Priority of the genus name Clostridium Prazmowski 1880 (Approved Lists 1980) vs Sarcina Goodsir 1842 (Approved Lists 1980) and the creation of the illegitimate combinations Clostridium maximum (Lindner 1888) Lawson and Rainey 2016 and Clostridium ventriculi (Goodsir 1842) Lawson and Rainey 2016 that may not be used

Tindall, Brian J.

doi:10.1099/ijsem.0.001361

Cited by 14 publications

(5 citation statements)

References 18 publications

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“…This has previously been observed by others (Yutin and Galperin 2013; Weigand et al. 2015; Lawson and Rainey 2016; Tindall 2016; Udaondo et al. 2017) but to the best of our knowledge, clostridial taxonomy and evolution has not been revisited using the opportunity offered by next-generation sequencing for phylogenomic reclassification until now.…”

Section: Discussionmentioning

confidence: 53%

“…The paroxysm of the conflicting organization of the Clostridium genus is the fact that the Sarcina genus was proposed before (Goodsir 1842) the Clostridium genus (Prazmowski 1880), giving priority to the name Sarcina for the whole genus. Although such change may be excessive and could cause a great deal of confusion, it highlights the need to revisit the taxonomy using modern approaches (see Lawson and Rainey 2016; Tindall 2016 for an interesting discussion on this subject).…”

Section: Introductionmentioning

confidence: 99%

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Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update

Cruz-Morales

Orellana

Moutafis³

et al. 2019

Genome Biology and Evolution

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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.

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Section: Discussionmentioning

confidence: 53%

Section: Introductionmentioning

confidence: 99%

Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update

Cruz-Morales

Orellana

Moutafis³

et al. 2019

Genome Biology and Evolution

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“…A comparison to GTDB taxonomy (i.e., limited to type strains; n ϭ 19 in GTDB) again reveals a high level of congruency with the MiSI method, matching 74% (14/19; Data Set S3B) of the Clostridium designations. The points of disagreement are limited to Clostridium cavendishii, Clostridium fallax, Clostridium perfringens, Clostridium ventriculi (note that this is a validly published name but illegitimate [40]), and Clostridium intestinale, with C. intestinale being a borderline case (i.e., within a 99% confidence interval of the estimated genus inflection point). An updated taxonomy based on phylogenomics has recently proposed to include these five species in Clostridium cluster I (sensu stricto), in agreement with our results (41).…”

mentioning

confidence: 99%

A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

Barco

Scott

Amend

et al. 2020

mBio

254

232

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Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and Archaea. IMPORTANCE In recent decades, the taxonomy of Bacteria and Archaea, and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution.

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“…The nomenclature of the genus Sarcina is contested (and sometimes the genus name Clostridium is substituted) because Sarcina is phylogenetically situated within the "cluster I" group of Clostridia 44 , considered the "true" Clostridia, although these organisms are polyphyletic. A proposal was made to change the name Sarcina to Clostridium, but was not approved because the name Sarcina predates the name Clostridium and therefore has priority 45 .…”

Section: Resultsmentioning

confidence: 99%

A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone

Owens

Colitti

Hirji³

et al. 2021

Nat Commun

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Human and animal infections with bacteria of the genus Sarcina (family Clostridiaceae) are associated with gastric dilation and emphysematous gastritis. However, the potential roles of sarcinae as commensals or pathogens remain unclear. Here, we investigate a lethal disease of unknown etiology that affects sanctuary chimpanzees (Pan troglodytes verus) in Sierra Leone. The disease, which we have named “epizootic neurologic and gastroenteric syndrome” (ENGS), is characterized by neurologic and gastrointestinal signs and results in death of the animals, even after medical treatment. Using a case-control study design, we show that ENGS is strongly associated with Sarcina infection. The microorganism is distinct from Sarcina ventriculi and other known members of its genus, based on bacterial morphology and growth characteristics. Whole-genome sequencing confirms this distinction and reveals the presence of genetic features that may account for the unusual virulence of the bacterium. Therefore, we propose that this organism be considered the representative of a new species, named “Candidatus Sarcina troglodytae”. Our results suggest that a heretofore unrecognized complex of related sarcinae likely exists, some of which may be highly virulent. However, the potential role of “Ca. S. troglodytae” in the etiology of ENGS, alone or in combination with other factors, remains a topic for future research.

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Cited by 14 publications

References 18 publications

Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update

Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update

A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone

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