Abstract
Motivation The structure and function of diverse microbial communities is underpinned by ecological interactions that remain uncharacterized. With rapid adoption of metagenomic sequencing for studying microbiomes, data-driven inference of microbial interactions based on abundance correlations is widely used, but with the drawback that ecological interpretations may not be possible. Leveraging cross-sectional metagenomic datasets for unravelling ecological structure in a scalable manner thus remains an open problem.
Methods We present an expectation-maximization algorithm (BEEM-Static) that can be applied to cross-sectional datasets to infer interaction networks based on an ecological model (generalized Lotka-Volterra). The method exhibits robustness to violations in model assumptions by using statistical filters to identify and remove corresponding samples.
Results Benchmarking against 10 state-of-the-art correlation based methods showed that BEEM-Static can infer presence and directionality of ecological interactions even with relative abundance data (AUC-ROC>0.85), a task that other methods struggle with (AUC-ROC<0.63). In addition, BEEM-Static can tolerate a high fraction of samples (up to 40%) being not at steady state or coming from an alternate model. Applying BEEM-Static to a large public dataset of human gut microbiomes (n=4,617) identified multiple stable equilibria that better reflect ecological enterotypes with distinct carrying capacities and interactions for key species.
Conclusion BEEM-Static provides new opportunities for mining ecologically interpretable interactions and systems insights from the growing corpus of metagenomic data.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Chenhao Li: lich{at}gis.a-star.edu.sg, Tamar V. Av-Shalom: tamar.avshalom{at}mail.utoronto.ca, Jun Wei Gerald Tan: tanjunweigerald1997{at}gmail.com, Junmei Samantha Kwah: Samantha_Kwah{at}gis.a-star.edu.sg, Kern Rei Chng: CHNG_Kern_Rei{at}gis.a-star.edu.sg, Niranjan Nagarajan: nagarajann{at}gis.a-star.edu.sg