# Next-gen fermented food: Harnessing gut microbiome diversity and functions

Julien Tap, Vincent Hervé, Sophie Landaud, Dalal Werner, Marie-Helene Desmonts, Stéphane Chaillou

► To cite this version:

Julien Tap, Vincent Hervé, Sophie Landaud, Dalal Werner, Marie-Helene Desmonts, et al. Next-gen fermented food: Harnessing gut microbiome diversity and functions. Metabolomics & Fermented Foods, Netherlands Metabolomics Centre, Feb 2024, Utrecht, Netherlands. hal-04489205

HAL Id: hal-04489205

https://hal.inrae.fr/hal-04489205

Submitted on 4 Mar 2024

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> Next-gen fermented food: Harnessing gut microbiome diversity and functions.

Julien Tap

INRAE MICALIS

NMC Utrecht 2024

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> Different factors shapes the human gut microbiome

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> Diet and lifestyle effect host microbiome symbiosis

Are we uncoupling our
metagenome and our
genome?

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> Gut microbiome throughout life span

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Micobiota
Abundance &
diversity

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Factors
Influencing
the microbiota

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> Microbiome states resilience as key factor

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Healthy state

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Resistance

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Recovery

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Resilience

Healthy state

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Degraded state
> Several attempts to decipher the gut microbiome structure

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Arumugam, Raes et al (2010)

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Costea et al (2017)

Dirichlet Multinomial Mixture (DMM) modeling

Limits:

Few association with diet

Few stability assessment (e.g. with time-series)

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> 35,000 human gut microbiome samples analyzed

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New computational method that help observe **global and local structure** at the same time

Time-series analysis to detect microbiome states

Region of birth, Lifestyle, diet, and health modelization

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> Human Gut microbiome structured as branches

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« Healthy index »

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Alpha-diversity

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« Aerobiosis »
> Low-diversity tips of branches display functional shifts

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amino acid catabolism increase
in *Bacteroides* branch tip

oxidative stress response increase
in *Prevotella* branch tip
> Altered states showed functional differences within species

400 B. bifidum MAGS
phylogenomics

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*Bifidobacterium bifidum* strains may be enriched in phage-related genes in subjects with altered gut microbiomes states
> Dynamics between partitions are associated to branches

827 participants

2,998 samples

2,171 time-pairs

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c

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d

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e

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f

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Faecalibacterium/Bacteroides as a tipping element
explaining the switch between some states
> Gut microbiome alternative stable states hypothesis

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> Branches help to monitor gut microbiome recovery

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AMERICAN
GUT PROJECT

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<figure><img src="image_39.png" /><figcaption>> Gut microbiome states are differentially associated with host and env factors</figcaption></figure>

Sex, exercises frequency and **region of birth** associated differentially between branches

Lifestyle and hygiene associated with altered state within *Bacteroides* branch

Specialized diet associated with altered state within *Prevotella* branch
> Do we already observe a intergenerationally mass extinction ?

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> Harnessing the microbial potential of fermented foods to avoid the point of no return

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> Food microbiome engraftment is gut microbiome baseline dependent

Modular coalescence between gut and biotics species

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"Engraftment" as function of existing niche and metabolic pathway

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> Food microbiome clinical effect is gut microbiome baseline dependent

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flatulogenic diet (61% carbohydrates, 25% proteins and 14% fat, 27 g of fiber per day)

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After FMP consumption, FMP active strains detected by metatranscriptomics

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c

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After FMP intake (TP5), higher responder group showed higher methanogenesis activity than low-responders
> From gut microbiome states to next-gen fermented foods design

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INRAE

Utrecht 2024

29.02.24 / Julien Tap / fme.micalis.fr

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Prevent gut microbiome critical transition to strengthen its resilience using next-gen fermented foods

Trends in Microbiology
> Towards selecting strains with abilities to prevent tipping point in gut microbiota

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Increase of peptidoglycan levels for cell wall formation *F.prau*

Lebas, Derrien and colleagues (2020)

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> Fermented food microbiome is shaped by deterministic dynamic processes

N = 4973 samples

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Food categories

Kimchi dynamics

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days

Junker et al. Biorxiv (2024)

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> Plant-based matrices metabolome matters

<figure><img src="image_57.png" /><figcaption>Unfermented plant-based
NMR profiles</figcaption></figure>

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cabbage

turnip

carrot

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SayFood
Food & Bioproduct Engineering

Vincent Hervé

Aerial
> Fermented plant-based food metabolome converge despite different synthetic consortia inoculation

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Hexanal
Pentanal

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3 different
synthetic consortia

Acetate

Esters

Volatile Sulfur Compounds

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> Take home messages

* Gut microbiome ecological landscape is made of **local states** that are dynamically linked within **"branches"** where **critical transition** occurred

* Fermented food can help but **effects may be personalized** thank to gut **microbiota states at baseline**

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* Prototyping next-gen fermented food should include **gut tipping elements** and **food matrix metabolites** during screening for better **personalized and beneficial effects**.

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> Acknowledgments

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UC San Diego

Rob Knight's lab
Daniel McDonald
Franck Lejzerowicz
...

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Vall d'Hebron
Institut de Recerca

Chays Mannichanh
Fernando Azpiroz
Iñigo Oyarzun
...

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INRAO

Utrecht 2024

29.02.24 / Julien Tap / fme.micalis.fr

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DANONE
NUTRICIA
RESEARCH

Muriel Derrien
Patrick Veiga
Boris Le Nevé
...

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Vincent Hervé
Sophie Landaud
...

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Aerial

Dalal Werner
Marie Hélène Desmonts
...

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Food Microbial Ecology Lab

≡

Food Microbial Ecology lab

INRAE | Micalis institute | Université Paris
Saclay

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Join us

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Marie-Christine Champomier-Vergès
Stéphane Chaillou
...