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Table 2 The 10 phyla (=divisions) of the kingdom Bacteria* recognized here

From: Rooting the tree of life by transition analyses

Formal name Informal names Examples
Subkingdom Negibacteria* (invariably with acyl-ester phospholipid-containing outer membrane: OM)
   Infrakingdom Glidobacteria* infraking. nov. (Description: gliding motility only; primitively lack flagella, endospores, and haem catalase III. Type order: Nostocales)
Superdivision Eobacteria* superking. nov. (earlier infrakingdom and division [1]. Description: no lipopolysaccharide or diaminopimelic acid, TolC or TonB)
Phylum Chlorobacteria green non-sulphur bacteria  
  (Chloroflexi, Thermomicrobia, GNS group) Dehalococcoides
Phylum Hadobacteria Deinococcus/Thermus group Thermus
Superdivision Cyanobacteria* superking. nov. (Description: flagella entirely absent; with lipopolysaccharide, diaminopimelic acid, oxygenic photosynthesis, TolC, TonB).
Phylum Cyanobacteria cyanobacteria, blue-green algae Nostoc
   Infrakingdom Eurybacteria* infraking. nov.1 (typically with endospores; external flagella or gliding motility)
Phylum Eurybacteria* div. nov.1 Classes: Selenobacteria* cl. nov.2 Sporomusa
  incl. Heliobacteriales ord. nov. Heliobacterium
  Fusobacteria cl. nov.3 Leptotrichia
  Togobacteria (Thermotogales) Thermotoga
   Infrakingdom Gracilicutes infraking. nov.4 (murein sacculus very thin or absent; no endospores)
Phylum Spirochaetae spirochaetes and leptospiras (endoflagella) Treponema
Phylum Sphingobacteria (fast gliding; mostly non-flagellate; unique MotB homologue – see text)
Class Chlorobea Chlorobi Chlorobium
Class Flavobacteria CFB group and Fibrobacteres Cytophaga
Superphylum Exoflagellata (external rotary flagella with both L- and P-rings; no sulfonolipids)
Phylum Proteobacteria proteobacteria (flagella; sometimes gliding; always murein)
   Subphylum Rhodobacteria purple bacteria; α-, β- and γ-proteobacteria Escherichia
   Rhizobium, Spirillum
   Subphylum Thiobacteria δ- and ε-proteobacteria Desulfovibrio
  (including gliding Myxobacteria) Geobacter, Bdellovibrio
  plus Aquificales Helicobacter, Aquifex
   Subphylum Geobacteria Deferribacteres, Chrysiogenetes and Acidobacteria groups Geovibrio
Phylum Planctobacteria5 Planctomycetales (flagella; no murein) and Chlamydiae/Verrucomicrobia group Pirellula
Subkingdom Unibacteria* (ancestrally with only a single cell surface membrane; absence of OM with acyl-ester phospholipids and of slime-secretion or pilus-based gliding motility)
Phylum Posibacteria* Gram-positive bacteria (ancestrally very thick murein with lipoprotein sortases; both lost only in Mollicutes)
   Subphylum Endobacteria6 'low-GC Gram-positives'6 + Dictyoglomus
  i.e. Teichobacteria (murein) Bacillus, Clostridium
  Mollicutes (no murein) Mycoplasma
   Subphylum Actinobacteria* high-GC Gram-positives7 Mycobacterium
Phylum Archaebacteria archaebacteria, archaea (isoprenoid ether lipids and N-linked glycoproteins; no murein or lipoprotein)
   Subphylum Euryarchaeota euryarchaeotes (e.g. methanogens, halophiles) Thermoplasma
   Subphylum Crenarchaeota crenarchaeotes Sulfolobus
  1. Informal names are mostly as used in GenBank. The formal, validly published names are explained in detail in [1] with key defining characters, except for four modifications here, i.e. accepting Eurybacteria [69] as a genuine, but slightly revised, phylum and Selenobacteria as a class (originally phylum [142]), placing both Selenobacteria and Thermotogales in Eurybacteria, and revising the circumscription of Gracilicutes. I use the name Proteobacteria more broadly than usual to include also Geobacteria and Aquificales [1]. All 10 phyla are monophyletic on the backbone bacterial tree, except for Posibacteria and Proteobacteria (the grouping there of typical ε-proteobacteria with Sphingobacteria and exclusion of Geobacteria from Proteobacteria are all arguably artefacts of tree reconstruction related to the almost non-existent resolution at the base of eubacteria on single-gene trees [1]) and the artifactual attraction of the hyperthermophiles Aquifex and Thermotoga towards the long-branch archaebacterial outgroup. The latter artifactual attraction is not seen on a 31 protein 191 species tree [175] on which all my phyla would be monophyletic if just three branches (the position of none strongly supported) were moved, as discussed in responses to referee 3; that tree even puts Acidobacteria within Proteobacteria (98% bootstrap support), being thus and in other ways much superior to single-gene trees (including rRNA). Note that the early definition of 10 major eubacterial 'taxa' (actually clades, not taxa) based on 16S rRNA signature sequences [201] was remarkably good and durable, better in some respects (e.g. treatment of what was a little later named Posibacteria [29] as a single phylum) than later ideas based on trees [68], which can be misled by such artefacts; all 10 of those early-recognised major clades are represented as high-level taxa in the present system, six as phyla and four as subphyla (within Proteobacteria and Sphingobacteria); the only phylum in this table not foreshadowed by that rRNA signature analysis is Eurybacteria, which if they are indeed paraphyletic would not have exclusive rRNA signatures, unless they were lost during the formation of Posibacteria.
  2. Many, possibly all, of the so-called 16S rRNA 'deep' branches from thermophilic organisms (whether cultured, e.g. Thermotoga, Aquifex, Dictyoglomus, Thermodesulfobacter, Coprothermobacter, or environmental) that have convergently acquired high GC likely to bias analyses are likely to be phylogenetically misplaced members of one of these 10 phyla rather than genuinely distinct lineages [1, 46]. Bergey's Manual [202] and GenBank use too many small 'phyla', not recognising Sphingobacteria or Planctobacteria even though both are robustly holophyletic on concatenated rRNA trees [18], and Sphingobacteria is strongly supported by indel analysis [83] and recovered by the 31 protein tree [175]; see [1, 69, 142] for a more preferable, organismally oriented, high-level bacterial classification that underlies the simpler system and phylum and subkingdom names used here, and is comprehensive to the class level (but note that the classes suggested for Actinobacteria are probably unsound; they are better retained as a single class [49], pending further research), and in which all names were validly published. *Probably paraphyletic taxa are marked with an asterisk.
  3. 1Formal description: Eurybacteria ([69] but not yet validated by a listing in IJSEM) phyl. nov. Negibacteria, usually with outer membrane lipopolysaccharide, but lacking the two domain insertions in RNA polymerase that characterise Gracilicutes; flagella often present, with L-rings and P-rings; endospores frequently present. Murein, if present, with cadaverine. If anoxygenic photosynthesis present, with bacteriochlorophyll g and no chlorosomes. Etym. Gk eury broad (because of broad range of phenotypes) bacterion rod. Type order Heliobacteriales ord. nov. Description: anaerobic flagellate or sometimes gliding photoheterotrophic (non-CO2 fixing) endospore-forming negibacteria with a homodimeric photosystem similar to photosystem I and bacteriochlorophyll g; type genus Heliobacterium. Etym. Gk helios sun bacterion rod. After type genus.
  4. 2Formal description: Selenobacteria (Cavalier-Smith 1992 as phylum [142], name based on included genus Selenomonas) cl. nov. Often flagellate negibacteria that are endospore formers or have secondarily lost endospores. Type order Sporomusales ord. nov. non-photosynthetic endospore-forming negibacteria and negibacterial descendants without spores. Etym. Derived from the type genus Sporomusa. The class also includes Heliobacteriales. (Selenobacteria are inappropriately lumped by many with Endobacteria under the informal name 'low-GC Gram-positives').
  5. 3Formal description: Fusobacteria (Cavalier-Smith 1998 as phylum [69] cl. nov. Non-spore forming, heterotrophic non-flagellate negibacteria with lipopolysaccharide and Omp85 in outer membrane but lacking the two domain insertions in RNA polymerase that characterise Gracilicutes (Fig. 7 legend); type order Fusobacteriales ord. nov. description as for Fusobacteria, type genus Fusobacterium; Etym Gk fus- spindle bacterion rod, after type genus.
  6. 4 Formal description: Gracilicutes (Gibbons and Murray 1978 [203], originally a division that excluded spirochaetes) infraking. nov. Negibacteria in which the peptidoglycan sacculus, if present, is invariably very thin, and with one or both of two distinct inserts in RNA polymerase: αβ-β' module domain 1 inserted into the universally conserved second sandwich barrel hybrid motif domain in the β-subunit; a long helical module in subunit σ; outer membrane with lipopolysaccharide or lipo-oligosaccharide and Omp85. Type order Chlorobiales.
  7. 5 Monophyly of Planctobacteria, repeatedly questioned since the relationship between Planctomyces and Chlamydia and the name were first proposed [30], is now well supported by multiple protein trees [204] as well as by concatenated rRNA trees [18].
  8. 6 Unlike in [1] Endobacteria now excludes Selenobacteria and Thermotogales because they are now established as Negibacteria (see text). 'Low GC-Gram positives' in most recent usages include the genetically related, but phenotypically non-Gram-positive, Selenobacteria and Mollicutes; by embracing two major and phenotypically very different non Gram-positive classes it is now descriptively profoundly misleading in this sense; the term 'low GC-Gram positives would be best restricted to Teichobacteria alone or else abandoned. The now frequently synonymous name Firmicutes also is not used here, as it has become thoroughly ambiguous and is probably best forgotten; it was originally invented for Actinobacteria plus Teichobacteria, but is now commonly contradictorily and inappropriately used instead for Teichobacteria, mycoplasmas and Selenobacteria collectively, a probably paraphyletic and phenotypically most heterogeneous assemblage, just because these taxa usually form a single branch on 16S rRNA trees. This usage destroys the whole point of the name, which was to contrast the thick-walled unimembranous Actinobacteria/Teichobacteria with the wall-less unimembranous mycoplasmas (Molli- soft; Firmi- hard; cutes skin in Greek). Confusingly the older usage still occurs, but often inappropriately modified to include Mollicutes. The now most prevalent misuse of Firmicutes comprises one group with one membrane and no wall, one with two membranes and a thin wall, and only one of the two groups that have a single membrane and thick wall; probably this group is not holophyletic, but a pseudoclade arising because actinobacteria are artifactually excluded from it because of their very high rRNA GC composition and/or elevated evolutionary rate and because the dramatic quantum evolution and persisting higher evolutionary rate of neomuran rRNA also artifactually drives them still further away [1]. Applying any name – even were it appropriate – to this artifactual pseudogroup is a taxonomically meaningless prime example of how not to use the potentially very valuable information that 16S rRNA trees can provide; like all other information, 16S RNA trees must by tested by their congruence (or incongruence in this case) with independent lines of evidence.
  9. 7A few early branching genera of 'high-GC Gram-positives' (e.g. Symbiobacterium [51]; Rubrobacterales [205]) are more like Endobacteria in some respects, showing that the original distinction between Endobacteria and Actinobacteria has broken down (see discussion in text). The status of such borderline organisms needs clarifying by a taxonomically broad and critical phylogenetic analysis of many conserved proteins and is potentially very important for understanding the origins of actinobacteria and neomura.