{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T00:38:24Z","timestamp":1792802304300,"version":"4.5.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008972","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,6,2]],"date-time":"2021-06-02T00:00:00Z","timestamp":1622592000000}}],"reference-count":83,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2021,5,7]],"date-time":"2021-05-07T00:00:00Z","timestamp":1620345600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ENIGMA"},{"name":"ENIGMA"},{"name":"ENIGMA"},{"DOI":"10.13039\/100015911","name":"Joint Genome Institute","doi-asserted-by":"crossref","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100015911","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100017223","name":"National Energy Research Scientific Computing Center","doi-asserted-by":"crossref","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100017223","id-type":"DOI","asserted-by":"crossref"}]},{"name":"U.S. Department of Energy Office of Science User Facilities","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"https:\/\/ror.org\/01bj3aw27","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/lmlui\/Jorg\" xlink:type=\"simple\">https:\/\/github.com\/lmlui\/Jorg<\/jats:ext-link>\n                    and is available on the DOE Systems Biology KnowledgeBase as a beta app.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1008972","type":"journal-article","created":{"date-parts":[[2021,5,7]],"date-time":"2021-05-07T15:25:27Z","timestamp":1620401127000},"page":"e1008972","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":38,"title":["A method for achieving complete microbial genomes and improving bins from metagenomics data"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8720-5268","authenticated-orcid":true,"given":"Lauren 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J."},{"key":"pcbi.1008972.ref002","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1038\/nmeth.4458","article-title":"Critical Assessment of Metagenome Interpretation\u2014A benchmark of metagenomics software","volume":"14","author":"A Sczyrba","year":"2017","journal-title":"Nat Methods."},{"key":"pcbi.1008972.ref003","first-page":"126","article-title":"A history of DNA sequence assembly","volume":"58","author":"EW Myers","year":"2016","journal-title":"it\u2014Inf Technol"},{"key":"pcbi.1008972.ref004","doi-asserted-by":"crossref","first-page":"e0169662","DOI":"10.1371\/journal.pone.0169662","article-title":"Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist\u2019s Perspective\u2014Not Only Size Matters!","volume":"12","author":"J Vollmers","year":"2017","journal-title":"PLoS One"},{"key":"pcbi.1008972.ref005","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1093\/bib\/bbz020","article-title":"New approaches for metagenome assembly with short reads","volume":"21","author":"M Ayling","year":"2020","journal-title":"Brief Bioinform"},{"key":"pcbi.1008972.ref006","doi-asserted-by":"crossref","first-page":"2196","DOI":"10.1126\/science.287.5461.2196","article-title":"A whole-genome assembly of Drosophila","volume":"287","author":"EW Myers","year":"2000","journal-title":"Science (80-)."},{"key":"pcbi.1008972.ref007","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1101\/gr.126953.111","article-title":"Efficient de novo assembly of large genomes using compressed data structures","volume":"22","author":"JT Simpson","year":"2012","journal-title":"Genome Res"},{"key":"pcbi.1008972.ref008","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1101\/gr.1917404","article-title":"Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs","volume":"14","author":"B Chevreux","year":"2004","journal-title":"Genome 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Nicholls","year":"2019","journal-title":"Gigascience"},{"key":"pcbi.1008972.ref012","doi-asserted-by":"crossref","first-page":"3673","DOI":"10.1093\/nar\/8.16.3673","article-title":"A new computer method for the storage and manipulation of DNA gel reading data","volume":"8","author":"R Staden","year":"1980","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008972.ref013","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1111\/j.1462-2920.2004.00624.x","article-title":"Application of tetranucleotide frequencies for the assignment of genomic fragments","volume":"6","author":"H Teeling","year":"2004","journal-title":"Environ Microbiol"},{"key":"pcbi.1008972.ref014","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1126\/science.aac4812","article-title":"Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples","volume":"349","author":"T Korem","year":"2015","journal-title":"Science (80-)."},{"key":"pcbi.1008972.ref015","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2018.00711","article-title":"Background adjusted alignment-free dissimilarity measures improve the detection of horizontal gene transfer","volume":"9","author":"K Tang","year":"2018","journal-title":"Front Microbiol"},{"key":"pcbi.1008972.ref016","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","author":"DH Parks","year":"2017","journal-title":"Nat Microbiol"},{"key":"pcbi.1008972.ref017","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"DH Parks","year":"2015","journal-title":"Genome 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Bacteria","volume":"523","author":"CT Brown","year":"2015","journal-title":"Nature"},{"key":"pcbi.1008972.ref022","doi-asserted-by":"crossref","DOI":"10.3390\/microorganisms8030320","article-title":"Complete genome of a member of a new bacterial lineage in the microgenomates group reveals an unusual nucleotide composition disparity between two strands of dna and limited metabolic potential","volume":"8","author":"V V Kadnikov","year":"2020","journal-title":"Microorganisms"},{"key":"pcbi.1008972.ref023","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/nbt.2579","article-title":"Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes","volume":"31","author":"M Albertsen","year":"2013","journal-title":"Nat Biotechnol"},{"key":"pcbi.1008972.ref024","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s40168-018-0499-z","article-title":"Stable isotope informed genome-resolved metagenomics reveals that 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Nelson","year":"2020","journal-title":"PLoS One"},{"key":"pcbi.1008972.ref038","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1016\/j.scitotenv.2018.05.256","article-title":"Multi \u2018omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone","volume":"642","author":"EB Graham","year":"2018","journal-title":"Sci Total Environ"},{"key":"pcbi.1008972.ref039","doi-asserted-by":"crossref","first-page":"3188","DOI":"10.1002\/2017JG003967","article-title":"Carbon Inputs From Riparian Vegetation Limit Oxidation of Physically Bound Organic Carbon Via Biochemical and Thermodynamic Processes","volume":"122","author":"EB Graham","year":"2017","journal-title":"J Geophys Res Biogeosciences"},{"key":"pcbi.1008972.ref040","doi-asserted-by":"crossref","first-page":"2106","DOI":"10.1038\/ismej.2016.25","article-title":"Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer","volume":"10","author":"TNM Jewell","year":"2016","journal-title":"ISME J"},{"key":"pcbi.1008972.ref041","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1038\/s41564-017-0098-y","article-title":"Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface","volume":"3","author":"AJ Probst","year":"2018","journal-title":"Nat Microbiol"},{"key":"pcbi.1008972.ref042","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1038\/ismej.2017.94","article-title":"Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community","volume":"11","author":"L Momper","year":"2017","journal-title":"ISME J."},{"key":"pcbi.1008972.ref043","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"pcbi.1008972.ref044","article-title":"MetaSPAdes: A new versatile metagenomic assembler","author":"S Nurk","year":"2017","journal-title":"Genome Res"},{"key":"pcbi.1008972.ref045","doi-asserted-by":"crossref","first-page":"e7359","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"2019","author":"DD Kang","year":"2019","journal-title":"PeerJ"},{"key":"pcbi.1008972.ref046","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database","volume":"36","author":"P-A Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"pcbi.1008972.ref047","doi-asserted-by":"crossref","first-page":"e129","DOI":"10.1093\/nar\/gkt371","article-title":"Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach","volume":"41","author":"C Hahn","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008972.ref048","doi-asserted-by":"crossref","first-page":"1699","DOI":"10.1093\/bioinformatics\/btq268","article-title":"Gap5\u2014editing the billion fragment sequence assembly","volume":"26","author":"JK Bonfield","year":"2010","journal-title":"Bioinformatics"},{"key":"pcbi.1008972.ref049","first-page":"133","volume-title":"Genome walkingCereal Genomics Methods in Molecular Biology (Methods and Protocols).","author":"FM Shapter","year":"2014"},{"key":"pcbi.1008972.ref050","doi-asserted-by":"crossref","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement.","volume":"9","author":"BJ Walker","year":"2014","journal-title":"PLoS One"},{"key":"pcbi.1008972.ref051","article-title":"GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes","author":"A Orakov","year":"2020","journal-title":"bioRxiv."},{"key":"pcbi.1008972.ref052","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0","volume":"59","author":"S Guindon","year":"2010","journal-title":"Syst Biol"},{"key":"pcbi.1008972.ref053","doi-asserted-by":"crossref","first-page":"W232","DOI":"10.1093\/nar\/gkw256","article-title":"W-IQ-TREE: A Fast Online Phylogenetic Tool for Maximum Likelihood Analysis\u2014PubMed","volume":"44","author":"J Trifinopoulos","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008972.ref054","article-title":"Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.","author":"RR Wick","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1008972.ref055","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1139\/o95-086","article-title":"Genomic evolution drives the evolution of the translation system","volume":"73","author":"SG Andersson","year":"1995","journal-title":"Biochem cell Biol"},{"key":"pcbi.1008972.ref056","first-page":"217","volume-title":"Archaea","author":"P Londei","year":"2007"},{"key":"pcbi.1008972.ref057","doi-asserted-by":"crossref","first-page":"2876","DOI":"10.1128\/jb.171.5.2876-2878.1989","article-title":"Novel arrangement of rRNA genes in Mycoplasma gallisepticum: Separation of the 16S gene of one set from the 23S and 5S genes","volume":"171","author":"X Chen","year":"1989","journal-title":"J Bacteriol"},{"key":"pcbi.1008972.ref058","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1099\/00222615-48-1-59","article-title":"Isolation of Borrelia burgdorferi from ticks in the Highlands of Scotland","volume":"48","author":"MM Davidson","year":"1999","journal-title":"J Med Microbiol"},{"key":"pcbi.1008972.ref059","doi-asserted-by":"crossref","first-page":"1883","DOI":"10.1073\/pnas.0604851104","article-title":"Genome dynamics in a natural archaeal population","volume":"104","author":"EE Allen","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1008972.ref060","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/0378-1119(94)00910-K","article-title":"Characterization of a putative 23S-5S rRNA operon of buchnera aphidicola (endosymbiont of aphids) unlinked to the 16S rRNA-encoding gene","volume":"155","author":"D Rouhbakhsh","year":"1995","journal-title":"Gene"},{"key":"pcbi.1008972.ref061","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/0378-1119(95)00539-I","article-title":"Characterization of the unlinked 16S rDNA and 23S-5S rRNA operon of Wolbachia pipientis, a prokaryotic parasite of insect gonads","volume":"165","author":"N Bensaadi-Merchermek","year":"1995","journal-title":"Gene"},{"key":"pcbi.1008972.ref062","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1038\/s41396-019-0552-3","article-title":"Unlinked rRNA genes are widespread among bacteria and archaea","volume":"14","author":"TE Brewer","year":"2020","journal-title":"ISME J."},{"key":"pcbi.1008972.ref063","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","article-title":"Infernal 1.1: 100-fold faster RNA homology searches","volume":"29","author":"EP Nawrocki","year":"2013","journal-title":"Bioinformatics"},{"key":"pcbi.1008972.ref064","first-page":"452","article-title":"Mycoplasma fermentans simplifies our view of the catalytic core of ribonuclease P RNA","volume":"2","author":"RW Siegel","year":"1996","journal-title":"RNA"},{"key":"pcbi.1008972.ref065","doi-asserted-by":"crossref","first-page":"22493","DOI":"10.1073\/pnas.1013969107","article-title":"Discovery of a minimal form of RNase P in Pyrobaculum","volume":"107","author":"LB Lai","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1008972.ref066","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/S0168-6445(99)00014-5","article-title":"Ribonuclease P: the diversity of a ubiquitous RNA processing enzyme","volume":"23","author":"A Sch\u00f6n","year":"1999","journal-title":"FEMS Microbiol Rev"},{"key":"pcbi.1008972.ref067","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1093\/bioinformatics\/btp250","article-title":"VARNA: Interactive drawing and editing of the RNA secondary structure","volume":"25","author":"K Darty","year":"2009","journal-title":"Bioinformatics"},{"key":"pcbi.1008972.ref068","doi-asserted-by":"crossref","first-page":"11063","DOI":"10.1073\/pnas.1106501108","article-title":"Multiplexed RNA structure characterization with selective 2\u2019-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).","volume":"108","author":"JB Lucks","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1008972.ref069","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/s41586-020-2007-4","article-title":"Clades of huge phages from across Earth\u2019s ecosystems","volume":"578","author":"B Al-Shayeb","year":"2020","journal-title":"Nature"},{"key":"pcbi.1008972.ref070","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1101\/gr.241299.118","article-title":"Plasmid detection and assembly in genomic and metagenomic data sets","volume":"29","author":"D Antipov","year":"2019","journal-title":"Genome Res"},{"key":"pcbi.1008972.ref071","article-title":"VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences","author":"K Kieft","year":"2020","journal-title":"Microbiome"},{"key":"pcbi.1008972.ref072","article-title":"SCAPP: An algorithm for improved plasmid assembly in metagenomes.","author":"D Pellow","year":"2020","journal-title":"bioRxiv"},{"key":"pcbi.1008972.ref073","first-page":"236","volume-title":"Science.","author":"PSG Chain","year":"2009"},{"key":"pcbi.1008972.ref074","volume-title":"mBio.","author":"A Shaiber","year":"2019"},{"key":"pcbi.1008972.ref075","doi-asserted-by":"crossref","first-page":"e62856","DOI":"10.1371\/journal.pone.0062856","article-title":"Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly","volume":"8","author":"Y-C Chen","year":"2013","journal-title":"PLoS 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