SubCom analysis: dissecting microbial community functions into taxon-specific contributions and interaction contexts.

Abstract

Background: Microbial communities play fundamental roles in industrial processes and ecosystem stability. However, understanding how individual members and their interactions give rise to community-level function remains challenging because such functions emerge from complex interactions among diverse members.

Results: In this study, we developed SubCom analysis, a subcommunity-based experimental-computational workflow for inferring candidate taxon-specific contributions and interaction contexts underlying microbial community function. Using an aniline-degrading microbial community, we generated paired composition-function data from 558 randomly assembled, low-complexity subcommunities constructed using a dilution-and-dispense strategy. We then trained decision-tree-based models to predict community function from composition, achieving high predictive performance (r = 0.77-0.89). Interpretation of the learned decision rules identified taxa with consistent functional association: specific Pseudomonas and Acinetobacter taxa were associated with increased community-level aniline utilization, whereas an Achromobacter taxon exhibited a negative association despite its presumed role in downstream metabolism. The models further suggested potential functional interactions, including attenuation of the positive contributions of Pseudomonas and Acinetobacter in the presence of a Corynebacterium taxon, highlighting functional relationships that are not readily inferred from genome-based approaches alone. An augmentation assay using representative isolates supported the predicted direction of several effects and enabled targeted improvement of community function.

Conclusions: These results demonstrate the potential of SubCom analysis as a practical framework for inferring taxon-specific contributions and interaction contexts in complex, nonsynthetic microbial communities. Video Abstract.