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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


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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

Valorisation of the Nestlé Culture Collection: from gene to function

LABIP Expert Workshop

  • S. Duboux, Nestlé Research Center
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CONFIDENTIAL 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

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  • S. Duboux, NRC

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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

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Sequencing of the Nestlé Culture Collection

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)

  • S. Duboux, NRC

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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

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Exploring NCC using the «From gene to function» approach

Genomic sequences

  • btained by Illumina &

PacBio

  • S. Duboux, NRC

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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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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

«From gene to function» proof of concept activities

30.01.2017

  • 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 Probiotic Fermentation Enzymes - Example 1: Novel glucanotransferase converting starch into slowly digestible fibers

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A new class of α-glucanotransferase able to synthesize slowly digestible starch derivatives

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  • S. Duboux, NRC

GH70 GH13

Glucansucrases (GSs) Starch modifying enzymes Lactic acid bacteria Bacteria Archaea Eukaryotes

GtfB

GtfB-like proteins

Leemhuis et al. Appl Microbiol Biotechnol (2013) 97:181–193.

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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

Natural GtfB variants in the Nestlé Culture Collection

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  • S. Duboux, NRC

 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

Gangoiti et al. 2017, submitted

 GtfB-like novel variant found in L. fermentum NCC 2970

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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

NCC 2970 GtfB produces a novel slowly digestible (α1→3) glucan

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  • S. Duboux, NRC

Gangoiti et al. Sci Rep. 2017 Jan 6;7:39761

Open questions

  • In vivo digestibility and impact on glycemic response ?
  • Applicability in product matrix ?
  • Impact on microbiome ?
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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

«From gene to function» proof of concept activities

30.01.2017

  • 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 Probiotic Fermentation Probiotic - Example 2: β-galactosidase producing probiotics for lactose maldigestion

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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

Can probiotics compensate digestive enzyme defficiencies ?

Lactase deficiency as a proof of concept

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  • S. Duboux, NRC

Misselwitz et al. United European Gastroenterol J. 2013 Jun;1(3):151-9

Normal lactose digestion Lactose maldigestion (lactase deficiency)

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β-galactosidase producing probiotics

  • S. thermophilus vs B. longum

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  • S. Duboux, NRC

Streptococcus thermophilus Bifidobacterium longum

From Donaldson et al. 2016, Nature

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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

β-galactosidase producing probiotics

  • S. thermophilus significantly improved lactose digestion

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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

  • B. longum vs S. thermophilus

PoC clinical trial on 37 lactose maldigestor subjects Primary outcome: lactose maldigestion (exhaled hydrogen)

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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

Conclusion & outlook

  • “From 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

  • ur products.

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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

Acknowledgments

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  • S. Duboux, NRC

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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

  • Tech. Microbiology

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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CONFIDENTIAL Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation

How industry can embrace new technologies to improve genetic diversity of LABs

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  • S. Duboux, NRC

Should industry first evaluate the full potential of natural diversity before/instead of “improving” it ?