Speaker
Description
Microbiomes, their composition and stability have been a topic of great interest in recent years as they turn out to influence human health much more than previously thought. However, the mechanisms determining microbiome health remain unclear. As microbiomes are complex, consisting of many species, attacking this problem through modelling is a challenge \cite{G18,K19}. Several unknown population dynamical parameters must be determined for every species, making accurate modelling a daunting task. We attempt to get around this issue by proposing a highly simplified model of microbiome assembly and stability. Instead of determining the full population dynamics using a typical, Lotka-Volterra-based modelling framework, we propose looking at species existence or absence as a binary variable. The interaction parameters between species we likewise model as binary relationships: bacterial species may produce or require a given nutrient, and they may each be in a commensal or antagonistic relationship with every other species. Pairs of antagonists are entirely unable to coexist. Despite these (over-)simplified assembly and coexistence rules, the model communities exhibit rich dynamics including multistability and mass-extinction events. We derive conditions for the establishment of a healthy, diverse microbiome and for its collapse. It is our hope that this model will present a new and useful approach to understanding how microbial communities assemble, remain stable, or break down.
Bibliography
@article{G18,
title = {Current understanding of the human microbiome},
volume = {24},
issn = {1078-8956, 1546-170X},
url = {https://www.nature.com/articles/nm.4517},
doi = {10.1038/nm.4517},
language = {en},
number = {4},
urldate = {2026-02-14},
journal = {Nature Medicine},
author = {Gilbert, Jack A and Blaser, Martin J and Caporaso, J Gregory and Jansson, Janet K and Lynch, Susan V and Knight, Rob},
month = apr,
year = {2018},
pages = {392--400},
}
@article{K19,
title = {Modelling approaches for studying the microbiome},
volume = {4},
issn = {2058-5276},
url = {https://www.nature.com/articles/s41564-019-0491-9},
doi = {10.1038/s41564-019-0491-9},
language = {en},
number = {8},
urldate = {2026-02-14},
journal = {Nature Microbiology},
author = {Kumar, Manish and Ji, Boyang and Zengler, Karsten and Nielsen, Jens},
month = jul,
year = {2019},
pages = {1253--1267},
}
