# Modeling Microbial Communities: Toward Digital Twins

Simon Labarthe

► To cite this version:

Simon Labarthe. Modeling Microbial Communities: Toward Digital Twins. Microbes 2025 - 20e congrès national de la SFM "Microbes dans un monde de transition", SFM, Sep 2025, Bordeaux, France. hal-05459251

HAL Id: hal-05459251

https://hal.inrae.fr/hal-05459251v1

Submitted on 15 Jan 2026

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Distributed under a Creative Commons CC BY 4.0 - Attribution - International License
> Modeling Microbial Communities:
Toward Digital Twins

Simon Labarthe

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Univ. Bordeaux, INRAE, BIOGECO

Univ. Bordeaux, Inria-Inrae, Pléiade

simon.labarthe@inrae.fr

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slabarthe@mathstodon.xyz

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simon-labarthe-0302a435

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# Model-guided microbial community steering

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# Model-guided microbial community steering

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Digital twin ?
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**Digital twin**

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**Microbial
system**
$$y = f_i(t, s | \theta)$$

instanciation

$i = k$

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$$y = f_k(t, s | \theta)$$

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**Digital twin**

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**Microbial**
**system**

in line
control

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Biotech
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# Digital Twin: boosting interdisciplinarity

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# Digital Twin: boosting interdisciplinarity

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# Digital Twin: boosting interdisciplinarity

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Research object

p. 14
# Digital Twin: boosting interdisciplinarity

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SynCom growth experiments

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Sthyve Tatho
PhD Mistic

Goal : metabolism-informed inference

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Inference

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metabolic model

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multi-omics

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individual
contributions,
trophic interactions

Individual
metabolism
Residuals

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$$ \hat{\nu}(t) := \arg \min_{\nu_t} \sum_{m \in \mathcal{M}} \| R_{m,t} - \sum_{b \in \mathcal{B}_m} \chi_t^{(b)} \nu_{m,t}^{(b)} \|_2^2 + \lambda \mathcal{R}(\nu) $$

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Regularization

Metatranscp.

Subject to

$$ S^b \nu_{m,t}^{(b)} = 0 $$

$$ C_{min} \leq \nu_{m,t}^{(b)} \leq C_{max} $$

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Metabolic constraints

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Competition

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Co-production

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Cross-feeding

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# Digital Twin: boosting interdisciplinarity

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# Speeding-up metabolic prediction with surrogate FBA

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<figure><img src="image_50.png" /><figcaption>C.Frioux</figcaption></figure>

<figure><img src="image_51.png" /><figcaption>P.Ugalde</figcaption></figure>

<figure><img src="image_52.png" /><figcaption>C.Muller</figcaption></figure>

<figure><img src="image_53.png" /><figcaption>Aex Slimmest</figcaption></figure>

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# Toy model: Salmonella infection

a. Luminal Compartment

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c. Luminal Compartment: reduced molecules

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b. Luminal Compartment

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<figure><img src="image_58.png" /><figcaption>C.Frioux</figcaption></figure>

<figure><img src="image_59.png" /><figcaption>P.Ugalde</figcaption></figure>

<figure><img src="image_60.png" /><figcaption>C.Muller</figcaption></figure>

<figure><img src="image_61.png" /><figcaption>Aex Slimmest</figcaption></figure>

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INRAO

Modelling the metabolism of microbial communities with numerical models

18/03/2025, S.Labarthe, Pléiade (INRAe, Inria).

Frioux et al., ESAIM PROC, 2023

https://doi.org/10.1051/proc/202373187
# Toy model: Salmonella infection

a. Luminal Compartment

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c. Luminal Compartment: reduced molecules

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b. Luminal Compartment

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Good approximation

Speed-up = 50 times faster

<figure><img src="image_67.png" /><figcaption>P.Ugalde</figcaption></figure>

<figure><img src="image_68.png" /><figcaption>C.Muller</figcaption></figure>

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Aex Slimmest

Inria

<figure><img src="image_70.png" /></figure>

INRAO

Modelling the metabolism of microbial communities with numerical models

18/03/2025, S.Labarthe, Pléiade (INRAe, Inria).

Frioux et al., ESAIM PROC, 2023

https://doi.org/10.1051/proc/202373187
# Conclusion

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Digital twins can foster interdisciplinary science

Science fronts all along the pipeline

Increase accuracy, increase speed

ML for data integration & surrogate models

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2 postdoc positions
in Mistic project

https://jobs.inrae.fr/

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