{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T18:10:37Z","timestamp":1789150237292,"version":"build-2803163510"},"reference-count":59,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003500","name":"University of Padova","doi-asserted-by":"crossref","award":["DOR-DAFNAE 2023"],"award-info":[{"award-number":["DOR-DAFNAE 2023"]}],"id":[{"id":"10.13039\/501100003500","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    16S rDNA is the historical gold standard for bacterial identification, particularly in metabarcoding approaches reliant on sequence similarity thresholds. We analyzed 6,660\n                    <jats:italic>Rhizobium<\/jats:italic>\n                    16S rRNA gene sequences from GenBank to examine the relationship between sequence identity and three metadata: species name, host plant, and geographic origin. Using an iterative BLAST-based pipeline, we detected 116,069 pairwise matches and assessed concordance among sequences (average length 1,328 bp) sharing 100% identity. For those in which the organism name, host plant and country of isolation were present in the record, surprisingly, 66.59% of identical sequence pairs showed full discordance across all three metadata, while only 1.40% shared the same name, host, and country. The most widespread sequence, detected 371 times, was associated with over 56 different host plants across 25 countries and bore multiple species name designations. These results highlight a striking mismatch between the 16S barcode and the taxonomic, ecological, and phenotypic variability it is assumed to reflect, likely arising from the slow evolution of rRNA genes contrasted with the mobility of ecologically relevant genes via horizontal transfer on plasmids, transposons, and phages. Our findings further challenge the limitations of relying on 16S rRNA alone for fine-scale taxonomic and metadata-based inference in capturing the true functional and ecological diversity of bacteria, endorsing the critical importance of polyphasic taxonomic approaches that integrate genomic, phenotypic, and ecological data. An interesting byproduct of the analysis was to realize the possibility of treating these data as if they were \u2018citations.\u2019 The more one finds the same query sequence, the more that sequence can be considered biologically \u2018cited\u2019, i.e., re-proposed elsewhere in the world. Thus, one can also analyze the h-index of such a ranking. In our\n                    <jats:italic>Rhizobium<\/jats:italic>\n                    dataset, we calculated an h-index\u2009=\u2009201, meaning the sequence ranked 201\n                    <jats:sup>st<\/jats:sup>\n                    had 202 identical homologues in GenBank. Although the research effort on given species is directly connected with it, this number provides a quantitative indicator of a taxon\u2019s sequence recurrence and distribution within public databases, independent of nomenclatural inconsistencies, offering a novel framework for assessing bacterial representation across global datasets.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0357973","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T17:44:29Z","timestamp":1789148669000},"page":"e0357973","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["GenBank mining reveals novel insights into Rhizobium phylogeny: Identical 16S rRNA sequences are mainly uncoupled from species designation, host plant, and geographic origin: How this search suggested the definition of a direct \u2018microbial h-index\u2019"],"prefix":"10.1371","volume":"21","author":[{"given":"Rosella","family":"Muresu","sequence":"first","affiliation":[{"name":"Institute for the Animal Production System in Mediterranean Environment-National Research Council (ISPAAM CNR)","place":["Sassari, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8926-2987","authenticated-orcid":true,"given":"Monica","family":"Rodriguez","sequence":"additional","affiliation":[{"name":"University of Sassari","place":["Viale Italia, Sassari, Italy"],"department":["Department of Agricultural Sciences"]},{"name":"University of Sassari","place":["Alghero, Sassari, Italy"],"department":["Interdepartmental Center for the Conservation and Valorization of Plant Biodiversity"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1961-1165","authenticated-orcid":true,"given":"Andrea","family":"Squartini","sequence":"additional","affiliation":[{"name":"Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Viale dell\u2019Universit\u00e0 16","place":["Legnaro, Padova, Italy"],"department":["Department of Agronomy"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"pone.0357973.ref001","volume-title":"Legumes of the World","author":"G Lewis","year":"2005"},{"issue":"1","key":"pone.0357973.ref002","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1128\/mr.59.1.124-142.1995","article-title":"The Rhizobium-plant symbiosis","volume":"59","author":"P van Rhijn","year":"1995","journal-title":"Microbiol 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