Brayon Fremin

The authors have declared no competing interest. Data availability Raw data used for this study are available at https://portal.nersc.gov/dna/microbial/prokpubs/spacer_database_resources/, and from NCBI SRA using accession numbers listed in the file “ Supplementary_Data_File_2_samples.tsv”. Access to the spacer database including spacer information and spacer hits against IMG/VR and IMG/PR is documented at https://spacers.jgi.doe.gov.

Abstract Background Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RNA motifs primarily due to computational limitations.