Fibrobacteres

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]

Fibrobacteres
Scientific classification
Domain:
Superphylum:
Phylum:
Fibrobacteres

Garrity & Holt 2012
Classes
  • ”Chitinispirillia”
  • Chitinivibrionia
  • Fibrobacteria

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]

  • Class "Chitinispirillia" ♠ Sorokin et al. 2016
    • Order "Chitinispirillales" Sorokin et al. 2016
      • Family "Chitinispirillaceae" ♠ Sorokin et al. 2016
        • Genus "Chitinispirillum" ♠ Sorokin et al. 2016
          • Species "Chitinispirillum alkaliphilum" ♠ Sorokin et al. 2016
  • Class Chitinivibrionia Sorokin et al. 2014
    • Order Chitinivibrionales Sorokin et al. 2014
      • Family Chitinivibrionaceae Sorokin et al. 2014
        • Genus Chitinivibrio Sorokin et al. 2014
          • Species Chitinivibrio alkaliphilus Sorokin et al. 2014
  • Class Fibrobacteria Spain et al. 2012
    • Order "Candidatus Fibromonadales" ♠ Abdul Rahman et al. 2016
      • Family "Candidatus Fibromonadaceae" ♠ Abdul Rahman et al. 2016
        • Genus "Candidatus Fibromonas" ♠ Abdul Rahman et al. 2016
          • Species "Candidatus Fibromonas termitidis" ♠ Abdul Rahman et al. 2016
    • Order Fibrobacterales Spain et al. 2012
      • Family Fibrobacteraceae Spain et al. 2012
        • 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
Fibrobacteres
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 (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. ^ 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.
  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. ^ 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. PMC 1112041. PMID 15901698.CS1 maint: Uses authors parameter (link)
  9. ^ 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.
  10. ^ a b c 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. PMC 1610327. PMID 17021231.CS1 maint: Uses authors parameter (link)
  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 (7): 472–482. doi:10.1016/j.syapm.2015.07.004. PMID 26283320.
  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 978-0-683-00603-2.CS1 maint: Extra text: authors list (link)

External links

Bacterial phyla

The bacterial phyla are the major lineages, known as phyla or divisions, of the domain Bacteria.

In the scientific classification established by Carl von Linné, each bacterial strain has to be assigned to a species (binary nomenclature), which is a lower level of a hierarchy of ranks. Currently, the most accepted mega-classification system is under the three-domain system, which is based on molecular phylogeny. In that system, bacteria are members of the domain Bacteria and "phylum" is the rank below domain, since the rank "kingdom" is disused at present in bacterial taxonomy. When bacterial nomenclature was controlled under the Botanical Code, the term division was used, but now that bacterial nomenclature (with the exception of cyanobacteria) is controlled under the Bacteriological Code, the term phylum is preferred.

In this classification scheme, Bacteria is (unofficially) subdivided into 30 phyla with representatives cultured in a lab. Many major clades of bacteria that cannot currently be cultured are known solely and somewhat indirectly through metagenomics, the analysis of bulk samples from the environment. If these possible clades, candidate phyla, are included, the number of phyla is 52 or higher. Therefore, the number of major phyla has increased from 12 identifiable lineages in 1987, to 30 in 2014, or over 50 including candidate phyla. The total number has been estimated to exceed 1,000 bacterial phyla.At the base of the clade Bacteria, close to the last universal common ancestor of all living things, some scientists believe there may be a definite branching order, whereas other scientists, such as Norman Pace, believe there was a large hard polytomy, a simultaneous multiple speciation event.

Bacteroidetes

The phylum Bacteroidetes is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals. Bacteroidetes spp. are part of normal, healthy placental microbiome.Although some Bacteroides spp. can be opportunistic pathogens, many Bacteroidetes are symbiotic species highly adjusted to the gastrointestinal tract. Bacteroides are highly abundant in intestines, reaching up to 1011 cells g−1 of intestinal material. They perform metabolic conversions that are essential for the host, such as degradation of proteins or complex sugar polymers. Bacteroidetes colonize the gastrointestinal already in infants, as non-digestible oligosaccharides in mother milk support the growth of both Bacteroides and Bifidobacterium spp. Bacteroides spp., is selectively recognized by the immune system of the host through specific interactions.

Bacteroidia

The class Bacteroidia is composed of a single order of environmental bacteria. By far, the Bacteroidales order are the most well-studied of the Bacteroidetes. Some members of the genus Bacteroides are opportunistic pathogens. Before the fourth volume of Bergey's Manual of Systematic Bacteriology came out, it was referred to as class Bacteroidetes.

Bergey's Manual of Systematic Bacteriology

Bergey’s Manual of Systematic Bacteriology is the main resource for determining the identity of prokaryotic organisms, emphasizing bacterial species, using every characterizing aspect.

The manual was published subsequent to the Bergey's Manual of Determinative Bacteriology, though the latter is still published as a guide for identifying unknown bacteria. First published in 1923 by David Hendricks Bergey, it is used to classify bacteria based on their structural and functional attributes by arranging them into specific familial orders. However, this process has become more empirical in recent years.The Taxonomic Outline of Bacteria and Archaea (TOBA) is a derived publication indezing taxon names from version two of the manual. It used to be available for free from the Bergey's manual trust website until September 2018. Michigan State University provides an alternative version that indexes NamesforLife records.

Chitinophagaceae

Chitinophagaceae is an aerobic or faculatively anaerobic and rod-shaped family of bacteria in the order of Sphingobacteriales.

Chlorobium

Chlorobium (also known as Chlorochromatium) is a genus of green sulfur bacteria. They are photolithotrophic oxidizers of sulfur and most notably utilise a noncyclic electron transport chain to reduce NAD+. Photosynthesis is achieved using a Type 1 Reaction Centre using bacteriochlorophyll (BChl) a. Two photosynthetic antenna complexes aid in light absorption: the Fenna-Matthews-Olson complex ("FMO", also containing BChl a), and the chlorosomes which employ mostly BChl c, d, or e. Hydrogen sulfide is used as an electron source and carbon dioxide its carbon source.Chlorobium species exhibit a dark green color; in a Winogradsky column, the green layer often observed is composed of Chlorobium. This genus lives in strictly anaerobic conditions below the surface of a body of water, commonly the anaerobic zone of a eutrophic lake.Chlorobium aggregatum is a species which exists in a symbiotic relationship with a colorless, nonphotosynthetic bacteria. This species looks like a bundle of green bacteria, attached to a central rod-like cell which can move around with a flagellum. The green, outer bacteria use light to oxidize sulfide into sulfate. The inner cell, which is not able to perform photosynthesis, reduces the sulfate into sulfide. These bacteria divide in unison, giving the structure a multicellular appearance which is highly unusual in bacteria.Chlorobium species are thought to have played an important part in mass extinction events on Earth. If the oceans turn anoxic (due to the shutdown of ocean circulation) then Chlorobium would be able to out compete other photosynthetic life. They would produce huge quantities of methane and hydrogen sulfide which would cause global warming and acid rain. This would have huge consequences for other oceanic organisms and also for terrestrial organisms. Evidence for abundant Chlorobium populations is provided by chemical fossils found in sediments deposited at the Cretaceous mass extinction.

The complete C. tepidum genome, which consists of 2.15 megabases (Mb), was sequenced and published in 2002. It synthesizes chlorophyll a and bacteriochlorophylls (BChls) a and c, of which the model organism has been used to elucidate the biosynthesis of BChl c. Several of its carotenoid metabolic pathways (including a novel lycopene cyclase) have similar counterparts in cyanobacteria.

Chrysiogenaceae

Chrysiogenaceae is a bacterial family.

Deferribacteraceae

The Deferribacteraceae are a family of gram-negative bacteria which make energy by anaerobic respiration.

Fibrobacter succinogenes

Fibrobacter succinogenes is a cellulolytic bacterium species in the genus Fibrobacter. It is present in the rumen of cattle. Beta glucans are its substrate of choice in the rumen and its products after digestion include formate, acetate and succinate. Fibrobacter succinogenes forms characteristic extensive grooves in crystalline cellulose, and is also rather readily detached from its substrate during sample preparation.

Flavobacteriales

The order Flavobacteriales comprises three families of environmental bacteria.

FtsZ-DE RNA motif

The ftsZ-DE RNA motif is a conserved RNA structure that was discovered by bioinformatics.ftsZ-DE motifs are found in bacteria belonging to the genus Fibrobacter.

It is ambiguous whether ftsZ-DE RNAs function as cis-regulatory elements or whether they operate in trans as small RNAs.

ftsZ-DE RNAs are consistently located immediately downstream of predicted operons, one of whose genes is predicted as ftsZ. ftsZ genes encode a GTPase

that is involved in cell division.

This genomic arrangement could suggest that ftsZ-DE RNAs function as cis-regulatory elements as part of the 3' untranslated regions of these operons. However, these locations rarely contain cis-regulatory RNAs in bacteria. Another possibility that was proposed is that ftsZ-DE RNAs represent an unusual form of Rho-independent transcription terminators that are specific to the under-studied phylum Fibrobacteres, to which Fibrobacter belongs. However, the ftsZ-DE motif exhibits some features that are not found in many Rho-independent terminators, especially that it consists of two hairpins. The function of ftsZ-DE RNAs has not, as of 2018, been established.

List of bacteria genera

This article lists the genera of the bacteria.

List of bacterial orders

This article lists the orders of the Bacteria.

Oceanospirillales

The Oceanospirillales are an order of Proteobacteria with seven families.

Sneathia

Sneathia is a Gram-negative,rod-shaped, non-spore-forming and non-motile genus of bacteria from the family of Leptotrichiaceae. Sneathia is named of the microbiologist H. A. Snaeth.

Sphingobacteria (phylum)

Sphingobacteria is a division (phylum), created by Cavalier-Smith, which contains the classes Chlorobea, Fibrobacteres, Bacteroidetes and Flavobacteria.It is however not followed by the larger scientific community. The group is commonly referred to as the "FCB group" with the rank of superphylum and the subdivisions are of the rank phylum and are referred to as:

Chlorobi (Chlorobea in Cavalier-Smith megaclassification)

Bacteroidetes, which differs from Cavalier-Smith megaclassification as it is composed of the classes Bacteroidia (equivalent to Cavalier-Smith's Bacteroidetes), Cytophagia and Flavobacteria and Sphingobacteria

FibrobacteresAn analogous situation is seen with the PVC group/Planctobacteria.

Sphingobacteriales

The order Sphingobacteriales comprises four families of environmental bacteria.

TG3 (candidate phylum)

Candidate phylum TG3 is a candidate phylum that is closely related to the phylum Fibrobacteres based on 16S rRNA gene phylogeny. Originally thought to be composed solely of sequences from termite guts, it was later found to be more widespread in nature.

Ureaplasma urealyticum

Ureaplasma urealyticum is a bacterium belonging to the genus Ureaplasma and the family Mycoplasmataceae in the order Mycoplasmatales. This family consists of the genera Mycoplasma and Ureaplasma. Its type strain is T960.

Prokaryotes: Bacteria classification (phyla and orders)
G-/
OM
G+/
no OM
Incertae
sedis
Extant Life phyla/divisions by domain

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