Paraclostridium dentum, a novel species with pathogenic features isolated from human dental plaque sample

Urvashi, .; Choksket, Stanzin; Jain, Ashish; Sharma, Deepika; Grover, Vishakha; Korpole, Suresh

doi:10.1016/j.anaerobe.2020.102239

Cited by 4 publications

(7 citation statements)

References 60 publications

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“…Within this clade, most species are separated by short branches and the two Paeniclostridium species exhibited polyphyletic branching. Similar branching of these species has been reported in earlier studies [4–8, 51]. A close relationship amongst the species from this clade is also suggested by the results from AAI analysis ( and S1).…”

Section: Resultssupporting

confidence: 89%

“…In both our core protein tree and the 16S rRNA tree (Figs 1 and 2), although these two Clostridioides species formed a monophyletic cluster, they are separated from each other by a long branch. Similar distal branching of these two species has been observed in phylogenetic trees reconstructed in earlier studies [4–8, 51]. Based on their relative evolutionary distances, the GTDB taxonomy places these species into two separate genera.…”

Section: Resultssupporting

confidence: 75%

“…(4) The results presented here also show that although the two known Clostridioides species group together in phylogenetic trees, they differ considerably from each other in terms of evolutionary distance and genetic properties. In all reconstructed trees presented here (Figs 1 and 2) and in earlier studies [4][5][6][7][8]51], these two species are separated by long branches. In the GTDB, which uses relative evolutionary distances to classify phylum to genus-level ranks, these two species are placed into two different genera [17].…”

Section: Discussionsupporting

confidence: 71%

“…In different phylogenetic trees reconstructed in this work (Figs 1 and 2), and in earlier studies [5,51], one effectively but nonvalidly published species 'Clostridium dakarense' consistently branches within the Peptostreptococcaceae sensu stricto clade. 2.…”

Section: Csis Demarcating the Romboutsia Sensu Stricto Clade And Line...supporting

confidence: 59%

“…In different phylogenetic trees reconstructed in this work (Figs 1 and 2), and in earlier studies [5, 51], one effectively but non-validly published species ‘ Clostridium dakarense’ consistently branches within the Peptostreptococcaceae sensu stricto clade. Although this species shares an immediate node with the Romboutsia sensu stricto clade (), it branches in a different position in the 16S rRNA gene tree ().…”

Section: Resultsmentioning

confidence: 51%

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Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers

Bello,

McQuay,

Rudra

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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The family Peptostreptococcaceae, which contains 15 genera including Clostridioides, presently lacks proper circumscription. Using 52 available genomes for Peptostreptococcaceae species, we report comprehensive phylogenomic and comparative analyses to reliably discern their evolutionary relationships. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, the examined species formed a strongly supported clade designated as Peptostreptococcaceae sensu stricto. This clade encompassed the genera Peptostreptococcus (type genus), Asaccharospora, Clostridioides, Intestinibacter, Paeniclostridium, Paraclostridium, Peptacetobacter, Romboutsia and Terrisporobacter, and two misclassified species (viz. Eubacterium tenue and ‘Clostridium dakarense’). The distinctness of this clade is strongly supported by eight identified conserved signature indels (CSIs), which are specific for the species from this clade. Based on the robust evidence provided by presented studies, we are proposing the emendment of family Peptostreptococcaceae to only the genera within the Peptostreptococcaceae sensu stricto clade. We also report 67 other novel CSIs, which reliably demarcate different Peptostreptococcaceae species clades and clarify the classification of some misclassified species. Based on the consistent evidence obtained from different presented studies, we are making the following proposals to clarify the classification of Peptostreptococcaceae species: (i) transfer of Eubacterium tenue, Paeniclostridium ghonii and Paeniclostridium sordellii as comb. nov. into the genus Paraclostridium; (ii) transfer of Clostridioides mangenotii as a comb. nov. into Metaclostridioides gen. nov.; (iii) classification of ‘Clostridium dakarense’ as a novel species Faecalimicrobium dakarense gen. nov., sp. nov. (type strain FF1T; genome and 16S rRNA accession numbers GCA_000499525.1 and KC517358, respectively); (iv) transfer of two misclassified species, Clostridium paradoxum and Clostridium thermoalcaliphilum, into Alkalithermobacter gen. nov.; and (v) proposals for two novel families, Peptoclostridiaceae fam. nov. and Tepidibacteraceae fam. nov., to accommodate remaining unclassified Peptostreptococcaceae genera. The described CSIs specific for different families and genera provide novel and reliable means for the identification, diagnostics and biochemical studies on these bacteria.

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Section: Resultssupporting

confidence: 89%

Section: Resultssupporting

confidence: 75%

Section: Discussionsupporting

confidence: 71%

Section: Csis Demarcating the Romboutsia Sensu Stricto Clade And Line...supporting

confidence: 59%

Section: Resultsmentioning

confidence: 51%

See 3 more Smart Citations

Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers

Bello,

McQuay,

Rudra

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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Anticandidal Efficacy of Green Synthesized Silver Nanoparticles Using Trans-Himalayan Plant Extracts Against Drug Resistant Clinical Isolates of Candida auris

Verma,

Riyaz,

Kaur

et al. 2024

Indian J Microbiol

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Genomic insights from Paraclostridium bifermentans HD0315_2: General features and pathogenic potential

et al. 2022

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BackgroundParaclostridium bifermentans is the most diverse distributed species of Paraclostridium and can cause fatal human infections under rare conditions. However, its pathogenic mechanisms and adaptation ability behind infections remain unclear. Herein, we reported the complete genome sequence of P. bifermentans HD0315_2 isolated from the feces of a patient with Crohn's disease. Then, we performed genomic analyses to understand its pathogenic mechanisms and adaptation ability.ResultsThe de novo assembly revealed that the HD0315_2 strain carried a circular chromosome of 3.27 Mb and six circular plasmids (19.41 to 139.50 kb). The phylogenomic analysis assigned the HD0315_2 strain as P. bifermentans and reclassified some previously non-P. bifermentans strains into this clade. The general genomic features showed that this species harbored a flexible genomic pool characterized by variable genome length and multiple plasmids. Then, the HD0315_2 strain was predicted as a human pathogen with high probability, and Listeria LIPI-1 virulence proteins were identified on its genome. Besides, abundant antibiotics/metal/stress resistant genes, such as asrABCH, cat, mccF, macB, entS, albA, bcrA, and tetB, were carried by either the genome or the plasmids. Furthermore, we proposed that transposase-directed horizontal gene transfer was responsible for the distribution of multiple copies of the hin gene in the plasmids.ConclusionThe flexible genomic pool of P. bifermentans encodes abundant functions for antimicrobial or oxidative stress resistance, helping it successfully inhabit and adapt to diverse environments. Moreover, P. bifermentans HD0315_2 might infect hosts via a Listeria LIPI-1-like cycle, with the help of a plasmid expressing the Hin DNA invertase to evade host immune responses.

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Paraclostridium dentum, a novel species with pathogenic features isolated from human dental plaque sample

Cited by 4 publications

References 60 publications

Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers

Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers

Anticandidal Efficacy of Green Synthesized Silver Nanoparticles Using Trans-Himalayan Plant Extracts Against Drug Resistant Clinical Isolates of Candida auris

Genomic insights from Paraclostridium bifermentans HD0315_2: General features and pathogenic potential

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