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Valorisation of the Nestlé Culture Collection: from gene to function

LABIP Expert Workshop

S. Duboux, Nestlé Research Center

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The Nestlé Culture CollectionThe Nestlé central repository of food grade bacteria

More than 3000 isolates

10.05.2017 S. Duboux, NRC2

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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

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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

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«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

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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.

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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

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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 ?

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«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

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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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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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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)

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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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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.

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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 ?