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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\u2009946 prokaryotic genomes. Using covariance models, we identified 86\u2009485 riboswitches across 12\u2009916 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.<\/jats:p>","DOI":"10.1139\/gen-2026-0048","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T21:37:05Z","timestamp":1790631425000},"page":"1-17","update-policy":"https:\/\/doi.org\/10.1139\/csp-crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Phylogeny and ecosystem jointly shape metabolite sensing by structured noncoding RNAs"],"prefix":"10.1139","volume":"69","author":[{"given":"Senthilkumar","family":"Kailasam","sequence":"first","affiliation":[{"name":"McGill University","place":["Montreal, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1727-9269","authenticated-orcid":false,"given":"Rashmi","family":"Panigrahi","sequence":"additional","affiliation":[{"name":"Memorial University of Newfoundland","place":["St. John\u2019s, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"155","reference":[{"key":"refg1\/ref1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0603-3"},{"key":"refg2\/ref2","doi-asserted-by":"publisher","DOI":"10.4161\/rna.8.1.13864"},{"key":"refg3\/ref3","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1111\/j.1442-9993.2001.01070.pp.x","volume":"26","author":"Anderson M.J.","year":"2001","journal-title":"Austral. 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