Biology:Fibrobacteres

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Short description: Phylum of bacteria

Fibrobacteres
Scientific classification
Domain:
Bacteria
Superphylum:
FCB group
Phylum:
Fibrobacteres

Garrity & Holt 2012
Classes
  • Chitinivibrionia
  • Fibrobacteria
  • "Raymondbacteria"
Synonyms
  • Fibrobacteraeota Oren et al. 2015
  • "Fibrobacterota" Whitman et al. 2018
  • "Raymondbacteria" Anantharaman et al. 2016

Fibrobacteres is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus Fibrobacter (the only genus of Fibrobacteres) was removed from the genus Bacteroides in 1988.[1]

Phylogeny and Comparative Genomic Studies

Although Fibrobacteres, which consists of a single genus Fibrobacter containing two species, is currently recognized as a distinct phylum, phylogenetic studies based RpoC and Gyrase B protein sequences, indicate that Fibrobacter succinogenes is closely related to the species from the phyla Bacteroidetes and Chlorobi.[2] The species from these three phyla also branch in the same position based upon conserved signature indels in a number of important proteins.[3] Lastly and most importantly, comparative genomic studies have identified two conserved signature indels (a 5-7 amino acid insert in the RpoC protein and a 13-16 amino acid insertion in serine hydroxymethyltransferase) and one signature protein (PG00081) that are uniquely shared by all of the species from these three phyla.[4] All of these results provide compelling evidence that the species from these three phyla shared a common ancestor exclusive of all other bacteria and it has been proposed that they should all recognized as part of a single “FCB”superphylum.[2][4]

Phylogeny

Phylogeny of Fibrobacteres.

16S rRNA-based LTP release 132 by The All-Species Living Tree Project[5] Annotree v1.2.0[6][7] which uses the GTDB 05-RS95 (Genome Taxonomy Database)[8][9]
Fibrobacteres
 

Chitinivibrio alkaliphilus

 
Fibrobacter
 

F. intestinalis

 
F. succinogenes
 

F. s. elongatus

 
 

F. s. succinogenes

 
 
 
 
 
 

"Raymondbacteria"

 
 
Chitinivibrionales
 

Chitinispirillum alkaliphilum

 
 

Chitinivibrio alkaliphilus

 
 
Fibrobacterales
 

"Ca. Fibromonas termitidis"

 
Fibrobacter
 

F. intestinalis

 
F. succinogenes
 

F. s. elongatus

 
 

F. s. succinogenes

 
 
 
 
 
 

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[10] and the National Center for Biotechnology Information (NCBI).[11]

  • Class "Raymondbacteria" [GTDB tag: OXYB2-FULL-49-7] (RIF7)
  • Class Chitinivibrionia Sorokin et al. 2014 [Chitinispirillia Sorokin et al. 2016]
    • Order Chitinivibrionales Sorokin et al. 2014 [Chitinispirillales Sorokin et al. 2016]
      • Family Chitinivibrionaceae Sorokin et al. 2014
        • Genus Chitinivibrio Sorokin et al. 2014
          • Species C. alkaliphilus Sorokin et al. 2014
      • Family Chitinispirillaceae Sorokin et al. 2016
        • Genus Chitinispirillum Sorokin et al. 2016
          • Species C. alkaliphilum Sorokin et al. 2016
  • Class Fibrobacteria Spain et al. 2012
    • Order Fibrobacterales Spain et al. 2012 ["Fibromonadales" Abdul Rahman et al. 2016]
      • Family Fibrobacteraceae Spain et al. 2012 [Fibromonadaceae" Abdul Rahman et al. 2016]
        • Genus "Hallerella" Wylensek et al. 2020
          • Species "H. porci" Wylensek et al. 2021
          • Species "H. succinigenes" Wylensek et al. 2020
        • Genus "Candidatus Fibromonas" Abdul Rahman et al. 2016
          • Species "Ca. F. termitidis" Abdul Rahman et al. 2016
        • Genus Fibrobacter Montgomery et al. 1988
          • Species F. intestinalis Montgomery et al. 1988
          • Species F. succinogenes (Hungate 1950) Montgomery et al. 1988
            • Subspecies F. s. elongatus Montgomery et al. 1988
            • Subspecies F. s. succinogenes (Hungate 1950) Montgomery et al. 1988
phylum Fibrobacteres and some of its phylogenetic neighbours

Distribution

The phylum Fibrobacteres is considered to be closely related to the CFB [Cytophaga-Flavibacterium-Bacteroides].[4] The only genus in this phylum is Fibrobacter that contains strains from the guts of many mammals including cattle and pigs.[12] The two described species in this genus namely, Fibrobacter succinogenes and Fibrobacter intestinalis are important members of fibrolytic communities in mammalian guts and have received a lot of attention in recent decades due to the long-standing interest microbes capable of degrading plant fiber.

Molecular evidence based on the amplification of 16rRNA genes from various environments suggest that the phylum is much more widespread than previously thought.[13][14] Most of the clones from mammalian environments group along with the known isolates in what has been called Fibrobacteres subphylum 1.[14] Members of Fibrobacteres subphylum 2 however, have so far been found only in the gut of termites.[14][15] and in some litter-feeding cockroaches.[16] The predominance of Fibrobacteres subphylum 2 in cellulolytic fibre-associated bacterial communities in hindguts of wood-feeding Nasutitermes corniger suggests that they play an important role in the breakdown of plant material in higher termites.[17]

See also

References

  1. ↑ "Transfer of Bacteroides succinogenes (Hungate) to Fibrobacter gen. nov. as Fibrobacter succinogenes comb. nov. and description of Fibrobacter intestinalis sp. nov". Int. J. Syst. Bacteriol. 38 (4): 430–435. 1988. doi:10.1099/00207713-38-4-430. 
  2. ↑ 2.0 2.1 Gupta, R. S. (2004). "The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes". Critical Reviews in Microbiology 30 (2): 123–140. doi:10.1080/10408410490435133. PMID 15239383. 
  3. ↑ Griffiths, E; Gupta, RS (2001). "The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga- Flavobacterium-Bacteroides division". Microbiology 147 (9): 2611–22. doi:10.1099/00221287-147-9-2611. PMID 11535801. 
  4. ↑ 4.0 4.1 4.2 Gupta, R. S.; Lorenzini, E. (2007). "Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species". BMC Evolutionary Biology 7: 71. doi:10.1186/1471-2148-7-71. PMID 17488508. 
  5. ↑ All-Species Living Tree Project."16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database. https://itol.embl.de/tree/37201229170412631528207598. Retrieved 2015-08-20. 
  6. ↑ "AnnoTree v1.2.0". https://annotree.uwaterloo.ca/app/. 
  7. ↑ Mendler, K; Chen, H; Parks, DH; Hug, LA; Doxey, AC (2019). "AnnoTree: visualization and exploration of a functionally annotated microbial tree of life". Nucleic Acids Research 47 (9): 4442–4448. doi:10.1093/nar/gkz246. PMID 31081040. PMC 6511854. https://academic.oup.com/nar/article/47/9/4442/5432638. 
  8. ↑ "GTDB release 05-RS95". https://gtdb.ecogenomic.org/about#4%7C. 
  9. ↑ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea.". Nature Biotechnology 38 (9): 1079–1086. doi:10.1038/s41587-020-0501-8. PMID 32341564. https://www.researchgate.net/publication/340954053. 
  10. ↑ "Fibrobacteres". List of Prokaryotic names with Standing in Nomenclature (LPSN). https://lpsn.dsmz.de/search?word=Fibrobacteres. 
  11. ↑ Sayers. "Fibrobacteres". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=65842&lvl=3&lin=f&keep=1&srchmode=1&unlock. 
  12. ↑ Qi, M. and Nelson, K.E. and Daugherty, S.C. and Nelson, W.C. and Hance, I.R. and Morrison, M. and Forsberg, C.W. (2005). "Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as determined by suppressive subtractive hybridization". Journal of Bacteriology 187 (11): 3739–3751. doi:10.1128/jb.187.11.3739-3751.2005. PMID 15901698. 
  13. ↑ McDonald, JE; Lockhart, RJ; Cox, MJ; Allison, HE; McCarthy, AJ (2008). "Detection of novel Fibrobacter populations in landfill sites and determination of their relative abundance via quantitative PCR". Environmental Microbiology 10 (5): 1310–1319. doi:10.1111/j.1462-2920.2007.01544.x. PMID 18266756. 
  14. ↑ 14.0 14.1 14.2 Hongoh, Y. and Deevong, P. and Hattori, S. and Inoue, T. and Noda, S. and Noparatnaraporn, N. and Kudo, T. and Ohkuma, M. (2006). "Phylogenetic diversity, localization, and cell morphologies of members of the candidate phylum TG3 and a subphylum in the phylum Fibrobacteres, recently discovered bacterial groups dominant in termite guts". Applied and Environmental Microbiology 72 (10): 6780–6788. doi:10.1128/aem.00891-06. PMID 17021231. 
  15. ↑ Mikaelyan, A.; Dietrich, C.; Köhler, T.; Poulsen, M.; Sillam-Dussès, D.; Brune, A. (2015). "Diet is the primary determinant of bacterial community structure in the guts of higher termites". Molecular Ecology 24 (20): 5824–5895. doi:10.1111/mec.13376. PMID 26348261. 
  16. ↑ Mikaelyan, A.; Köhler, T.; Lampert, N.; Rohland, J.; Boga, H.; Meuser, K.; Brune, A. (2015). "Classifying the bacterial gut microbiota of termites and cockroaches: A curated phylogenetic reference database (DictDb)". Systematic and Applied Microbiology 38 (7): 472–482. doi:10.1016/j.syapm.2015.07.004. PMID 26283320. 
  17. ↑ Mikaelyan, A.; Strassert, J.; Tokuda, G.; Brune, A. (2014). "The fibre-associated cellulolytic bacterial community in the hindgut of wood-feeding higher termites (Nasutitermes spp.)". Environmental Microbiology 16 (9): 2711–2722. doi:10.1111/1462-2920.12425. 
  • Holt JG (editor) (1994). Bergey's Manual of Determinative Bacteriology (9th ed.). Williams & Wilkins. ISBN 978-0-683-00603-2. 

External links

Wikidata ☰ Q1200941 entry




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