Strain-specific higher-order interactions break phylogenetic conservatism in microbial communities

Authors

Cordero-Martinez, E., Navarro-Miranda, M., Ramirez-Sanchez, O., Bustos-Diaz, E. D., Higareda-Alvear, V. M., Moreno-Hagelsieb, G., Rocha, J. G., Hernandez-Rosales, M., Olmedo-Alvarez, G.

Abstract

Whether strains of the same species sharing the same ecological role are truly interchangeable has not been directly tested experimentally in communities, where higher-order interactions govern outcomes. Using 79 co-occurring Bacillaceae isolates from the Cuatrocienegas Basin, we combined whole-genome analyses with systematic strain substitutions in BARS, a three-species community in which a resistant strain protects a sensitive strain from an antagonist. Trait conservatism strongly predicted pairwise antagonistic outcomes. Yet across 34 assembled triads, 13 showed rescue beyond pairwise expectations and five showed suppression; single-strain substitutions rarely restored protection, although protection was recovered in one fully reconfigured triad. These outcomes could not be inferred from taxonomic relatedness, pangenomic content or pairwise assays; phylogenetic conservatism thus reaches its limit at the transition from pairwise to higher-order interactions. To explain this limit, we propose that strains behave as non-equivalent biological tiles whose interaction edges must align, a dynamic biological tessellation.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 17 Oct 2026.

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