Multiple stable states in microbial communities explained by the stable marriage problem

TL;DR

This paper introduces a novel model based on the stable marriage problem to predict multiple stable states and transitions in microbial communities, using nutrient preferences and competitive abilities to understand coexistence and resilience.

Contribution

The authors develop a new conceptual model that predicts stable states and transitions in microbial communities using only nutrient preference and competitive ability rankings.

Findings

The model predicts all possible stable states of microbial communities.

Mutual complementarity in nutrient preferences promotes coexistence.

The approach can forecast community shifts due to nutrient or microbe changes.

Abstract

Experimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics and diet shifts, result in transitions to other states. Can we reliably both predict such stable states as well as direct and control transitions between them? Here we present a new conceptual model inspired by the stable marriage problem in game theory and economics in which microbial communities naturally exhibit multiple stable states, each state with a different species' abundance profile. Our model's core ingredient is that microbes utilize nutrients one at a time while competing with each other. Using only two ranked tables, one with microbes' nutrient preferences and one with their competitive abilities, we can determine all possible stable states as well as predict inter-state transitions, triggered by the removal or addition of a specific nutrient or microbe. Further, using an example of 7 Bacteroides species common to the human gut utilizing 9 polysaccharides, we predict that mutual complementarity in nutrient preferences enables these species to coexist at high abundances.