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Coriobacteriia

Coriobacteriia
Scientific classification
Kingdom:
Phylum:
Class:
Coriobacteriia König 2013 emend. Gupta et al. 2013
Orders and families
  • Coriobacteriales Stackebrandt et al. 1997 emend. Gupta et al. 2013
    • Atopobiaceae Gupta et al. 2013
    • Coriobacteriaceae Stackebrandt et al. 1997 emend. Gupta et al. 2013
  • Eggerthellales Gupta et al. 2013
    • Eggerthellaceae Gupta et al. 2013
Synonyms
  • Coriobacteridae Stackebrandt et al. 1997 emend. Zhi et al. 2009

The Coriobacteriia are a class of Gram-positive bacteria within the Actinobacteria phylum.[1][2] Species within this group are nonsporulating, strict or facultative anaerobes that are capable of thriving in a diverse set of ecological niches.[3][4][5][6] 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.[7][8] Eggerthella species have been associated with severe blood bacteraemia and ulcerative colitis.[9]

Taxonomy

The Coriobacteriia class currently consists of 16 genera within two orders and three families.[10][11] The Coriobacteriales order consists of two families, the Coriobacteriaceae and Atopobiaceae. The Coriobacteriaceae family contains the Collinsella, Coriobacterium, Enorma, Parvibacter, and Senegalimassilia genera, while the Atopobiaceae contain Atopobium and Olsenella. The Eggerthellales consist of a single family (Eggerthellaceae) and the remaining Coriobacteriia genera (Adlercreutzia , Asaccharobacter, Cryptobacterium, Denitrobacterium, Eggerthella, Enterorhabdus, Gordonibacter, Paraeggerthella, and Slackia).

Molecular signatures and phylogenetic position

Historically, all Coriobacteriia species were placed within a single order (Coriobacteriales) and a single family (Coriobacteriaceae).[1][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.[11] 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.[16] 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.[1][2][11]

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 Actinobacteria.[11] The Coriobacteriia are an early branching lineage within the Actinobacteria phylum[2][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 actinobacterial 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 Actinobacteria species, and absent from all other bacteria.[11] This CSI provides unambiguous support for Coriobacteriia’s membership within the Actinobacteria.[11][16]

Phylogeny

The currently accepted taxonomy is based on the National Center for Biotechnology Information (NCBI).[10]

  • Order Coriobacteriales Stackebrandt et al. 1997 emend. Gupta et al. 2013
    • Family Atopobiaceae Gupta et al. 2013
      • Genus Atopobium Collins & Wallbanks 1993
        • Atopobium deltae Cools et al. 2014
        • Atopobium fossor (Bailey & Love 1986) Kageyama, Benno & Nakase 1999
        • Atopobium minutum (Hauduroy et al. 1937) Collins & Wallbanks 1993
        • Atopobium parvulum (Weinberg, Nativelle & Prevot 1937) Collins & Wallbanks 1993
        • Atopobium rimae (Olsen et al. 1991) Collins & Wallbanks 1993
        • Atopobium vaginae Rodriguez Jovita et al. 1999
      • Genus Olsenella Dewhirst et al. 2001 emend. Kraatz et al. 2011
    • Family Coriobacteriaceae Stackebrandt et al. 1997 emend. Gupta et al. 2013
      • Genus Collinsella Kageyama et al. 1999 emend. Kageyama & Benno 2000
      • Genus Coriobacterium Haas & Konig 1988
        • Coriobacterium glomerans Haas & Konig 1988
      • Genus Enorma Mishra et al. 2013
      • Genus Parvibacter Clavel et al. 2013
        • Parvibacter caecicola Clavel et al. 2013
      • Genus Senegalimassilia corrig. Lagier et al. 2014
        • Senegalimassilia anaerobia corrig. Lagier et al. 2014
  • Order Eggerthellales Gupta et al. 2013
    • Family Eggerthellaceae Gupta et al. 2013
      • Genus Adlercreutzia Maruo et al. 2008
        • Adlercreutzia equilofaciens Maruo et al. 2008
      • Genus Asaccharobacter Minamida et al. 2008
      • Genus Cryptobacterium Nakazawa et al. 1999
      • Genus Denitrobacterium Anderson et al. 2000
        • Denitrobacterium detoxificans Anderson et al. 2000
      • Genus Eggerthella Wade et al. 1999 emend. Würdemann et al. 2009
        • Eggerthella lenta (Eggerth 1935) Wade et al. 1999 emend. Maruo et al. 2008
        • Eggerthella sinensis Lau et al. 2006 emend. Maruo et al. 2008
      • Genus Enterorhabdus Clavel et al. 2009 emend. Clavel et al. 2010
        • Enterorhabdus caecimuris Clavel et al. 2010
        • Enterorhabdus mucosicola Clavel et al. 2009
      • Genus Gordonibacter Wurdemann et al. 2009
        • Gordonibacter faecihominis Jin et al. 2015
        • Gordonibacter pamelaeae Wurdemann et al. 2009
        • Gordonibacter urolithinfaciens Selma et al. 2014
      • Genus Paraeggerthella Wurdemann et al. 2009
        • Paraeggerthella hongkongensis (Lau et al. 2006) Wurdemann et al. 2009
      • Genus Slackia Wade et al. 1999 emend. Nagai, Watanabe & Morotomi 2010

References

  1. ^ a b c Ludwig, W., Euze´ by, J., Schumann, P., Busse, H. J., Trujillo, M. E.,Ka¨ mpfer, 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
  2. ^ a b c Clavel T, Lepage P & Charrier C. (2014). The family Coriobacteriaceae. In: The Prokaryotes, pp. 201-238. Springer-:Berlin Heidelberg
  3. ^ 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.
  4. ^ 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.
  5. ^ 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. PMID 19502325.
  6. ^ 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.
  7. ^ 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.
  8. ^ 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.
  9. ^ 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.
  10. ^ a b Sayers; et al. "Coriobacteriia". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-10-27.
  11. ^ a b c d e f 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.
  12. ^ 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.
  13. ^ 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.
  14. ^ 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.
  15. ^ 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.
  16. ^ 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.