Challenges in interpreting functional redundancy and quantifying functional selection in microbial communities.

Abstract

Microbiomes often show similar functional profiles despite highly variable taxonomic compositions, a phenomenon attributed to "functional redundancy" and presumed selection for functional traits. However, this link between functional variability and selection remains vaguely defined. We demonstrate that reduced functional variability can arise from statistical averaging when aggregating taxonomic abundances and does not necessarily imply selection. We introduce an empirical null model that accounts for this statistical averaging effect. Applying this model to microbial communities from bromeliad foliage, we find no evidence of functional selection. In contrast, soil and human gut communities grown in vitro exhibit selection for metabolic functions. We also find that correlations between functions and taxonomic abundances can produce misleading signals of selection. Using an extended null model, we show that apparent functional selection in Human Microbiome Project data is artifactual. Our framework clarifies the conditions under which functional selection can be meaningfully inferred from microbiome data.