Enterotype-like microbiome stratification as emergent structure in complex adaptive systems: A mathematical model

Abstract

AbstractBackgroundMetagenomics has provided valuable insight into human gut microbiome composition together with its structure and function. Studies suggest that the adult gut microbial community possess a certain amount of stability and resilience. The architecture of host-microbial symbiotic states suggested by microbiome clustering findings and co-occurrence functional networks might be involved in these properties. Models for understanding the underlying structure (including enterotypes) and derived properties are in demand by researchers.Principal findingsWe propose a simple random function system as a model approach of the adaption and self-organization of the microbiome space when fostering the optimal functioning of the system. The construction of this model is based on key facts of microbiota functioning reported in recent studies. We aim to demonstrate the existence of a probability distribution as a microbiome attractor resulting from an intermittent adaption process. Its mathematical structural properties explain the stability of gut microbiota and its ability for restoration after occasional perturbations. The model is consistent with microbiome clustering results and provides precise mathematical meaning to the gradient among enterotypes previously reported. The model also explains how intermittent perturbations, such as long-term dietary patterns, might affect the microbiome structure, and these results are consistent with previously reported experimental results.Conclusions/significanceThese mathematical facts implied by the model unveil an underlying mechanism that may explain gut microbiome structure and related experimental findings. Within this framework, stability and resilience properties of human gut microbiota are explained as a consequence of the model.