Coriobacteriia
| Coriobacteriia | |
|---|---|
Scientific classification  | |
| Domain: | Bacteria |
| Phylum: | Actinomycetota |
| Class: | Coriobacteriia König 2013[1] |
| Orders[2] | |
| Synonyms | |
| |
The Coriobacteriia are a class of Gram-positive bacteria within the Actinomycetota phylum.[3][4] Species within this group are nonsporulating, strict or facultative anaerobes that are capable of thriving in a diverse set of ecological niches.[5][6][7][8] Gordonibacter species are the only members capable of motility by means of flagella within the class. Several species within the Coriobacteriia class have been implicated with human diseases that range in severity. Atopobium, Olsenella, and Cryptobacterium species have responsible for human oral infections including periodontitis, halitosis, and other endodontic infections.[9][10] Eggerthella species have been associated with severe blood bacteraemia and ulcerative colitis.[11]
Molecular signatures and phylogenetic position
[edit]Historically, all Coriobacteriia species were placed within a single order (Coriobacteriales) and a single family (Coriobacteriaceae).[3][12][13][14][15] This view, however, was not reflective of accurate evolutionary interrelationships within the class. The current taxonomic view is justified by the presence of several conserved signature indels (CSIs) that have been found at the different taxonomic ranks.[16] These CSIs are specific and represent synapomorphic characteristics that can be used to distinguish groups within the Coriobacteriia, both at the family and order levels.[17] The distinction of the orders within the Coriobacteriia is also supported phylogenetic tree branching and by consistent characteristics; members belonging to the Coriobacteriales are glucose-fermenting, saccharolytic species while the Eggerthellales order has species that are consistently unable to ferment glucose and are asaccharolytic.[3][4][16]
CSIs have also been used to resolve the phylogenetic position of the Coriobacteriia among all bacteria where they have been found exclusively for all species within the class, delineating them from other Actinomycetota.[16] The Coriobacteriia are an early branching lineage within the Actinomycetota phylum[4][14][15] The deep branching of the class has led to dispute over its membership within the phylum and whether or not it is a true Actinomycetota group.[12][13][14] A CSI in the form of a single amino acid insert in the enzyme deoxyuridine 59-triphosphate (dUTP) nucleotidohydrolase has been found that is shared by all Coriobacteriia members, as well as several Actinomycetota species, and absent from all other bacteria.[16] This CSI provides unambiguous support for Coriobacteriia's membership within the Actinomycetota.[16][17]
Phylogeny
[edit]The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[2] and National Center for Biotechnology Information (NCBI).[18]
| 16S rRNA based LTP_08_2023[19][20][21] | 120 marker proteins based GTDB 08-RS214[22][23][24] | |||
|---|---|---|---|---|
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References
[edit]- ^ König H (2012). "Class III. Coriobacteriia class nov.". In Goodfellow M, Kämpfer P, Trujillo ME, Ludwig W, Whitman WB (eds.). Bergey's Manual of Systematic Bacteriology. Vol. 5 (The Actinobacteria), part B (2nd ed.). New York: Springer. p. 1975.
- ^ a b Euzéby JP, Parte AC. "Coriobacteriia". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved June 23, 2021.
- ^ a b c Ludwig, W., Euzéby, J., Schumann, P., Busse, H. J., Trujillo, M. E.,Kämpfer, P. & Whitman, W. B. (2012). Road map of the phylum Actinobacteria. In: Bergey's Manual of Systematic Bacteriology, pp. 1–28. Eds. M. Goodfellow, P. Ka¨mpfer, H. J. Busse, M. E. Trujillo, K. Suzuki, W. Ludwig & W. B. Whitman. Springer-:New York
- ^ a b c Clavel T, Lepage P & Charrier C. (2014). The family Coriobacteriaceae. In: The Prokaryotes, pp. 201-238. Springer-:Berlin Heidelberg
- ^ Stackebrandt E, Zeytun A, Lapidus A, et al. (2013). "Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug)". Stand Genomic Sci. 8 (1): 15–25. doi:10.4056/sigs.3507020. PMC 3739169. PMID 23961308.
- ^ Nakazawa F, Poco SE, Ikeda T, Sato M, Kalfas S, Sundqvist G, Hoshino E (1999). "Cryptobacterium curtum gen. nov., sp. nov., a new genus of gram-positive anaerobic rod isolated from human oral cavities". Int J Syst Bacteriol. 49 (Pt 3): 1193–200. doi:10.1099/00207713-49-3-1193. PMID 10425779.
- ^ Würdemann D, Tindall BJ, Pukall R, et al. (2009). "Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn's disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov". Int J Syst Bacteriol. 59 (Pt 6): 1405–15. doi:10.1099/ijs.0.005900-0. hdl:10536/DRO/DU:30125259. PMID 19502325.
- ^ Mavrommatis K, Pukall R, Rohde C, et al. (2009). "Complete genome sequence of Cryptobacterium curtum type strain (12-3)". Stand Genomic Sci. 1 (2): 93–100. doi:10.4056/sigs.12260. PMC 3035227. PMID 21304644.
- ^ Copeland A, Sikorski J, Lapidus A, et al. (2009). "Complete genome sequence of Atopobium parvulum type strain (IPP 1246)". Stand Genomic Sci. 1 (2): 166–73. doi:10.4056/sigs.29547. PMC 3035223. PMID 21304653.
- ^ Göker M, Held B, Lucas S, et al. (2010). "Complete genome sequence of Olsenella uli type strain (VPI D76D-27C)". Stand Genomic Sci. 3 (1): 76–84. doi:10.4056/sigs.1082860. PMC 3035265. PMID 21304694.
- ^ Saunders E, Pukall R, Abt B, et al. (2009). "Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255)". Stand Genomic Sci. 1 (2): 174–82. doi:10.4056/sigs.33592. PMC 3035228. PMID 21304654.
- ^ a b Gao B, Gupta RS (2005). "Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria". Int J Syst Evol Microbiol. 55 (Pt 6): 2401–2412. doi:10.1099/ijs.0.63785-0. PMID 16280504.
- ^ a b Gao B, Paramanathan R, Gupta RS (2006). "Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups". Antonie van Leeuwenhoek. 90 (1): 69–91. doi:10.1007/s10482-006-9061-2. PMID 16670965. S2CID 25817892.
- ^ a b c Gao B, Gupta RS (2012). "Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria". Microbiol Mol Biol Rev. 76 (1): 66–112. doi:10.1128/MMBR.05011-11. PMC 3294427. PMID 22390973.
- ^ a b Zhi XY, Li WJ, Stackebrandt E (2009). "An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa". Int J Syst Evol Microbiol. 59 (Pt 3): 589–608. doi:10.1099/ijs.0.65780-0. PMID 19244447.
- ^ a b c d e Gupta RS, Chen WJ, Adeolu M, Chai Y (2010). "Molecular signatures for the class Coriobacteriia and its different clades; Proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov". Int J Syst Evol Microbiol. 63 (3): 3379–97. doi:10.1099/ijs.0.048371-0. PMID 23524353.
- ^ a b Gupta RS (2016). "Impact of genomics on the understanding of microbial evolution and classification: The importance of Darwin's views on classification". FEMS Microbiol Rev. 40 (4): 520–53. doi:10.1093/femsre/fuw011. PMID 27279642.
- ^ Sayers; et al. "Coriobacteriia". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
- ^ "The LTP". Retrieved 20 November 2023.
- ^ "LTP_all tree in newick format". Retrieved 20 November 2023.
- ^ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
- ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
- ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
- ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.