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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
CONFIDENTIAL
Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation
The Nestlé Culture CollectionThe Nestlé central repository of food grade bacteria
More than 3000 isolates
10.05.2017 S. Duboux, NRC2
CONFIDENTIAL
Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation
10.05.2017
Sequencing of the Nestlé Culture CollectionA 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, NRC3
CONFIDENTIAL
Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation10.05.2017
Exploring NCC using the «From gene to function» approach
Genomic sequences
obtained by Illumina &
PacBio
S. Duboux, NRC4
Genome storage, comparison & screeningAssembly, 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
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 geneto function
Enzymes ProbioticFermentation
Enzymes - Example 1:
Novel glucanotransferase
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
A new class of α-glucanotransferase able to synthesize slowly digestible starch derivatives
10.05.20176 S. Duboux, NRC
GH70
GH13
Glucansucrases
(GSs)
Starch modifying
enzymes
Lactic acid bacteria
BacteriaArchaeaEukaryotes
GtfB
GtfB-like
proteins
Leemhuis et al. Appl Microbiol Biotechnol (2013) 97:181–193.
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
10.05.20177 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
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
10.05.20178 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 ?
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 geneto function
Enzymes ProbioticFermentation
Probiotic - Example 2:
β-galactosidase producing
probiotics for lactose
maldigestion
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
10.05.201710 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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Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation
β-galactosidase producing probioticsS. thermophilus vs B. longum
10.05.201711 S. Duboux, NRC
Streptococcus thermophilus Bifidobacterium longum
From Donaldson et al. 2016, Nature
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Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation
β-galactosidase producing probioticsS. thermophilus significantly improved lactose digestion
12
Milk 18g lactose + B. longum
Milk 18g lactose + S. thermophilus
Milk 18g lactose
Lactose free milk
POS vs B. longumPOS vs S. thermophilus
POS vs NEGNEG vs B. longum
NEG vs S. thermophilusB. longum vs S. thermophilus
PoC clinical trial on 37 lactose maldigestor subjects
Primary outcome: lactose maldigestion (exhaled hydrogen)
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
our products.
10.05.201713 S. Duboux, NRC
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Proprietary information of Nestlé S. A., Vevey, Switzerland – This document should not be reproduced or disclosed without prior authorisation
Acknowledgments
10.05.2017 S. Duboux, NRC14
Nestlé Intitute of Health Sciences
Functional GenomicsDéborah MoineCoralie FournierMohamed KassamPatrick DescombesPeter Sperisen
Institute of Food Safety & Analytical Sciences
Applied MathematicsAndreas RytzCaroline BarrettoCatherine Ngom-BruAnne-Catherine Portmann
Institute of Materials Science
EnzymesYvette Fleury-ReyChristina VafeiadiJean-Luc Sauvageat
Tech. MicrobiologyAliénor GenevazJosette Sidoti
Anne BruttinChristoph Bolten
Prototyping groupJulia TanguyAudrey VissièresPierre-Alain Richon
R&D Konolfingen
Fermentation technologyBiljana BogicevicGuenolée Prioult
Institute of Nutritional Science
Gut EcosystemAnnick MercenierGabriela Bergonzelli
Clinical Development Unit
Rafael CrabbeEmma WynnAude ChevalierMaurice Beaumont et al.Frederik DelodderDominik GrathwohlAntonio De CastroTung Nguyen
François Rechenmann et al.
Lubbert Dijkhuisen et al.
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
10.05.201715 S. Duboux, NRC
Should industry first evaluate the full potential of natural diversity
before/instead of “improving” it ?