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Fibrobacterota

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Fibrobacteres
Scientific classification
Domain:
Bacteria
Phylum:
Fibrobacteres

Garrity and Holt 2012
Classes

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]

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN),[5] National Center for Biotechnology Information (NCBI)[6] and the 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project.[7]

phylum Fibrobacteres and some of its phylogenetic neighbours

Notes: ♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN)

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.[8] 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.[9][10] Most of the clones from mammalian environments group along with the known isolates in what has been called Fibrobacteres subphylum 1.[10] Members of Fibrobacteres subphylum 2 however, have so far been found only in the gut of termites.[10][11] and in some litter-feeding cockroaches.[12] 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.[13]

See also

References

  1. ^ 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.
  2. ^ a b Gupta, R. S. (2004). "The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes". Critical Reviews in Microbiology. 30: 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: 2611–22. doi:10.1099/00221287-147-9-2611.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  4. ^ 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  5. ^ J.P. Euzéby. "Fibrobacteres". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-06-05.
  6. ^ Sayers; et al. "Fibrobacteres". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-06-05.
  7. ^ 'The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-06-05.
  8. ^ "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. 2005. doi:10.1128/jb.187.11.3739-3751.2005. {{cite journal}}: Unknown parameter |authors= ignored (help)
  9. ^ "Detection of novel Fibrobacter populations in landfill sites and determination of their relative abundance via quantitative PCR". Environmental Microbiology. 10 (5). Wiley Online Library: 1310–1319. 2008. doi:10.1111/j.1462-2920.2007.01544.x.
  10. ^ a b c "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). Am Soc Microbiol: 6780–6788. 2006. doi:10.1128/aem.00891-06. {{cite journal}}: Unknown parameter |authors= ignored (help)
  11. ^ 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.
  12. ^ 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: 472–482. doi:10.1016/j.syapm.2015.07.004.
  13. ^ 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 0-683-00603-7. {{cite book}}: |author= has generic name (help)
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