Vol. 43, No. 14 6761–6771 Kanehisa et al. Nucleic Acids Res. 2012 Jan; 40 (Database issue): D109–D114.
Functional in silico screening: genes & pathways
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Glucansucrases (GSs) Starch modifying enzymes Lactic acid bacteria Bacteria Archaea Eukaryotes
GtfB
Leemhuis et al. Appl Microbiol Biotechnol (2013) 97:181–193.
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106 genes encoding GtfB-like enzymes in NCC:
plantarum, L. reuteri, L. helveticus, L. sanfranciscensis and S. thermophilus strains
Gangoiti et al. 2017, submitted
GtfB-like novel variant found in L. fermentum NCC 2970
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Gangoiti et al. Sci Rep. 2017 Jan 6;7:39761
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Misselwitz et al. United European Gastroenterol J. 2013 Jun;1(3):151-9
Normal lactose digestion Lactose maldigestion (lactase deficiency)
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Streptococcus thermophilus Bifidobacterium longum
From Donaldson et al. 2016, Nature
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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
PoC clinical trial on 37 lactose maldigestor subjects Primary outcome: lactose maldigestion (exhaled hydrogen)
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Nestlé Intitute of Health Sciences Functional Genomics Déborah Moine Coralie Fournier Mohamed Kassam Patrick Descombes Peter Sperisen Institute of Food Safety & Analytical Sciences Applied Mathematics Andreas Rytz Caroline Barretto Catherine Ngom-Bru Anne-Catherine Portmann Institute of Materials Science Enzymes Yvette Fleury-Rey Christina Vafeiadi Jean-Luc Sauvageat
Aliénor Genevaz Josette Sidoti Anne Bruttin Christoph Bolten Prototyping group Julia Tanguy Audrey Vissières Pierre-Alain Richon R&D Konolfingen Fermentation technology Biljana Bogicevic Guenolée Prioult Institute of Nutritional Science Gut Ecosystem Annick Mercenier Gabriela Bergonzelli Clinical Development Unit Rafael Crabbe Emma Wynn Aude Chevalier Maurice Beaumont et al. Frederik Delodder Dominik Grathwohl Antonio De Castro Tung Nguyen François Rechenmann et al. Lubbert Dijkhuisen et al.
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