cMFA for multi-omics data integration in microbial
community models

Sthyve Junior Tatho Djeanou, Simon Labarthe, Valentina Baldazzi

► To cite this version:

Sthyve Junior Tatho Djeanou, Simon Labarthe, Valentina Baldazzi. cMFA for multi-omics data integration in microbial community models. Population Dynamics: From Data to Models 2025, Mar 2025, Sophia antipolis, France. hal-04996155

HAL Id: hal-04996155

https://inria.hal.science/hal-04996155v1

Submitted on 18 Mar 2025

**HAL** is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# cMFA for multi-omics data integration in microbial community models

**Sthyve Tatho, Simon Labarthe, Valentina Baldazzi**
# Biology-informed inference from multi-omics data

<figure><img src="image_2.png" /></figure>

## Context :

* Developing a mathematical inference method based on metabolic networks.

* Inferring metabolic fluxes by integrating multi-omics data.

## Objectives :

* Estimating the contribution of each microorganism to the community.

* Reconstruction internal fluxes of individual micro-organisms.
cMFA for community models

<figure><img src="image_3.png" /></figure>

Gerken Starepravo et al., Digit. Chem. Eng. (2022)

$$ \hat{v}(t) := \arg \min \sum_{m \in \mathcal{M}} \left\| \underbrace{R_{m,t}}_{\text{Data rate}} - \underbrace{\sum_{b \in \mathcal{B}_m} \chi_t^{(b)} \nu_{m,t}^{(b)}}_{\substack{\text{Model} \\ \text{Biomass}}} \right\|_2^2 + \underbrace{\lambda \mathcal{R}(\nu)}_{\text{Regularization term}} $$

$$ \text{biological information} \left\{ \begin{array}{l} \stackrel{\text{stoichiometry matrix}}{\overbrace{S^{(b)} \cdot \nu^{(b)} = 0,}} \\ C_{\text{min}}^{(b)} \le \nu^{(b)} \le C_{\text{max}}^{(b)}. \\ \underbrace{\text{Fluxes}} \end{array} \right. $$
Benchmark result for two-species communities

<figure><img src="image_4.png" /></figure>

Comparison of simulated dFBA vs cMFA for Multiple Organisms

<figure><img src="image_5.png" /></figure>

More on the poster