Phylogeny and ecosystem jointly shape metabolite sensing by structured noncoding RNAs

Non-coding RNAs (ncRNAs) regulate gene expression through diverse structural and sequence-based mechanisms, often acting without protein intermediates. Riboswitches are cis-regulatory ncRNAs that directly sense small molecule metabolites to control gene expression. Many riboswitches operate through kinetic control, meaning the rate at which a ligand binds to the aptamer domain determines whether gene expression is turned ON or OFF. Here, we present a comparative survey of riboswitch repertoires across eight microbiomes: human gut, oral, skin, vaginal, mouse gut, pig gut, sheep rumen, and marine environment, spanning 13,946 prokaryotic genomes. Using covariance models, we identified 86,485 riboswitches across 12,916 genomes (92.6%), representing 23 metabolite-sensing classes, with six dominant classes accounting for ~70% of all riboswitch hits. Riboswitch composition varied significantly across ecosystems, but variance partitioning showed this structure is driven primarily by phylogeny: phylum explained 25.5% of compositional variance, whereas the fraction uniquely attributable to ecosystem after conditioning on taxonomy, was only 2.2%. Overall riboswitch distributions reflect both phylogenetic and ecological influences, highlighting their role in shaping metabolite-responsive regulatory strategies across microbial life.