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Fibrobacterota

Fibrobacterota
Scientific classification Edit this classification
Domain: Bacteria
Clade: FCB group
Phylum: Fibrobacterota
Garrity & Holt 2021[1]
Classes
Synonyms
  • "Fibrobacteraeota" Oren et al. 2015
  • "Fibrobacteres" Garrity and Holt 2001
  • "Fibrobacterota" Whitman et al. 2018
  • "Raymondbacteria" Anantharaman et al. 2016

Fibrobacterota 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 Fibrobacterota) was removed from the genus Bacteroides in 1988.[2]

Phylogeny and comparative genomic studies

Although Fibrobacterota 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.[3] The species from these three phyla also branch in the same position based upon conserved signature indels in a number of important proteins.[4] 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.[5] 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.[3][5]

Phylogeny

Phylogeny of Fibrobacterota.

16S rRNA based LTP_12_2021[6][7][8] 120 single copy marker proteins based GTDB 08-RS214[9][10][11]
Chitinivibrionia
Fibrobacteria

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[12] and the National Center for Biotechnology Information (NCBI).[13]

phylum Fibrobacterota and some of its phylogenetic neighbours

Distribution

The phylum Fibrobacterota is considered to be closely related to the CFB [Cytophaga-Flavibacterium-Bacteroidota].[5] It contains the genus Fibrobacter, which has strains present in the guts of many mammals including cattle and pigs.[14] 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.[15][16] Most of the clones from mammalian environments group along with the known isolates in what has been called subphylum 1.[16] Members of subphylum 2 however, have so far been found only in the gut of termites.[16][17] and in some litter-feeding cockroaches.[18] The predominance of 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.[19]

See also

References

  1. ^ Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987. S2CID 239887308.
  2. ^ Montgomery L, Flesher B, Stahl D (1988). "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. doi:10.1099/00207713-38-4-430.
  3. ^ a b 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. S2CID 24565648.
  4. ^ 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.
  5. ^ a b c 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. PMC 1887533. PMID 17488508.
  6. ^ "The LTP". Retrieved 23 February 2021.
  7. ^ "LTP_all tree in newick format". Retrieved 23 February 2021.
  8. ^ "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
  9. ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  10. ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  11. ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
  12. ^ Euzéby JP. "Fibrobacteres". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-03-20.
  13. ^ Sayers. "Fibrobacteres". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  14. ^ Qi, M.; Nelson, K.E.; Daugherty, S.C.; Nelson, W.C.; Hance, I.R.; Morrison, M.; 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. PMC 1112041. PMID 15901698.
  15. ^ 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.
  16. ^ a b c Hongoh, Y.; Deevong, P.; Hattori, S.; Inoue, T.; Noda, S.; Noparatnaraporn, N.; Kudo, T.; 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. Bibcode:2006ApEnM..72.6780H. doi:10.1128/aem.00891-06. PMC 1610327. PMID 17021231.
  17. ^ 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. S2CID 206182668.
  18. ^ 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.
  19. ^ 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, ed. (1994). Bergey's Manual of Determinative Bacteriology (9th ed.). Williams & Wilkins. ISBN 978-0-683-00603-2.
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