# Metabolite mediated modeling of microbial community dynamics captures emergent behavior more effectively than species-species modeling

## TL;DR

This study demonstrates that modeling microbial communities through species-metabolite interactions more accurately captures emergent behaviors than direct species-species models, improving predictions of community dynamics.

## Contribution

It introduces and validates species-metabolite interaction models as superior to species-species models for predicting microbial community behavior.

## Key findings

- Species-metabolite models better predict community growth outcomes.
- Species-species models cannot capture complex community dynamics.
- Species-metabolite models explain diverse interdependent growth patterns.

## Abstract

Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We seek a modeling strategy that can capture emergent behavior when built from sets of universal individual interactions. Our investigation reveals that species-metabolite interaction modeling is better able to capture emergent behavior in community composition dynamics than direct species-species modeling. Using publicly available data, we examine the ability of species-species models and species-metabolite models to predict trio growth experiments from the outcomes of pair growth experiments. We compare quadratic species-species interaction models and quadratic species-metabolite interaction models, and conclude that only species-metabolite models have the necessary complexity to to explain a wide variety of interdependent growth outcomes. We also show that general species-species interaction models cannot match patterns observed in community growth dynamics, whereas species-metabolite models can. We conclude that species-metabolite modeling will be important in the development of accurate, clinically useful models of microbial communities.