Habitat Fluctuations Drive Species Covariation in the Human Microbiota

TL;DR

This study demonstrates that habitat fluctuations significantly influence species covariation in the human microbiota, with mathematical modeling revealing predictable abundance correlations driven by shared resources and phylogenetic relationships.

Contribution

The paper introduces a mathematical framework linking habitat variability to microbiota species covariation, highlighting the role of functional pathways and phylogenetic relatedness in abundance patterns.

Findings

Habitat fluctuations explain intra-bodysite species correlations.

Phylogenetically related species show positive abundance correlations.

Key metabolic and cell wall pathways underpin shared resource niches.

Abstract

Two species with similar resource requirements respond in a characteristic way to variations in their habitat -- their abundances rise and fall in concert. We use this idea to learn how bacterial populations in the microbiota respond to habitat conditions that vary from person-to-person across the human population. Our mathematical framework shows that habitat fluctuations are sufficient for explaining intra-bodysite correlations in relative species abundances from the Human Microbiome Project. We explicitly show that the relative abundances of phylogenetically related species are positively correlated and can be predicted from taxonomic relationships. We identify a small set of functional pathways related to metabolism and maintenance of the cell wall that form the basis of a common resource sharing niche space of the human microbiota.