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ribosomal operon sequencing

Studies of bacterial microbiota using short read sequencing (V1–V6 variable regions of the 16S rRNA gene) report identifications at the genus through phylum level.  Long read sequencing (Oxford Nanopore MinION, PacBio SMRT) of near full-length ribosomal operons provides robust, strain-level identification for complex natural samples.

Below is a link to a database of bacterial ribosomal operons spanning the small subunit (16S) to the large subunit (23S) and everything between including the internal transcribed spacer region and associated tRNAs (such as tRNA-Ile, tRNA-Ala).  This database was extracted from prokaryotic genome sequences in RefSeq at NCBI. The result is over 300,000 rRNA operons for your strain-level tastes!

The rRNA Operon Database was created by a collaboration between the following associations:


Department of Marine & Coastal Sciences, Rutgers–the State University of New Jersey in New Brunswick, NJ


U.S. Army Combat Capabilities Development Command - Chemical Biological Center, Aberdeen Proving Ground, MD


Department of Biochemistry & Microbiology, Rutgers–the State University of New Jersey in New Brunswick, NJ

Australian Institute of Marine Sciences, Queensland, Australia

U.S. Deptartment of Agriculture-Agricultural Research Services, Genetic Improvement for Fruits & Vegetables Laboratory, Chatsworth, NJ 

The Joint Program Executive Office for Chemical Biological Nuclear & Radiological Defense, Aberdeen Proving Ground, MD

To download a zip-compressed file of the ribosomal operon database in fasta formatting, click on the link below:

     rOPBD zip file

If you wish to receive notifications when the ribosomal operon database is updated, please fill out the subscription form below.

We will send you a confirmatory e-mail of your rOPDB registration and database update notifications as they occur.  Please note: the confirmatory response may end up in your junk mailbox so check there within 24 h if you do not see an e-mail from us.

Thanks for your interest!
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