{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T00:59:57Z","timestamp":1778633997672,"version":"3.51.4"},"reference-count":45,"publisher":"American Society for Microbiology","issue":"1","license":[{"start":{"date-parts":[[2007,1,1]],"date-time":"2007-01-01T00:00:00Z","timestamp":1167609600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2007,1]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene\n            <jats:italic>rpoB<\/jats:italic>\n            . Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such \u201cheterogeneity hot spots\u201d occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below.\n            <jats:italic>rpoB<\/jats:italic>\n            provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as\n            <jats:italic>rpoB<\/jats:italic>\n            could complement the information provided by the 16S rRNA gene.\n          <\/jats:p>","DOI":"10.1128\/aem.01177-06","type":"journal-article","created":{"date-parts":[[2006,12,26]],"date-time":"2006-12-26T18:42:45Z","timestamp":1167158565000},"page":"278-288","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":488,"title":["Use of 16S rRNA and\n            <i>rpoB<\/i>\n            Genes as Molecular Markers for Microbial Ecology Studies"],"prefix":"10.1128","volume":"73","author":[{"given":"Rebecca J.","family":"Case","sequence":"first","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences"},{"name":"The Centre for Marine Biofouling and Bio-Innovation, University of New South Wales, Sydney 2052, Australia"}]},{"given":"Yan","family":"Boucher","sequence":"additional","affiliation":[{"name":"Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, 5859 University Avenue, Halifax B3H 4H7, Canada"}]},{"given":"Ingela","family":"Dahllo\u0308f","sequence":"additional","affiliation":[{"name":"The National Environmental Research Institute, Roskilde, Denmark"}]},{"given":"Carola","family":"Holmstro\u0308m","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences"},{"name":"The Centre for Marine Biofouling and Bio-Innovation, University of New South Wales, Sydney 2052, Australia"}]},{"given":"W. Ford","family":"Doolittle","sequence":"additional","affiliation":[{"name":"Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, 5859 University Avenue, Halifax B3H 4H7, Canada"}]},{"given":"Staffan","family":"Kjelleberg","sequence":"additional","affiliation":[{"name":"School of Biotechnology and Biomolecular Sciences"},{"name":"The Centre for Marine Biofouling and Bio-Innovation, University of New South Wales, Sydney 2052, Australia"}]}],"member":"235","reference":[{"key":"e_1_3_1_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.67.7.2922-2926.2001"},{"key":"e_1_3_1_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature02649"},{"key":"e_1_3_1_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.9.2629-2635.2004"},{"key":"e_1_3_1_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.8.4935-4941.2003"},{"key":"e_1_3_1_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.3.1748-1758.2003"},{"key":"e_1_3_1_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.12.3980-3990.2004"},{"key":"e_1_3_1_8_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2005.00793.x"},{"key":"e_1_3_1_9_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-3-2"},{"key":"e_1_3_1_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/sj.jim.2900546"},{"key":"e_1_3_1_11_2","doi-asserted-by":"publisher","DOI":"10.2144\/03344rr01"},{"key":"e_1_3_1_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.8.3376-3380.2000"},{"key":"e_1_3_1_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.soilbio.2004.03.011"},{"key":"e_1_3_1_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.5.2555-2562.2003"},{"key":"e_1_3_1_15_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00227-005-1614-9"},{"key":"e_1_3_1_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2004.04.015"},{"key":"e_1_3_1_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1236"},{"key":"e_1_3_1_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/345060a0"},{"key":"e_1_3_1_19_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.3672135"},{"key":"e_1_3_1_20_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2005.00018.x"},{"key":"e_1_3_1_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.4.1328-1333.2000"},{"key":"e_1_3_1_22_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.1.181"},{"key":"e_1_3_1_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0167-7012(02)00026-X"},{"key":"e_1_3_1_24_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1103289"},{"key":"e_1_3_1_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.171.11.6234-6242.1989"},{"key":"e_1_3_1_26_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1472-765X.2002.01183.x"},{"key":"e_1_3_1_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(05)97021-3"},{"key":"e_1_3_1_28_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/21.22.5264"},{"key":"e_1_3_1_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.64.10.3724-3730.1998"},{"key":"e_1_3_1_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/14.9.817"},{"key":"e_1_3_1_31_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.180094797"},{"key":"e_1_3_1_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.fm.2003.10.002"},{"key":"e_1_3_1_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.fm.2005.01.019"},{"key":"e_1_3_1_34_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2004.00617.x"},{"key":"e_1_3_1_35_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2001.tb00775.x"},{"key":"e_1_3_1_36_2","unstructured":"Swofford D. 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