Branching order of bacterial phyla (Ciccarelli et al., 2006)

Last updated

There are several models of the Branching order of bacterial phyla, one of these was proposed in 2006 by Ciccarelli et al. for their iTOL project. [1]

This tree is based on a concatenated set of conserved protein and not 16S rRNA (cf. Branching order of bacterial phyla (Woese, 1987)).

There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.

"Neomura"
 

Domain Eukaryotes (nuclear genome)

 
 

Domain Archaea

 
 
Domain  Bacteria
 

Firmicutes

 
 
 
 
 

Actinobacteria

 
 
 

Planctomycetes

 
 

Spirochaetes

 
 
 
 
 

Chlamydiae

 
 
 

Fibrobacter

 
 
 

Chlorobium

 
 

Bacteroidetes

 
 
 
 
 
 
 
 
 

Fusobacterium

 
 
 

Aquifex

 
 

Thermotoga

 
 
 
 
 

Cyanobacteria

 
 
 

Dehalococcoides (Chloroflexi)

 
 

Deinococcus-Thermus

 
 
 
 
 
 

Proteobacteria subclade

 
 
 

Deltaproteobacteria

 
 

Acidobacteria

 
 
 
 
 
 

The arrangement of the various phyla differs from that of 16S, but may be due to long branch attraction and due to the limited sampling (many phyla have a sole sequenced representative, whereas the Firmicutes and the Proteobacteria are over-represented). The Proteobacteria is not monophyletic in this phylogram, but this may be erroneous given the large amount of literature in favour of basal Acidobacteria. Contrary to 16S trees, the deepest branching clade is the Firmicutes. Nevertheless, the last common ancestor was between Bacteria and Archaea+Eukarya.

In phylogenetics, long branch attraction (LBA) is a form of systematic error whereby distantly related lineages are incorrectly inferred to be closely related. LBA arises when the amount of molecular or morphological change accumulated within a lineage is sufficient to cause that lineage to appear similar to another long-branched lineage, solely because they have both undergone a large amount of change, rather than because they are related by descent. Such bias is more common when the overall divergence of some taxa results in long branches within a phylogeny. Long-branches are often attracted to the base of a phylogenetic tree, because the lineage included to represent an outgroup is often also long-branched. The frequency of true LBA is unclear and often debated, and some authors view it as untestable and therefore irrelevant to empirical phylogenetic inference. Although often viewed as a failing of parsimony-based methodology, LBA could in principle result from a variety of scenarios and be inferred under multiple analytical paradigms.

Firmicutes phylum of bacteria

The Firmicutes are a phylum of bacteria, most of which have gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer membrane that causes them to stain gram-negative. Scientists once classified the Firmicutes to include all gram-positive bacteria, but have recently defined them to be of a core group of related forms called the low-G+C group, in contrast to the Actinobacteria. They have round cells, called cocci, or rod-like forms (bacillus).

See also

There are several models of the Branching order of bacterial phyla, the most cited of these was proposed in 1987 paper by Carl Woese. This cladogram was later expanded by Rappe and Giovanoni in 2003 to include newly discovered phyla.

There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla. One feature of the cladogram obtained with this method is the clustering of cell wall morphology from monoderms to transitional diderms to traditional diderms.

There are several models of the Branching order of bacterial phyla, one of these was proposed in 2002 and 2004 by Thomas Cavalier-Smith. In this frame of work, the branching order of the major lineage of bacteria are determined based on some morphological characters, such as cell wall structure, and not based on the molecular evidence.

Related Research Articles

Gram-positive bacteria bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their cell wall

Gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their cell wall.

Gram-negative bacteria group of bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation

Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the gram-staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane.

Proteobacteria phylum of Gram-negative bacteria

Proteobacteria is a major phylum of gram-negative bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia, Legionellales and many other notable genera. Others are free-living (non-parasitic) and include many of the bacteria responsible for nitrogen fixation.

Domain (biology) Taxonomic rank

In biological taxonomy, a domain [/də(ʊ)ˈmeɪn/], also superkingdom or empire, is the highest taxonomic rank of organisms in the three-domain system of taxonomy designed by Carl Woese et.al. in 1990.

The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. The name 'Aquificae' was given to this phylum based on an early genus identified within this group, Aquifex, which is able to produce water by oxidizing hydrogen. They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods. They are true bacteria as opposed to the other inhabitants of extreme environments, the Archaea.

Bacteroidetes phylum of Gram-negative bacteria

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.

Mollicutes is a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis, and cutis. Individuals are very small, typically only 0.2–0.3 μm in size and have a very small genome size. They vary in form, although most have sterols that make the cell membrane somewhat more rigid. Many are able to move about through gliding, but members of the genus Spiroplasma are helical and move by twisting. The best-known genus in the Mollicutes is Mycoplasma.

The Thermotogae are a phylum of the domain Bacteria. The phylum Thermotogae is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.

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 was removed from the genus Bacteroides in 1988.

Gracilicutes infrakingdom of bacteria

Gracilicutes is a controversial taxon in bacterial taxonomy.

Monera is a kingdom that contains unicellular organisms with a prokaryotic cell organization, such as bacteria. They are single-celled organisms with no true nuclear membrane.

Bacterial phyla

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

Bacterial taxonomy is the taxonomy, i.e. the rank-based classification, of bacteria.

The Negativicutes are a class of bacteria in the phylum Firmicutes, whose members have a peculiar cell wall with a lipopolysaccharide outer membrane which stains gram-negative, unlike most other members of the Firmicutes. Although several neighbouring Clostridia species also stain gram-negative, the proteins responsible for the unusual diderm structure of the Negativicutes may have actually been laterally acquired from Proteobacteria. Additional research is required to confirm the origin of the diderm cell envelope in the Negativicutes.

There are several models of the Branching order of bacterial phyla, one of these was proposed in 2004 by Battistuzzi and Hedges, note the coinage of the taxa Terrabacteria and Hydrobacteria.

Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein.

References

  1. ↑ Ciccarelli, F. D.; Doerks, T; Von Mering, C; Creevey, CJ; Snel, B; Bork, P (2006). "Toward Automatic Reconstruction of a Highly Resolved Tree of Life". Science. 311 (5765): 1283–1287. Bibcode:2006Sci...311.1283C. CiteSeerX   10.1.1.381.9514 . doi:10.1126/science.1123061. PMID   16513982.

This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.