{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T07:17:22Z","timestamp":1771226242419,"version":"3.50.1"},"reference-count":113,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T00:00:00Z","timestamp":1771200000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      The\n                      <jats:italic>Mycobacterium<\/jats:italic>\n                      \u201c\n                      <jats:italic>Fortuitum-Vaccae<\/jats:italic>\n                      \u201d clade (FVC) contains many rapid-growing species and is increasingly reported in human infections globally. However, the clade\u2019s taxonomic composition and the exact association with human infections remain to be explored.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      In this study, we conducted a comprehensive genome-based analysis of the FVC, aiming to update its taxonomy and identify new taxa. We compiled a dataset of 298\n                      <jats:italic>Mycobacterium<\/jats:italic>\n                      species using public databases, ultimately including 222 type strain genomes for phylogenomic analysis\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      This revealed 106 species within the FVC. Subsequent curation of 11,534 public\n                      <jats:italic>Mycobacterium<\/jats:italic>\n                      identified 557 belonging to the FVC, from which we uncovered 86 new taxa (genomospecies) and resolved one new synonym pair. We reconstructed three core-protein phylogenomic trees and found the FVC comprising eight distinct subclades. Our analysis unveiled a remarkably complicated taxonomic landscape within the clade, encompassing 106 known species, among which 16 species, such as\n                      <jats:italic>M. syngnathidarum<\/jats:italic>\n                      and\n                      <jats:italic>M. yunnanensis<\/jats:italic>\n                      , have not previously been classified within the FVC. We detected a pair of synonyms:\n                      <jats:italic>M. murale<\/jats:italic>\n                      is a heterotypic synonym of\n                      <jats:italic>M. tokaiense<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>These findings highlight the remarkable taxonomic diversity within the FVC. The updated taxonomy and the curated database of genomes allow precise species identification in diagnostics, clinical reporting, epidemiological surveillance, and future studies on the ecology and pathogenesis. Accurate identification may uncover the disease spectrum, clinical manifestation, and prognosis of infections by individual FVC species, guiding countermeasures.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1728622","type":"journal-article","created":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T06:35:50Z","timestamp":1771223750000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Taxonomic landscape of the Mycobacterium \u201cFortuitum-Vaccae\u201d clade: a genome study"],"prefix":"10.3389","volume":"17","author":[{"given":"Chengcheng","family":"Wang","sequence":"first","affiliation":[{"name":"Center of Infectious Diseases, West China Hospital, Sichuan University","place":["Chengdu, China"]},{"name":"Division of Infectious Diseases, State Key Laboratory of Biotherapy","place":["Chengdu, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Feng","sequence":"additional","affiliation":[{"name":"Laboratory of Pathogen Research, West China Hospital, Sichuan University","place":["Chengdu, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dan","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, West China Hospital, Sichuan University","place":["Chengdu, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feifei","family":"Zhao","sequence":"additional","affiliation":[{"name":"Center of Infectious Diseases, West China Hospital, Sichuan University","place":["Chengdu, China"]},{"name":"Division of Infectious Diseases, State Key Laboratory of Biotherapy","place":["Chengdu, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuling","family":"Xiao","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, West China Hospital, Sichuan University","place":["Chengdu, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, West China Hospital, Sichuan University","place":["Chengdu, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alan","family":"McNally","sequence":"additional","affiliation":[{"name":"Department of Microbes, Infection and Microbiomes, School of Infection, Inflammation and Immunology, College of Medicine and Health, University of Birmingham","place":["Birmingham, United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiyong","family":"Zong","sequence":"additional","affiliation":[{"name":"Center of Infectious Diseases, West China Hospital, Sichuan University","place":["Chengdu, China"]},{"name":"Division of Infectious Diseases, State Key Laboratory of Biotherapy","place":["Chengdu, China"]},{"name":"Laboratory of Pathogen Research, West China Hospital, Sichuan University","place":["Chengdu, China"]},{"name":"State Key Laboratory of Respiratory Health and Multimorbidity","place":["Chengdu, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,2,16]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1099\/ijs.0.63969-0","article-title":"rpoB gene sequence-based characterization of emerging non-tuberculous mycobacteria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov., and Mycobacterium aubagnense sp. nov","volume":"56","author":"Adekambi","year":"2006","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"2095","DOI":"10.1099\/ijs.0.63094-0","article-title":"Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing","volume":"54","author":"Adekambi","year":"2004","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"3493","DOI":"10.1128\/JCM.00724-06","article-title":"Mycobacterium barrassiae sp. nov., a Mycobacterium moriokaense group species associated with chronic pneumonia","volume":"44","author":"Ad\u00e9kambi","year":"2006","journal-title":"J. Clin. Microbiol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1099\/00207713-36-2-246","article-title":"Rhodococcus chlorophenolicus sp. nov., a chlorophenol-mineralizing actinomycete","volume":"36","author":"Apajalahti","year":"1986","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1099\/00207713-42-4-529","article-title":"Mycobacterium alvei sp. nov","volume":"42","author":"Ausina","year":"1992","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"03019","DOI":"10.3389\/fmicb.2019.03019","article-title":"Key transitions in the evolution of rapid and slow growing mycobacteria identified by comparative genomics","volume":"10","author":"Bachmann","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1007\/s00284-014-0588-6","article-title":"Mycobacterium hippocampi sp. nov., a rapidly growing scotochromogenic species isolated from a seahorse with tail rot","volume":"69","author":"Balcazar","year":"2014","journal-title":"Curr. Microbiol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1099\/00221287-28-2-333","article-title":"Adansonian classification of mycobacteria","volume":"28","author":"Bojalil","year":"1962","journal-title":"J. Gen. Microbiol."},{"key":"ref10","first-page":"133","article-title":"Beschreibung der neuen Species Mycobacterium vaccae n. sp","volume":"192","author":"Bonicke","year":"1964","journal-title":"Zentralbl. Bakteriol. Orig."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1493","DOI":"10.1099\/00207713-49-4-1493","article-title":"Mycobacterium wolinskyi sp. nov. and Mycobacterium goodii sp. nov., two new rapidly growing species related to Mycobacterium smegmatis and associated with human wound infections: a cooperative study from the international working group on mycobacterial taxonomy","volume":"49","author":"Brown","year":"1999","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"4377","DOI":"10.1128\/JCM.00853-10","article-title":"Mycobacterium neoaurum and Mycobacterium bacteremicum sp. nov. as causes of mycobacteremia","volume":"48","author":"Brown-Elliott","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1016\/0041-3879(74)90039-7","article-title":"Mycobacterium gadium sp. nov. a new species of rapid-growing scotochromogenic mycobacteria","volume":"55","author":"Casal","year":"1974","journal-title":"Tubercle"},{"key":"ref14","first-page":"215","article-title":"M. farcinogenes agent causal du farcin du boeuf en Afrique","volume":"124","author":"Chamoiseau","year":"1973","journal-title":"Ann. Microbiol. Inst. Pasteur"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","article-title":"GTDB-Tk v2: memory friendly classification with the genome taxonomy database","volume":"38","author":"Chaumeil","year":"2022","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"005019","DOI":"10.1099\/ijsem.0.005019","article-title":"Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov., two new rapidly growing mycobacterial species","volume":"71","author":"Cheng","year":"2021","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"2385","DOI":"10.1099\/ijs.0.63238-0","article-title":"Mycobacterium cosmeticum sp. nov., a novel rapidly growing species isolated from a cosmetic infection and from a nail salon","volume":"54","author":"Cooksey","year":"2004","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"767895","DOI":"10.3389\/fmicb.2021.767895","article-title":"Comparative genomic study of vinyl chloride cluster and description of novel species, Mycolicibacterium vinylchloridicum sp. nov","volume":"12","author":"Cortes-Albayay","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref19","first-page":"297","article-title":"Mycobacterium fortuitum um novo bacillo acidoresistance pathogenico para o homen","volume":"1","author":"Da Costa Cruz","year":"1938","journal-title":"Acta Med."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"004438","DOI":"10.1099\/ijsem.0.004438","article-title":"Mycolicibacterium nivoides sp. nov isolated from a peat bog","volume":"71","author":"Dahl","year":"2021","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1016\/j.ijid.2022.10.013","article-title":"Global trends of pulmonary infections with nontuberculous mycobacteria: a systematic review","volume":"125","author":"Dahl","year":"2022","journal-title":"Int. J. Infect. Dis."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"2313","DOI":"10.1099\/ijs.0.03003-0","article-title":"Mycobacterium pyrenivorans sp. nov., a novel polycyclic-aromatic-hydrocarbon-degrading species","volume":"54","author":"Derz","year":"2004","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1099\/00207713-47-2-535","article-title":"Mycobacterium mageritense sp. nov","volume":"47","author":"Domenech","year":"1997","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1099\/ijsem.0.002978","article-title":"Mycobacterium syngnathidarum sp. nov., a rapidly growing mycobacterium identified in syngnathid fish","volume":"68","author":"Fogelson","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1099\/ijsem.0.001678","article-title":"Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization","volume":"67","author":"Gcebe","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1526","DOI":"10.1099\/ijsem.0.002707","article-title":"Mycobacterium komaniense sp. nov., a rapidly growing non-tuberculous Mycobacterium species detected in South Africa","volume":"68","author":"Gcebe","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"13011","DOI":"10.1038\/s41598-021-91737-8","article-title":"Phenotypic and genomic hallmarks of a novel, potentially pathogenic rapidly growing Mycobacterium species related to the Mycobacterium fortuitum complex","volume":"11","author":"Gharbi","year":"2021","journal-title":"Sci. Rep."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"2769","DOI":"10.1099\/ijs.0.65857-0","article-title":"Mycobacterium llatzerense sp. nov., a facultatively autotrophic, hydrogen-oxidizing bacterium isolated from haemodialysis water","volume":"58","author":"Gomila","year":"2008","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"206","DOI":"10.3389\/fmicb.2019.00206","article-title":"Commentary: genome-based taxonomic classification of the phylum Actinobacteria","volume":"10","author":"Gupta","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"67","DOI":"10.3389\/fmicb.2018.00067","article-title":"Phylogenomics and comparative genomic studies robustly support division of the genus Mycobacterium into an emended genus Mycobacterium and four novel genera","volume":"9","author":"Gupta","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"3279","DOI":"10.1099\/ijsem.0.002103","article-title":"Mycobacterium aquaticum sp. nov., a rapidly growing species isolated from haemodialysis water","volume":"67","author":"Hashemi Shahraki","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"e00625","DOI":"10.1128\/genomeA.00625-17","article-title":"Whole-genome sequence of the 1,4-dioxane-degrading bacterium Mycobacterium dioxanotrophicus PH-06","volume":"5","author":"He","year":"2017","journal-title":"Genome Announc."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1099\/ijs.0.65827-0","article-title":"Polycyclic aromatic hydrocarbon-degrading species isolated from Hawaiian soils: Mycobacterium crocinum sp. nov., Mycobacterium pallens sp. nov., Mycobacterium rutilum sp. nov., Mycobacterium rufum sp. nov. and Mycobacterium aromaticivorans sp. nov","volume":"59","author":"Hennessee","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"5650","DOI":"10.1128\/JCM.41.12.5650-5653.2003","article-title":"Characterization of a novel rapidly growing Mycobacterium species associated with sepsis","volume":"41","author":"Hong","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1078\/0723202042369866","article-title":"Mycobacterium fluoranthenivorans sp. nov., a fluoranthene and aflatoxin B1 degrading bacterium from contaminated soil of a former coal gas plant","volume":"27","author":"Hormisch","year":"2004","journal-title":"Syst. Appl. Microbiol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1735","DOI":"10.1007\/s10482-021-01638-z","article-title":"Genomic molecular signatures determined characterization of Mycolicibacterium gossypii sp. nov., a fast-growing mycobacterial species isolated from cotton field soil","volume":"114","author":"Huang","year":"2021","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1038\/s41579-020-0331-1","article-title":"Non-tuberculous mycobacteria and the rise of Mycobacterium abscessus","volume":"18","author":"Johansen","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1099\/00207713-30-1-77","article-title":"Mycobacterium sphagni sp. nov","volume":"30","author":"Kazda","year":"1980","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1099\/00207713-29-4-361","article-title":"Mycobacterium komossense sp. nov","volume":"29","author":"Kazda","year":"1979","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1099\/00207713-42-4-524","article-title":"Mycobacterium madagascariense sp. nov","volume":"42","author":"Kazda","year":"1992","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"2277","DOI":"10.1099\/ijs.0.000255","article-title":"Mycobacterium anyangense sp. nov., a rapidly growing species isolated from blood of Korean native cattle, Hanwoo (Bos taurus coreanae)","volume":"65","author":"Kim","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1099\/00207713-42-2-257","article-title":"Mycobacterium confluentis sp. nov","volume":"42","author":"Kirschner","year":"1992","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1099\/00207713-46-3-683","article-title":"Mycobacterium hodleri sp. nov., a new member of the fast-growing mycobacteria capable of degrading polycyclic aromatic hydrocarbons","volume":"46","author":"Kleespies","year":"1996","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"3694","DOI":"10.1099\/ijsem.0.001253","article-title":"Mycobacterium lutetiense sp. nov., Mycobacterium montmartrense sp. nov. and Mycobacterium arcueilense sp. nov., members of a novel group of non-pigmented rapidly growing mycobacteria recovered from a water distribution system","volume":"66","author":"Konjek","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref46","doi-asserted-by":"publisher","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":"ref47","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1099\/00207713-42-2-240","article-title":"Proposal of Mycobacterium peregrinum sp. nov., nom. Rev., and elevation of Mycobacterium chelonae subsp. abscessus (Kubica et al.) to species status: Mycobacterium abscessus comb. nov","volume":"42","author":"Kusunoki","year":"1992","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1099\/ijs.0.65222-0","article-title":"Mycobacterium setense sp. nov., a Mycobacterium fortuitum-group organism isolated from a patient with soft tissue infection and osteitis","volume":"58","author":"Lamy","year":"2008","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref49","first-page":"1","volume-title":"Atlas und Grundriss der Bakteriologie und Lehrbuch der speziellen Bakteriologishcen Diagnostik 2. Aufl","author":"Lehmann","year":"1899"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1099\/00207713-33-2-336","article-title":"Mycobacterium fallax sp. nov","volume":"33","author":"Levy-Frebault","year":"1983","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref4","year":"2022"},{"key":"ref52","first-page":"405","article-title":"Mycobacterium brumae sp. nov., a rapidly growing, nonphotochromogenic mycobacterium","volume-title":"Int. J. Syst. Bacteriol.","author":"Luquin","year":"1993"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"854078","DOI":"10.1155\/2015\/854078","article-title":"Use of MALDI-TOF MS for identification of nontuberculous Mycobacterium species isolated from clinical specimens","volume":"2015","author":"Mediavilla-Gradolph","year":"2015","journal-title":"Biomed. Res. Int."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"004922","DOI":"10.1099\/ijsem.0.004922","article-title":"Reconstituting the genus Mycobacterium","volume":"71","author":"Meehan","year":"2021","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/1471-2105-14-60","article-title":"Genome sequence-based species delimitation with confidence intervals and improved distance functions","volume":"14","author":"Meier-Kolthoff","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"i142","DOI":"10.1093\/bioinformatics\/bty266","article-title":"Versatile genome assembly evaluation with QUAST-LG","volume":"34","author":"Mikheenko","year":"2018","journal-title":"Bioinformatics"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"992610","DOI":"10.3389\/fmicb.2022.992610","article-title":"Characterization of Mycobacterium salfingeri sp. nov.: a novel nontuberculous mycobacteria isolated from a human wound infection","volume":"13","author":"Musser","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"3726","DOI":"10.1099\/ijsem.0.003039","article-title":"Description of a novel species of fast growing mycobacterium: Mycobacterium kyogaense sp. nov., a scotochromogenic strain received as Mycobacterium vaccae","volume":"68","author":"Nouioui","year":"","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"2007","DOI":"10.3389\/fmicb.2018.02007","article-title":"Genome-based taxonomic classification of the phylum Actinobacteria","volume":"9","author":"Nouioui","year":"","journal-title":"Front. Microbiol."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"1209","DOI":"10.1007\/s10482-018-1029-5","article-title":"Formal description of Mycobacterium neglectum sp. nov. and Mycobacterium palauense sp. nov., rapidly growing actinobacteria","volume":"111","author":"Nouioui","year":"","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"4948","DOI":"10.1099\/ijsem.0.002350","article-title":"Two novel species of rapidly growing mycobacteria: Mycobacterium lehmannii sp. nov. and Mycobacterium neumannii sp. nov","volume":"67","author":"Nouioui","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"3465","DOI":"10.1099\/ijsem.0.003644","article-title":"Mycolicibacterium stellerae sp. nov., a rapidly growing scotochromogenic strain isolated from Stellera chamaejasme","volume":"69","author":"Nouioui","year":"2019","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"005585","DOI":"10.1099\/ijsem.0.005585","article-title":"International code of nomenclature of prokaryotes. Prokaryotic code (2022 revision)","volume":"73","author":"Oren","year":"2023","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"1411","DOI":"10.1099\/ijsem.0.002711","article-title":"List of new names and new combinations previously effectively, but not validly, published","volume":"68","author":"Oren","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1099\/00207713-37-3-186","article-title":"Mycobacterium poriferae sp. nov., a scotochromogenic, rapidly growing species isolated from a marine sponge","volume":"37","author":"Padgitt","year":"1987","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"005595","DOI":"10.1099\/ijsem.0.005595","article-title":"Mycolicibacterium aurantiacum sp. nov. and Mycolicibacterium xanthum sp. nov., two novel actinobacteria isolated from mangrove sediments","volume":"72","author":"Pan","year":"2022","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"4345","DOI":"10.1099\/ijsem.0.002216","article-title":"Mycobacterium grossiae sp. nov., a rapidly growing, scotochromogenic species isolated from human clinical respiratory and blood culture specimens","volume":"67","author":"Paniz-Mondolfi","year":"2017","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref69","doi-asserted-by":"publisher","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":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"40443","DOI":"10.1038\/srep40443","article-title":"Mycobacterium massilipolynesiensis sp nov., a rapidly-growing mycobacterium of medical interest related to Mycobacterium phlei","volume":"7","author":"Phelippeau","year":"2017","journal-title":"Sci. Rep."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"2575","DOI":"10.1099\/ijs.0.64527-0","article-title":"Mycobacterium monacense sp. nov","volume":"56","author":"Reischl","year":"2006","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"1991","DOI":"10.1099\/00207713-52-6-1991","article-title":"Mycobacterium holsaticum sp. nov","volume":"52","author":"Richter","year":"2002","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref73","doi-asserted-by":"publisher","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":"ref74","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1099\/00207713-50-2-575","article-title":"Mycobacterium septicum sp nov., a new rapidly growing species associated with catheter-related bacteraemia","volume":"50","author":"Schinsky","year":"2000","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.1099\/ijs.0.02743-0","article-title":"Taxonomic variation in the Mycobacterium fortuitum third biovariant complex: description of Mycobacterium boenickei sp. nov., Mycobacterium houstonense sp. nov., Mycobacterium neworleansense sp. nov. and Mycobacterium brisbanense sp. nov. and recognition of Mycobacterium porcinum from human clinical isolates","volume":"54","author":"Schinsky","year":"2004","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1099\/00207713-47-1-86","article-title":"Mycobacterium hassiacum sp. nov., a new rapidly growing thermophilic mycobacterium","volume":"47","author":"Schroder","year":"1997","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref78","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1099\/ijs.0.064832-0","article-title":"Mycobacterium celeriflavum sp. nov., a rapidly growing scotochromogenic bacterium isolated from clinical specimens","volume":"65","author":"Shahraki","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref79","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1099\/ijs.0.043562-0","article-title":"Mycobacterium iranicum sp. nov., a rapidly growing scotochromogenic species isolated from clinical specimens on three different continents","volume":"63","author":"Shojaei","year":"2013","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"1205","DOI":"10.1099\/00207713-47-4-1205","article-title":"Mycobacterium novocastrense sp. nov., a rapidly growing photochromogenic Mycobacterium","volume":"47","author":"Shojaei","year":"1997","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"1817","DOI":"10.1099\/00207713-50-5-1817","article-title":"Mycobacterium elephantis sp. nov., a rapidly growing non-chromogenic Mycobacterium isolated from an elephant","volume":"50","author":"Shojaei","year":"2000","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"1729","DOI":"10.1099\/ijs.0.02999-0","article-title":"Mycobacterium canariasense sp. nov","volume":"54","author":"Soledad Jimenez","year":"2004","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1099\/00207713-45-2-262","article-title":"Phylogeny of the Mycobacterium chelonae-like organism based on partial sequencing of the 16S rRNA gene and proposal of Mycobacterium mucogenicum sp. nov","volume":"45","author":"Springer","year":"1995","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref84","first-page":"627","article-title":"A study of some fast-growing scotochromogenic mycobacteria including species descriptions of Mycobacterium gilvum (new species) and Mycobacterium duv alii (new species)","volume":"52","author":"Stanford","year":"1971","journal-title":"Br. J. Exp. Pathol."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"1901623","DOI":"10.1183\/13993003.01623-2019","article-title":"On the valid publication of names of mycobacteria","volume":"54","author":"Tortoli","year":"2019","journal-title":"Eur. Respir. J."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1099\/ijs.0.003459-0","article-title":"Mycobacterium insubricum sp. nov","volume":"59","author":"Tortoli","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"1900795","DOI":"10.1183\/13993003.00795-2019","article-title":"Same meat, different gravy: ignore the new names of mycobacteria","volume":"54","author":"Tortoli","year":"","journal-title":"Eur. Respir. J."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.meegid.2017.10.013","article-title":"The new phylogeny of the genus Mycobacterium: the old and the news","volume":"56","author":"Tortoli","year":"2017","journal-title":"Infect. Genet. Evol."},{"key":"ref89","doi-asserted-by":"publisher","first-page":"1839","DOI":"10.1099\/00207713-49-4-1839","article-title":"Mycobacterium tusciae sp. nov","volume":"49","author":"Tortoli","year":"1999","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref90","doi-asserted-by":"publisher","first-page":"103983","DOI":"10.1016\/j.meegid.2019.103983","article-title":"Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium","volume":"75","author":"Tortoli","year":"","journal-title":"Infect. Genet. Evol."},{"key":"ref91","doi-asserted-by":"publisher","first-page":"2007","DOI":"10.1099\/00207713-51-6-2007","article-title":"Mycobacterium doricum sp nov","volume":"51","author":"Tortoli","year":"2001","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref92","doi-asserted-by":"publisher","first-page":"4480","DOI":"10.1099\/ijsem.0.001377","article-title":"Mycobacterium sarraceniae sp. nov. and Mycobacterium helvum sp. nov., isolated from the pitcher plant Sarracenia purpurea","volume":"66","author":"Tran","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1099\/ijs.0.02938-0","article-title":"Mycobacterium psychrotolerans sp. nov., isolated from pond water near a uranium mine","volume":"54","author":"Trujillo","year":"2004","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref94","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1099\/00221287-45-2-253","article-title":"Adansonian classification of mycobacteria","volume":"45","author":"Tsukamura","year":"","journal-title":"J. Gen. Microbiol."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1099\/00221287-42-1-7","article-title":"Mycobacterium parafortuitum: a new species","volume":"42","author":"Tsukamura","year":"","journal-title":"J. Gen. Microbiol."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1111\/j.1348-0421.1967.tb00319.x","article-title":"Mycobacterium chitae: a new species","volume":"11","author":"Tsukamura","year":"1967","journal-title":"Jpn. J. Microbiol."},{"key":"ref97","first-page":"229","article-title":"Mycobacterium neoaurum Tsukamura sp. nov","volume":"85","author":"Tsukamura","year":"1972","journal-title":"Med. Biol."},{"key":"ref98","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1099\/00207713-31-3-247","article-title":"Numerical analysis of rapidly growing, nonphotochromogenic mycobacteria, including Mycobacterium agri (Tsukamura 1972) Tsukamura sp. nov., nom. Rev","volume":"31","author":"Tsukamura","year":"1981","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref99","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1099\/00207713-33-4-811","article-title":"Mycobacterium pulveris sp. nov., a nonphotochromatogenic mycobacterium with an intermediate growth rate","volume":"33","author":"Tsukamura","year":"","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref100","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1099\/00207713-31-3-263","article-title":"Numerical analysis of rapidly growing, scotochromogenic mycobacteria, including Mycobacterium obuense sp. nov. nom. Rev. Mycobacterium rhodesiae sp. nov. nom. Rev. Mycobacterium aichiense sp. nov. nom. Rev. Mycobacterium chubuense sp. nov. nom. Rev","volume":"31","author":"Tsukamura","year":"1981","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref101","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1099\/00207713-33-2-162","article-title":"Mycobacterium porcinum sp. nov., a porcine pathogen","volume":"33","author":"Tsukamura","year":"","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref102","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1099\/00207713-33-3-460","article-title":"Numerical taxonomy of rapidly growing, scotochromogenic mycobacteria of the Mycobacterium parafortuitum complex: Mycobacterium austroafricanum sp. nov. and mycobacterium diernhoferi sp. nov., nom. Rev","volume":"33","author":"Tsukamura","year":"","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1099\/00207713-36-2-333","article-title":"Mycobacterium moriokaense sp. nov., a rapidly growing, nonphotochromogenic Mycobacterium","volume":"36","author":"Tsukamura","year":"1986","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref104","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1016\/j.meegid.2019.01.017","article-title":"Nontuberculous mycobacteria: insights on taxonomy and evolution","volume":"72","author":"Turenne","year":"2019","journal-title":"Infect. Genet. Evol."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"2779","DOI":"10.1128\/JCM.41.6.2779-2782.2003","article-title":"Soft tissue infection caused by a novel pigmented, rapidly growing Mycobacterium species","volume":"41","author":"Turenne","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref9001","doi-asserted-by":"publisher","first-page":"2277","DOI":"10.1099\/ijs.0.008854-0","article-title":"Proposal to elevate Mycobacterium avium complex ITS sequevar MAC-Q to Mycobacterium vulneris sp. nov.","volume":"59","author":"van Ingen","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref106","doi-asserted-by":"publisher","first-page":"214","DOI":"10.5588\/ijtld.19.0194","article-title":"A global update on rare non-tuberculous mycobacteria in humans: epidemiology and emergence","volume":"24","author":"Varghese","year":"2020","journal-title":"Int. J. Tuberc. Lung Dis."},{"key":"ref107","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1099\/00207713-49-1-25","article-title":"A new rapidly growing mycobacterial species, Mycobacterium murale sp. nov., isolated from the indoor walls of a children's day care Centre","volume":"49","author":"Vuorio","year":"1999","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref108","doi-asserted-by":"publisher","first-page":"1715","DOI":"10.1099\/00207713-51-5-1715","article-title":"Mycobacterium frederiksbergense sp. nov., a novel polycyclic aromatic hydrocarbon-degrading Mycobacterium species","volume":"51","author":"Willumsen","year":"2001","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref109","doi-asserted-by":"publisher","first-page":"861291","DOI":"10.3389\/fmicb.2022.861291","article-title":"Mycolicibacterium lacusdiani sp. nov., an attached bacterium of Microcystis aeruginosa","volume":"13","author":"Xiao","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref110","doi-asserted-by":"publisher","first-page":"4081","DOI":"10.1099\/ijs.0.050567-0","article-title":"Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium","volume":"63","author":"Zhang","year":"2013","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref111","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1099\/ijs.0.033449-0","article-title":"Mycobacterium litorale sp. nov., a rapidly growing mycobacterium from soil","volume":"62","author":"Zhang","year":"2012","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref112","doi-asserted-by":"publisher","first-page":"1292897","DOI":"10.3389\/fmicb.2023.1292897","article-title":"Contraction and expansion dynamics: deciphering genomic underpinnings of growth rate and pathogenicity in Mycobacterium","volume":"14","author":"Zhu","year":"2023","journal-title":"Front. Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1728622\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T06:35:53Z","timestamp":1771223753000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1728622\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,16]]},"references-count":113,"alternative-id":["10.3389\/fmicb.2026.1728622"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1728622","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,16]]},"article-number":"1728622"}}