Bacterial phyla

Molecular phylogenetics

Traditionally, phylogeny was inferred and taxonomy established based on studies of morphology. Recently molecular phylogenetics has been used to allow better elucidation of the evolutionary relationship of species by analysing their DNA and protein sequences, for example their ribosomal DNA. The lack of easily accessible morphological features, such as those present in animals and plants, hampered early efforts of classification and resulted in erroneous, distorted and confused classification, an example of which, noted Carl Woese, is Pseudomonas whose etymology ironically matched its taxonomy, namely "false unit".

Initial sub-division

In 1987, Carl Woese, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences:

New cultured phyla

New species have been cultured since 1987, when Woese's review paper was published, that are sufficiently different that they warrant a new phylum. Most of these are thermophiles and often also chemolithoautotrophs, such as Aquificae, which oxidises hydrogen gas. Other non-thermophiles, such as Acidobacteria, a ubiquitous phylum with divergent physiologies, have been found, some of which are chemolithotrophs, such as Nitrospira (nitrile-oxidising) or Leptospirillum (Fe-oxidising)., some proposed phyla however do not appear in LPSN as they were insufficiently described or are awaiting approval or it is debated if they may belong to a pre-existing phylum. An example of this is the genus Caldithrix, consisting of C. palaeochoryensis and C. abyssi, which is considered Deferribacteres, however, it shares only 81% similarity with the other Deferribacteres (Deferribacter species and relatives) and is considered a separate phylum by Rappé and Giovannoni. Additionally the placement of the genus Geovibrio in the phylum Deferribacteres is debated.

Uncultivated Phyla and metagenomics

With the advent of methods to analyse environmental DNA (metagenomics), the 16S rRNA of an extremely large number of undiscovered species have been found, showing that there are several whole phyla which have no known cultivable representative and that some phyla lack in culture major subdivisions as is the case for Verrucomicrobia and Chloroflexi. The term Candidatus is used for proposed species for which the lack of information prevents it to be validated, such as where the only evidence is DNA sequence data, even if the whole genome has been sequenced. When the species are members of a whole phylum it is called a candidate division (or candidate phylum) and in 2003 there were 26 candidate phyla out of 52. A candidate phylum was defined by Hugenholtz and Pace in 1998, as a set of 16S ribosomal RNA sequences with less than 85% similarity to already-described phyla. More recently an even lower threshold of 75% was proposed. Three candidate phyla were known before 1998, prior to the 85% threshold definition by Hugenholtz and Pace:

Since then several other candidate phyla have been identified:)

Since then a candidate phylum called Poribacteria was discovered, living in symbiosis with sponges and extensively studied. (Note: the divergence of the major bacterial lineages predates sponges) Another candidate phylum, called Tectomicrobia, was also found living in symbiosis with sponges. And Nitrospina gracilis, which had long eluded phylogenetic placement, was proposed to belong to a new phylum, Nitrospinae.

Other candidate phyla that have been the center of some studies are TM7, the genomes of organisms of which have even been sequenced (draft), WS6 and Marine Group A.

Two species of the candidate phylum OP10, which is now called Armatimonadetes, where recently cultured: Armatimonas rosea isolated from the rhizoplane of a reed in a lake in Japan and Chthonomonas calidirosea from an isolate from geothermally heated soil at Hell's Gate, Tikitere, New Zealand.

One species, Caldisericum exile, of the candidate phylum OP5 was cultured, leading to it being named Caldiserica.

The candidate phylum VadinBE97 is now known as Lentisphaerae after Lentisphaera araneosa and Victivallis vadensis were cultured.

More recently several candidate phyla have been given provisional names despite the fact that they have no cultured representatives:

Despite these lineages not being officially recognised (due to the ever-increasing number of sequences belonging to undescribed phyla) the ARB-Silva database lists 67 phyla, including 37 candidate phyla (Acetothermia, Aerophobetes, Aminicenantes, aquifer1, aquifer2, Atribacteria, Calescamantes, CKC4, Cloacimonetes, GAL08, GOUTA4, Gracilibacteria, Fermentibacteria (Hyd24-12), Hydrogenedentes, JL-ETNP-Z39, Kazan-3B-09, Latescibacteria, LCP-89, LD1-PA38, Marinimicrobia, Microgenomates, OC31, Omnitrophica, Parcubacteria, PAUC34f, RsaHF231, S2R-29, Saccharibacteria, SBYG-2791, SHA-109, SM2F11, SR1, TA06, TM6, WCHB1-60, WD272, and WS6), the Ribosomal Database Project 10, lists 49 phyla, including 20 candidate phyla (Acetothermia, Aminicenantes, Atribacteria, BRC1, Calescamantes, Cloacimonetes, Hydrogenedentes, Ignavibacteriae, Latescibacteria, Marinimicrobia, Microgenomates, Nitrospinae, Omnitrophica, Parcubacteria, Poribacteria, SR1, Saccharibacteria, WPS-1, WPS-2, and ZB3), and NCBI lists 120 phyla, including 90 candidate phyla (AC1, Acetothermia, Aerophobetes, Aminicenantes, Atribacteria, Berkelbacteria, BRC1, CAB-I, Calescamantes, CPR1, CPR2, CPR3, EM 3, Fervidibacteria, GAL15, GN01, GN03, GN04, GN05, GN06, GN07, GN08, GN09, GN10, GN11, GN12, GN13, GN14, GN15, Gracilibacteria, Fermentibacteria (Hyd24-12), Hydrogenedentes, JL-ETNP-Z39, KD3-62, kpj58rc, KSA1, KSA2, KSB1, KSB2, KSB3, KSB4, Latescibacteria, marine group A, Marinimicrobia, Microgenomates, MSBL2, MSBL3, MSBL4, MSBL5, MSBL6, NC10, Nitrospinae, NPL-UPA2, NT-B4, Omnitrophica, OP2, OP4, OP6, OP7, OS-K, Parcubacteria, Peregrinibacteria, Poribacteria, RF3, Saccharibacteria, SAM, SBR1093, Sediment-1, Sediment-2, Sediment-3, Sediment-4, SPAM, SR1, TA06, TG2, TM6, VC2, WOR-1, WOR-3, WPS-1, WPS-2, WS1, WS2, WS4, WS5, WS6, WWE3, WYO, ZB3, and Zixibacteria).

Superphyla

Despite the unclear branching order for most bacterial phyla, several groups of phyla have clear clustering and are referred to as superphyla.

The FCB Group

The FCB group includes Bacteroidetes, the unplaced genus Caldithrix, Chlorobi, candidate phylum Cloacimonetes, Fibrobacteres, Gemmatimonadates, candidate phylum Ignavibacteriae, candidate phylum Latescibacteria, candidate phylum Marinimicrobia, and candidate phylum Zixibacteria.

The PVC Group

The PVC group includes Chlamydiae, Lentisphaerae, candidate phylum Omnitrophica, Planctomycetes, candidate phylum Poribacteria, and Verrucomicrobia.

Patescibacteria

The proposed superphylum, Patescibacteria, includes candidate phyla Gracilibacteria, Microgenomates, Parcubacteria, and Saccharibacteria and possibly Dependentiae. These same candidate phyla, along with candidate phyla Berkelbacteria, CPR2, CPR3, Kazan, Perigrinibacteria, SM2F11, WS6, and WWE3 were more recently proposed to belong to the larger CPR Group. To complicate matters, it has been suggested that several of these phyla are themselves actually superphyla (see the section on cryptic superphyla below).

Terrabacteria

The proposed superphylum, Terrabacteria, includes Actinobacteria, Cyanobacteria, Deinococcus–Thermus, Chloroflexi, Firmicutes, and candidate phylum OP10.

Proteobacteria as superphylum

It has been proposed that several of the classes of the phylum Proteobacteria are phyla in their own right, which would make Proteobacteria a superphylum.

Cryptic Superphyla

Several candidate phyla (Microgenomates, Omnitrophica, Parcubacteria, and Saccharibacteria) and several accepted phyla (Elusimicrobia, Caldiserica, and Armatimonadetes) have been suggested to actually be superphyla that were incorrectly described as phyla because rules for defining a bacterial phylum are lacking. For example, it is suggested that candidate phylum Microgenomates is actually a superphylum that encompasses 28 subordinate phyla and that phylum Elusimocrobia is actually a superphylum that encompasses 7 subordinate phyla.

Overview of phyla

As of January 2016, there are 30 phyla in the domain "Bacteria" accepted by LPSN. There are no fixed rules to the nomenclature of bacterial phyla. It was proposed that the suffix "-bacteria" be used for phyla, but generally the name of the phylum is generally the plural of the type genus, with the exception of the Firmicutes, Cyanobacteria, and Proteobacteria, whose names do not stem from a genus name (Actinobacteria instead is from Actinomyces).

Acidobacteria

The Acidobacteria (diderm Gram negative) is most abundant bacterial phylum in many soils, but its members are mostly uncultured. Additionally, they phenotypically diverse and include not only acidophiles, but also many non-acidophiles. Generally its members divide slowly, exhibit slow metabolic rates under low-nutrient conditions and can tolerate well fluctuations in soil hydration.

Actinobacteria

The Actinobacteria is a phylum of monoderm Gram positive bacteria, many of which notable secondary metabolite producers. There are only two phyla of monoderm Gram positive bacteria, the other being the Firmicutes; the actinobacteria generally have higher GC content so are sometimes called "high-CG Gram positive bacteria". Notable genera/species include Streptomyces (antibiotic production), Propionibacterium acnes (odorous skin commensal) and Propionibacterium freudenreichii (holes in Emmental)

Aquificae

The Aquificae (diderm Gram negative) contains only 14 genera (including Aquifex and Hydrogenobacter). The species are hyperthermophiles and chemolithotrophs (sulphur). According to some studies may be one of the most deep branching phyla.

Bacteroidetes

The Bacteroidetes (diderm Gram negative) is a member of the FBC superphylum. Some species are opportunistic pathogens, while other are the most common human gut commensal bacteria. Gained notoriety in the non-scientific community with the urban myth as a bacterial weight loss powder.

Caldiserica

This phylum was formerly known as candidate phylum OP5, Caldisericum exile is the sole representative.

Chlamydiae

The Chlamydiae (diderms, weakly Gram negative) is a phylum of the PVC superphylum. It is composed of only 6 genera of obligate intracellular pathogens with a complex life cycle. Species include Chlamydia trachomatis (chlamydia infection).

Chlorobi

Chlorobi is a member of the FBC superphylum. It contains only 7 genera of obligately anaerobic photoautotrophic bacteria, known colloquially as Green sulfur bacteria. The reaction centre for photosynthesis in Chlorobi and Chloroflexi (another photosynthetic group) is formed by a structures called the chlorosome as opposed to phycobilisomes of cyanobacteria (another photosynthetic group).

Chloroflexi

Chloroflexi,diverse phylum including thermophiles and halorespirers, known colloquially as Green non-sulfur bacteria.

Chrysiogenetes

Chrysiogenetes, only 3 genera (Chrysiogenes arsenatis, Desulfurispira natronophila, Desulfurispirillum alkaliphilum)

Cyanobacteria

Cyanobacteria, major photosynthetic clade believed to have caused Earth's oxygen atmosphere, also known as the blue-green algae

Deferribacteres

Deferribacteres

Deinococcus–Thermus

Deinococcus–Thermus, Deinococcus radiodurans and Thermus aquaticus are "commonly known" species of this phylum.

Dictyoglomi

Dictyoglomi

Elusimicrobia

Elusimicrobia, formerly candidate phylum Termite Group 1

Fibrobacteres

Fibrobacteres, member of the FBC superphylum.

Firmicutes

Firmicutes, Low-G+C Gram positive species most often spore-forming, in two/three classes: the class Bacilli such as the Bacillus spp. (e.g. B. anthracis, a pathogen, and B. subtilis, biotechnologically useful), lactic acid bacteria (e.g. Lactobacillus casei in yoghurt, Oenococcus oeni in malolactic fermentation, Streptococcus pyogenes, pathogen), the class Clostridia of mostly anaerobic sulphite-reducing saprophytic species, includes the genus Clostridium (e.g. the pathogens C. dificile, C. tetani, C. botulinum and the biotech C. acetobutylicum)

Fusobacteria

Fusobacteria

Gemmatimonadetes

Gemmatimonadetes, member of the FBC superphylum.

Lentisphaerae

Lentisphaerae, formerly clade VadinBE97, member of the PVC superphylum.

Nitrospirae

Nitrospirae

Planctomycetes

Planctomycetes, member of the PVC superphylum.

Proteobacteria

Proteobacteria, contains most of the "commonly known" species, such as Escherichia coli and Pseudomonas aeruginosa.

Spirochaetes

Spirochaetes, notable for compartmentalisation and species include Borrelia burgdorferi, which causes Lyme disease.

Synergistetes

The Synergistetes is a phylum whose members are diderm Gram negative, rod-shaped obligate anaerobes, some of which are human commensals.

Tenericutes

The Tenericutes includes the class Mollicutes, formerly/debatedly of the phylum Firmicutes (sister clades). Despite their monoderm Gram-positive relatives, they lack peptidoglycan. Notable genus: Mycoplasma.

Thermodesulfobacteria

The Thermodesulfobacteria is a phylum composed of only three genera in the same family (Thermodesulfobacteriaceae: Caldimicrobium, Thermodesulfatator and Thermodesulfobacterium). The members of the phylum are thermophilic sulphate-reducers.

Thermomicrobia

Thermomicrobia

Thermotogae

The Thermotogae is a phylum of whose members possess an unusual outer envelope called the toga and are mostly hyperthermophilic obligate anaerobic fermenters.

Verrucomicrobia

Verrucomicrobia is a phylum of the PVC superphylum. Like the Planctomycetes species, its members possess a compartmentalised cell plan with a condensed nucleoid and the ribosomes pirellulosome (enclosed by the intracytoplasmic membrane) and paryphoplasm compartment between the intracytoplasmic membrane and cytoplasmic membrane.

Branching order

The branching order of the phyla of bacteria is unclear. Different studies arrive at different results due to different datasets and methods. For example, in studies using 16S and few other sequences Thermotogae and Aquificae appear as the most basal phyla, whereas in several phylogenomic studies, Firmicutes are the most basal.