{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:48:57Z","timestamp":1787028537535,"version":"build-2736575974"},"reference-count":68,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2024,4,18]],"date-time":"2024-04-18T00:00:00Z","timestamp":1713398400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100011011","name":"Junta de Andaluc\u00eda","doi-asserted-by":"publisher","award":["P18-RT-3048"],"award-info":[{"award-number":["P18-RT-3048"]}],"id":[{"id":"10.13039\/501100011011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011011","name":"Junta de Andaluc\u00eda","doi-asserted-by":"publisher","award":["PPIT_2022E_025814"],"award-info":[{"award-number":["PPIT_2022E_025814"]}],"id":[{"id":"10.13039\/501100011011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008679","name":"Universidad de C\u00f3rdoba","doi-asserted-by":"publisher","award":["P18-RT-3048"],"award-info":[{"award-number":["P18-RT-3048"]}],"id":[{"id":"10.13039\/501100008679","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008679","name":"Universidad de C\u00f3rdoba","doi-asserted-by":"publisher","award":["PPIT_2022E_025814"],"award-info":[{"award-number":["PPIT_2022E_025814"]}],"id":[{"id":"10.13039\/501100008679","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fundaci\u00f3n Torres Guti\u00e9rrez, Spain","award":["P18-RT-3048"],"award-info":[{"award-number":["P18-RT-3048"]}]},{"name":"Fundaci\u00f3n Torres Guti\u00e9rrez, Spain","award":["PPIT_2022E_025814"],"award-info":[{"award-number":["PPIT_2022E_025814"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Molecular studies about cyanide biodegradation have been mainly focused on the hydrolytic pathways catalyzed by the cyanide dihydratase CynD or the nitrilase NitC. In some Pseudomonas strains, the assimilation of cyanide has been linked to NitC, such as the cyanotrophic model strain Pseudomonas pseudoalcaligenes CECT 5344, which has been recently reclassified as Pseudomonas oleovorans CECT 5344. In this work, a phylogenomic approach established a more precise taxonomic position of the strain CECT 5344 within the species P. oleovorans. Furthermore, a pan-genomic analysis of P. oleovorans and other species with cyanotrophic strains, such as P. fluorescens and P. monteilii, allowed for the comparison and identification of the cioAB and mqoAB genes involved in cyanide resistance, and the nitC and cynS genes required for the assimilation of cyanide or cyanate, respectively. While cyanide resistance genes presented a high frequency among the analyzed genomes, genes responsible for cyanide or cyanate assimilation were identified in a considerably lower proportion. According to the results obtained in this work, an in silico approach based on a comparative genomic approach can be considered as an agile strategy for the bioprospection of putative cyanotrophic bacteria and for the identification of new genes putatively involved in cyanide biodegradation.<\/jats:p>","DOI":"10.3390\/ijms25084456","type":"journal-article","created":{"date-parts":[[2024,4,18]],"date-time":"2024-04-18T10:30:52Z","timestamp":1713436252000},"page":"4456","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Genomic Insights into Cyanide Biodegradation in the Pseudomonas Genus"],"prefix":"10.3390","volume":"25","author":[{"given":"Lara P.","family":"S\u00e1ez","sequence":"first","affiliation":[{"name":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de C\u00f3rdoba, 14071 C\u00f3rdoba, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3058-5663","authenticated-orcid":false,"given":"Gema","family":"Rodr\u00edguez-Caballero","sequence":"additional","affiliation":[{"name":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de C\u00f3rdoba, 14071 C\u00f3rdoba, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8961-1099","authenticated-orcid":false,"given":"Alfonso","family":"Olaya-Abril","sequence":"additional","affiliation":[{"name":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de C\u00f3rdoba, 14071 C\u00f3rdoba, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Purificaci\u00f3n","family":"Cabello","sequence":"additional","affiliation":[{"name":"Departamento de Bot\u00e1nica, Ecolog\u00eda y Fisiolog\u00eda Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de C\u00f3rdoba, 14071 C\u00f3rdoba, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8149-5716","authenticated-orcid":false,"given":"Conrado","family":"Moreno-Vivi\u00e1n","sequence":"additional","affiliation":[{"name":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de C\u00f3rdoba, 14071 C\u00f3rdoba, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7173-8641","authenticated-orcid":false,"given":"Mar\u00eda Dolores","family":"Rold\u00e1n","sequence":"additional","affiliation":[{"name":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de C\u00f3rdoba, 14071 C\u00f3rdoba, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1447-4795","authenticated-orcid":false,"given":"V\u00edctor M.","family":"Luque-Almagro","sequence":"additional","affiliation":[{"name":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de C\u00f3rdoba, 14071 C\u00f3rdoba, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,4,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.envint.2015.02.001","article-title":"Exploring the planetary boundary for chemical pollution","volume":"78","author":"Diamond","year":"2015","journal-title":"Environ. Int."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"106616","DOI":"10.1016\/j.envint.2021.106616","article-title":"Chemical pollution: A growing peril and potential catastrophic risk to humanity","volume":"156","author":"Naidu","year":"2021","journal-title":"Environ. Int."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1126\/science.abg5433","article-title":"The global threat from plastic pollution","volume":"373","author":"MacLeod","year":"2021","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"44587","DOI":"10.1007\/s11356-021-14700-0","article-title":"Aluminum environmental pollution: The silent killer","volume":"28","author":"Alasfar","year":"2021","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Chrzanowski, L., and Lawniczak, L. (2020). Biodegradation of conventional and emerging pollutants. Molecules, 25.","DOI":"10.3390\/molecules25051186"},{"key":"ref_6","first-page":"137","article-title":"Bioresources for control of environmental pollution","volume":"147","author":"Sana","year":"2015","journal-title":"Adv. Biochem. Eng. Biotechnol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/j.scitotenv.2019.02.390","article-title":"Mitigation of environmental pollution by genetically engineered bacteria -current challenges and future perspectives","volume":"667","author":"Liu","year":"2019","journal-title":"Sci. Total Environ."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Sharma, N., Thakur, N., Raj, T., and Bhalla, T.C. (2017). Mining of microbial genomes for the novel sources of nitrilases. Biomed Res. Int., 2017.","DOI":"10.1155\/2017\/7039245"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2687","DOI":"10.1007\/s11033-021-06239-7","article-title":"Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria","volume":"48","author":"Oyewusi","year":"2021","journal-title":"Mol. Biol. Rep."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Caputo, A., Fournier, P.-E., and Raoult, D. (2019). Genome and pan-genome analysis to classify emerging bacteria. Biol. Direct, 14.","DOI":"10.1186\/s13062-019-0234-0"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Bobby, P., Raj, K.K., Murali, T.S., and Satyamoorthy, K. (2020). Species-specific genomic sequences for classification of bacteria. Comput. Biol. Med., 123.","DOI":"10.1016\/j.compbiomed.2020.103874"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"15929","DOI":"10.1007\/s11356-017-9081-7","article-title":"Cyanides in the environment-analysis-problems and challenges","volume":"24","author":"Jaszczak","year":"2017","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"5118","DOI":"10.1128\/AEM.00503-07","article-title":"Essential role of the cytochrome bd-related oxidase in cyanide resistance of Pseudomonas pseudoalcaligenes CECT5344","volume":"73","author":"Quesada","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1099\/mic.0.045286-0","article-title":"Cyanide degradation by Pseudomonas pseudoalcaligenes CECT5344 involves a malate: Quinone oxidoreductase and an associated cyanide-insensitive electro transfer chain","volume":"157","author":"Blasco","year":"2011","journal-title":"Microbiology"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Cabello, P., Luque-Almagro, V.M., Olaya-Abril, A., S\u00e1ez, L.P., Moreno-Vivi\u00e1n, C., and Rold\u00e1n, M.D. (2018). Assimilation of cyanide and cyano-derivatives by Pseudomonas pseudoalcaligenes CECT5344: From omic approaches to biotechnological applications. FEMS Microbiol. Lett., 1.","DOI":"10.1093\/femsle\/fny032"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e53720","DOI":"10.15252\/embr.202153720","article-title":"Bioremediation of cyanide-containing wastes. The potential of systems and synthetic biology for cleaning up the toxic leftovers from mining","volume":"22","author":"Cabello","year":"2021","journal-title":"EMBO Rep."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Olaya-Abril, A., Bie\u0142\u0142o, K., Rodr\u00edguez-Caballero, G., Cabello, P., S\u00e1ez, L.P., Moreno-Vivi\u00e1n, C., Luque-Almagro, V.M., and Rold\u00e1n, M.D. (2024). Bacterial tolerance and detoxification of cyanide, arsenic and heavy metals: Holistic approaches applied to bioremediation of industrial complex wastes. Microb. Biotechnol., 17.","DOI":"10.1111\/1751-7915.14399"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1111\/j.1758-2229.2012.00337.x","article-title":"The nit1C gene cluster of Pseudomonas pseudoalcaligenes CECT5344 involved in assimilation of nitriles is essential for growth on cyanide","volume":"4","author":"Estepa","year":"2012","journal-title":"Environ. Microbiol. Rep."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1099\/mic.0.000668","article-title":"Linkage of the Nit1C gene cluster to bacterial cyanide assimilation as a nitrogen source","volume":"164","author":"Jones","year":"2018","journal-title":"Microbiology"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Podar, M., Eads, J.R., and Richardson, R.H. (2005). Evolution of a microbial nitrilase gene family: A comparative and environmental genomics study. BMC Evol. Biol., 5.","DOI":"10.1186\/1471-2148-5-42"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Panwar, P., Williams, T.J., Allen, M.A., and Cavicchioli, R. (2022). Population structure of an Antarctic aquatic cyanobacterium. Microbiome, 10.","DOI":"10.1186\/s40168-022-01404-x"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e00777-21","DOI":"10.1128\/Spectrum.00777-21","article-title":"Alternative pathway for 3-cyanoalanine assimilation in Pseudomonas pseudoalcaligenes CECT5344 under noncyanotrophic conditions","volume":"9","author":"Cabello","year":"2021","journal-title":"Microbiol. Spectr."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"S\u00e1ez, L.P., Cabello, P., Ib\u00e1\u00f1ez, M.I., Luque-Almagro, V.M., Rold\u00e1n, M.D., and Moreno-Vivi\u00e1n, C. (2019). Cyanate assimilation by the alkaliphilic cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344: Mutational analysis of the cyn gene cluster. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20123008"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2386","DOI":"10.1099\/ijsem.0.002809","article-title":"Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI","volume":"68","author":"Ciufo","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1128\/AEM.71.2.940-947.2005","article-title":"Bacterial degradation of cyanide and its metal complexes under alkaline conditions","volume":"71","author":"Huertas","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2567","DOI":"10.1073\/pnas.0409727102","article-title":"Genomic insights that advance the species definition for prokaryotes","volume":"102","author":"Konstantinidis","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Bodilis, J., Nsigue-Mejlo, S., Besaury, L., and Quillet, L. (2012). Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in Pseudomonas. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0035647"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1677","DOI":"10.1099\/00221287-144-6-1677","article-title":"Cyanide hydrolysis in a cyanide-degrading bacterium, Pseudomonas stutzeri AK61, by cyanidase","volume":"144","author":"Watanabe","year":"1998","journal-title":"Microbiology"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1128\/aem.55.1.256-258.1989","article-title":"Cyanase-mediated utilization of cyanate in Pseudomonas fluorescens NCIB 11764","volume":"55","author":"Kunz","year":"1989","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"6280","DOI":"10.1128\/AEM.00916-08","article-title":"Characterization of the Pseudomonas pseudoalcaligenes CECT5344 cyanase, an enzyme that is not essential for cyanide assimilation","volume":"74","author":"Huertas","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1111\/j.1462-2920.2012.02875.x","article-title":"Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344","volume":"15","author":"Acera","year":"2013","journal-title":"Environ. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Lalucat, J., Gomila, M., Mulet, M., Zaruma, A., and Garc\u00eda-Vald\u00e9s, E. (2022). Past, present and future of the boundaries of the Pseudomonas genus: Proposal of Stutzerimonas gen. Nov. Syst. Appl. Microbiol., 45.","DOI":"10.1016\/j.syapm.2021.126289"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Gomila, M., Mulet, M., Garc\u00eda-Vald\u00e9s, E., and Lalucat, J. (2022). Genome-based taxonomy of the genus Stutzerimonas and proposal of S. frequens sp. nov. and S. degradans sp. nov. and emended descriptions of S. perfectomarina and S. chloritidismutans. Microorganisms, 10.","DOI":"10.3390\/microorganisms10071363"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1099\/00221287-43-2-159","article-title":"The aerobic pseudomonads: A taxonomic study","volume":"43","author":"Stanier","year":"1966","journal-title":"J. Gen. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2385","DOI":"10.1099\/00221287-146-10-2385","article-title":"Phylogeny of the genus Pseudomonas: Intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes","volume":"146","author":"Yamamoto","year":"2000","journal-title":"Microbiology"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1111\/j.1462-2920.2010.02181.x","article-title":"DNA sequence-based analysis of the Pseudomonas species","volume":"12","author":"Mulet","year":"2010","journal-title":"Environ. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1007\/s00284-009-9540-6","article-title":"Pseudomonas oleovorans subsp. lubricantis subsp. nov., and reclassification of Pseudomonas pseudoalcaligenes ATCC 17440T as later synonym of Pseudomonas oleovorans ATCC 8062 T","volume":"60","author":"Saha","year":"2010","journal-title":"Curr. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Gomila, M., Pe\u00f1a, A., Mulet, M., Lalucat, J., and Garc\u00eda-Vald\u00e9s, E. (2015). Phylogenomics and systematics in Pseudomonas. Front. Microbiol., 18.","DOI":"10.3389\/fmicb.2015.00214"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1111\/j.1574-6976.2011.00269.x","article-title":"Pseudomonas genomes: Diverse and adaptable","volume":"35","author":"Silby","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1016\/j.mib.2008.09.006","article-title":"Comparative genomics: The bacterial pan-genome","volume":"11","author":"Tettelin","year":"2008","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"3268","DOI":"10.1111\/1462-2920.13015","article-title":"Analysis of the core genome and pangenome of Pseudomonas putida","volume":"18","author":"Udaondo","year":"2016","journal-title":"Environ. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Kumari, K., Rawat, V., Shadan, A., Sharma, P.K., Deb, S., and Singh, R.P. (2023). In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1140249"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e00774-17","DOI":"10.1128\/genomeA.00774-17","article-title":"First insights into the genome sequence of Pseudomonas oleovorans DSM 1045","volume":"32","author":"Poehlein","year":"2017","journal-title":"Genome Announc."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"R1094","DOI":"10.1016\/j.cub.2019.08.012","article-title":"The ecology and evolution of pangenomes","volume":"29","author":"Brockhurst","year":"2019","journal-title":"Curr. Biol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.mib.2022.01.005","article-title":"Prokaryote pangenomes are dynamic entities","volume":"66","author":"Cummins","year":"2022","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Parra-S\u00e1nchez, \u00c1., Antequera-Zambrano, L., Mart\u00ednez-Navarrete, G., Zorrilla-Mu\u00f1oz, V., Paz, J.L., Alvarado, Y.J., Gonz\u00e1lez-Paz, L., and Fern\u00e1ndez, E. (2023). Comparative analysis of CRISPR-Cas systems in Pseudomonas genomes. Genes, 14.","DOI":"10.3390\/genes14071337"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1038\/s41396-020-00860-3","article-title":"CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa","volume":"15","author":"Wheatley","year":"2021","journal-title":"ISME J."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.jbiotec.2015.09.032","article-title":"DNA microarray analysis of the cyanotroph Pseudomonas pseudoalcaligenes CECT5344 in response to nitrogen starvation, cyanide and a jewelry wastewater","volume":"214","author":"Escribano","year":"2015","journal-title":"J. Biotechnol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1016\/j.str.2003.10.005","article-title":"The cyanide degrading nitrilase from Pseudomonas stutzeri AK61 is a two-fold symmetric, 14-subunit spiral","volume":"11","author":"Sewell","year":"2003","journal-title":"Structure"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"e01322-18","DOI":"10.1128\/MRA.01322-18","article-title":"Draft genome sequence of the cyanotroph Pseudomonas monteilii BCN3","volume":"8","author":"Jones","year":"2019","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"720","DOI":"10.1038\/s41396-023-01386-0","article-title":"Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies","volume":"17","author":"Guyet","year":"2023","journal-title":"ISME J."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Barbaccia, P., Gaglio, R., Dazzi, C., Miceli, C., Bella, P., Lo Papa, G., and Settanni, L. (2022). Plant growth-promoting activities of bacteria isolated from an anthropogenic soil located in Agrigento province. Microorganisms, 10.","DOI":"10.3390\/microorganisms10112167"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2182","DOI":"10.1038\/s41467-019-10210-3","article-title":"TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy","volume":"10","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: Fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: Consistent and rapid annotation of ribosomal RNA genes","volume":"35","author":"Lagesen","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: Architecture and applications. BMC Bioinform., 10.","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.-P., and G\u00f6ker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-60"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"D801","DOI":"10.1093\/nar\/gkab902","article-title":"TYGS and LPSN: A database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes","volume":"50","author":"Carbasse","year":"2022","journal-title":"Nucleic Acid Res."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"2798","DOI":"10.1093\/molbev\/msv150","article-title":"FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program","volume":"32","author":"Lefort","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1086\/282802","article-title":"Estimating phylogenetic trees from distance matrices","volume":"106","author":"Farris","year":"1972","journal-title":"Am. Nat."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"2946","DOI":"10.1093\/bioinformatics\/btx324","article-title":"PhyD3: A phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization","volume":"33","author":"Kreft","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1944-3277-9-2","article-title":"Complete genome sequence of DSM 30083T, the type strain (U5\/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy","volume":"9","author":"Hahnke","year":"2014","journal-title":"Stand. Genomic. Sci."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"4412","DOI":"10.1093\/bioinformatics\/btac504","article-title":"PanExplorer: A web-based tool for exploratory analysis and visualization of bacterial pan-genomes","volume":"38","author":"Dereeper","year":"2022","journal-title":"Bioinformatics"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Perrin, A., and Rocha, E.P.C. (2021). PanACoTA: A modular tool for massive microbial comparative genomics. NAR Genom. Bioinform., 3.","DOI":"10.1101\/2020.09.11.293472"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: An information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"W330","DOI":"10.1093\/nar\/gkac441","article-title":"FUNAGE-Pro: Comprehensive web server for gene set enrichment analysis of prokaryotes","volume":"50","author":"Jong","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2628","DOI":"10.1093\/bioinformatics\/btz931","article-title":"ShinyGO: A graphical gene-set enrichment tool for animals and plants","volume":"36","author":"Ge","year":"2020","journal-title":"Bioinformatics"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/8\/4456\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:30:08Z","timestamp":1760106608000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/8\/4456"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4,18]]},"references-count":68,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2024,4]]}},"alternative-id":["ijms25084456"],"URL":"https:\/\/doi.org\/10.3390\/ijms25084456","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,4,18]]}}}