Abstract
The gut microbiome ecosystem is a significant driver of host health and disease. High-throughput Longitudinal studies have begun to unravel the complex dynamics of these ecosystems, and quantitative frameworks are now being developed to understand their organizing principles. Dimensionality reduction offers unique insights into gut bacterial dynamics by leveraging collective abundance fluctuations of multiple bacteria across multiple subjects driven by similar underlying ecological factors. However, methods providing lower-dimensional representations of gut microbial dynamics both at the community and individual taxa level are currently missing. To that end, we develop EMBED: Essential Microbiome Dynamics. Similar to normal modes in structural biology, EMBED infers ecological normal modes (ECNs), which represent the unique set of orthogonal dynamical trajectories capturing the collective behavior of microbial communities across subjects. We show that a small number of ECNs accurately describe gut microbiome dynamics across multiple data sets. Importantly, we find that ECNs reflect specific ecological behaviors, providing natural templates along which the dynamics of individual bacteria may be partitioned. Moreover, the multi-subject treatment in EMBED systematically identifies subject-specific and universal dynamical processes. Collectively, our results highlight the utility of dimensionality reduction approaches to understanding the dynamics of the gut microbiome and provide a framework to study the dynamics of other high-dimensional systems as well.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
We extended the analysis to subject-specific variability in the microbiome
