{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T02:00:13Z","timestamp":1792202413743,"version":"4.4.0"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,5,11]],"date-time":"2019-05-11T00:00:00Z","timestamp":1557532800000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Australian Research Council Linkage","award":["LP150100087"],"award-info":[{"award-number":["LP150100087"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Clostridium is a large genus of obligate anaerobes belonging to the Firmicutes phylum of bacteria, most of which have a Gram-positive cell wall structure. The genus includes significant human and animal pathogens, causative of potentially deadly diseases such as tetanus and botulism. Despite their relevance and many studies suggesting that they are not a monophyletic group, the taxonomy of the group has largely been neglected. Currently, species belonging to the genus are placed in the unnatural order defined as Clostridiales, which includes the class Clostridia. Here, we used genomic data from 779 strains to study the taxonomy and evolution of the group. This analysis allowed us to 1) confirm that the group is composed of more than one genus, 2) detect major differences between pathogens classified as a single species within the group of authentic Clostridium spp. (sensu stricto), 3) identify inconsistencies between taxonomy and toxin evolution that reflect on the pervasive misclassification of strains, and 4) identify differential traits within central metabolism of members of what has been defined earlier and confirmed by us as cluster I. Our analysis shows that the current taxonomic classification of Clostridium species hinders the prediction of functions and traits, suggests a new classification for this fascinating class of bacteria, and highlights the importance of phylogenomics for taxonomic studies.<\/jats:p>","DOI":"10.1093\/gbe\/evz096","type":"journal-article","created":{"date-parts":[[2019,5,6]],"date-time":"2019-05-06T12:07:57Z","timestamp":1557144477000},"page":"2035-2044","source":"Crossref","is-referenced-by-count":129,"title":["Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update"],"prefix":"10.1093","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6751-8897","authenticated-orcid":false,"given":"Pablo","family":"Cruz-Morales","sequence":"first","affiliation":[{"name":"Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia"},{"name":"Joint BioEnergy Institute, Emeryville, CA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camila A","family":"Orellana","sequence":"additional","affiliation":[{"name":"Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Moutafis","sequence":"additional","affiliation":[{"name":"Zoetis, Parkville, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glenn","family":"Moonen","sequence":"additional","affiliation":[{"name":"Zoetis, Parkville, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gonzalo","family":"Rincon","sequence":"additional","affiliation":[{"name":"Zoetis, Parkville, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars K","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esteban","family":"Marcellin","sequence":"additional","affiliation":[{"name":"Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,5,10]]},"reference":[{"issue":"3","key":"2019072413222440700_evz096-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"issue":"Pt 4","key":"2019072413222440700_evz096-B2","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1099\/mic.0.2006\/002287-0","article-title":"A novel toxin homologous to large clostridial cytotoxins found in culture supernatant of Clostridium perfringens type C","volume":"153","author":"Amimoto","year":"2007","journal-title":"Microbiology (Reading, Engl)"},{"key":"2019072413222440700_evz096-B305"},{"issue":"Database issue","key":"2019072413222440700_evz096-B3","doi-asserted-by":"crossref","first-page":"D16","DOI":"10.1093\/nar\/gkj157","article-title":"GenBank","volume":"34","author":"Benson","year":"2006","journal-title":"Nucleic Acids Res"},{"issue":"Pt 2","key":"2019072413222440700_evz096-B4","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1099\/ijs.0.013169-0","article-title":"Clostridium hydrogeniformans sp. nov. and Clostridium cavendishii sp. nov., hydrogen-producing bacteria from chlorinated solvent-contaminated groundwater","volume":"60","author":"Bowman","year":"2010","journal-title":"Int J Syst Evol Microbiol"},{"key":"2019072413222440700_evz096-B5","doi-asserted-by":"crossref","first-page":"24373.","DOI":"10.1038\/srep24373","article-title":"BPGA\u2014an ultra-fast pan-genome analysis pipeline","volume":"6","author":"Chaudhari","year":"2016","journal-title":"Sci Rep"},{"issue":"4","key":"2019072413222440700_evz096-B6","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1099\/00207713-44-4-812","article-title":"The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations","volume":"44","author":"Collins","year":"1994","journal-title":"Int J Syst Bacteriol"},{"issue":"9","key":"2019072413222440700_evz096-B7","doi-asserted-by":"crossref","first-page":"fix086.","DOI":"10.1093\/femsec\/fix086","article-title":"Actinobacteria phylogenomics, selective isolation from an iron oligotrophic environment and siderophore functional characterization, unveil new desferrioxamine traits","volume":"93","author":"Cruz-Morales","year":"2017","journal-title":"FEMS Microbiol Ecol"},{"issue":"7682","key":"2019072413222440700_evz096-B8","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1038\/nature24661","article-title":"A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites","volume":"551","author":"Dodd","year":"2017","journal-title":"Nature"},{"key":"2019072413222440700_evz096-B304"},{"key":"2019072413222440700_evz096-B401"},{"key":"2019072413222440700_evz096-B9","first-page":"151.","article-title":"Defining pathogenic bacterial species in the genomic era","volume":"1","author":"Georgiades","year":"2010","journal-title":"Front Microbiol"},{"issue":"Pt 5","key":"2019072413222440700_evz096-B10","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1099\/ijs.0.059543-0","article-title":"Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov","volume":"64","author":"Gerritsen","year":"2014","journal-title":"Int J Syst Evol Microbiol"},{"key":"2019072413222440700_evz096-B11","first-page":"430","article-title":"History of a case in which a fluid periodically ejected from the stomach contained vegetable organisms of an undescribed form","volume":"57","author":"Goodsir","year":"1842","journal-title":"Edinb Med Surg J"},{"issue":"2","key":"2019072413222440700_evz096-B12","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1093\/molbev\/msp259","article-title":"SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building","volume":"27","author":"Gouy","year":"2010","journal-title":"Mol Biol Evol"},{"key":"2019072413222440700_evz096-B301"},{"issue":"1","key":"2019072413222440700_evz096-B13","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1128\/CMR.3.1.66","article-title":"Toxigenic 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pear orchard soil","volume":"60","author":"Jung","year":"2010","journal-title":"Int J Syst Evol Microbiol"},{"key":"2019072413222440700_evz096-B17","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"key":"2019072413222440700_evz096-B18","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.toxicon.2017.10.012","article-title":"The hypothetical protein P47 of Clostridium botulinum E1 strain Beluga has a structural topology similar to bactericidal\/permeability-increasing protein","volume":"147","author":"Lam","year":"2017","journal-title":"Toxicon"},{"issue":"5","key":"2019072413222440700_evz096-B19","first-page":"1070","article-title":"The taxonomy of the genus Clostridium: current status and future perspectives. Conference: the 7th National Conference of Microbial Resources & the International Symposium on Microbial Systematics and Taxonomy, at Hangzhou, China","volume":"43","author":"Lawson","year":"2016","journal-title":"Microbiol China"},{"key":"2019072413222440700_evz096-B20","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.anaerobe.2016.06.008","article-title":"Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O\u2019Toole 1935) Pr\u00e9vot 1938","volume":"40","author":"Lawson","year":"2016","journal-title":"Anaerobe"},{"issue":"2","key":"2019072413222440700_evz096-B21","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1099\/ijsem.0.000824","article-title":"Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species","volume":"66","author":"Lawson","year":"2016","journal-title":"Int J Syst Evol 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for estimating maximum likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"1A","key":"2019072413222440700_evz096-B25","first-page":"S1","article-title":"International code of nomenclature of prokaryotes","volume":"69","author":"Parker","year":"2015","journal-title":"Int J Syst Evol Microbiol"},{"issue":"3","key":"2019072413222440700_evz096-B26","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/S0966-842X(98)01430-9","article-title":"Clostridium perfringens: toxinotype and genotype","volume":"7","author":"Petit","year":"1999","journal-title":"Trends Microbiol"},{"key":"2019072413222440700_evz096-B27","author":"Prazmowski","year":"1880"},{"key":"2019072413222440700_evz096-B28","first-page":"654","volume-title":"The Prokaryotes: a handbook on the biology of bacteria: Vol. 4: bacteria: firmicutes, cyanobacteria","author":"Rainey","year":"2006","edition":"3rd 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