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.[Note 1] 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)[Note 2] 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.
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".
- Purple Bacteria and their relatives (later renamed Proteobacteria)
- alpha subdivision (purple non-sulfur bacteria, rhizobacteria, Agrobacterium, Rickettsiae, Nitrobacter)
- beta subdivision (Rhodocyclus, (some) Thiobacillus, Alcaligenes, Spirillum, Nitrosovibrio)
- gamma subdivision (enterics, fluorescent pseudomonads, purple sulfur bacteria, Legionella, (some) Beggiatoa)
- delta subdivision (Sulfur and sulfate reducers (Desulfovibrio), Myxobacteria, Bdellovibrio)
- Gram-positive Eubacteria[Note 3]
- High-G+C species (later renamed Actinobacteria) (Actinomyces, Streptomyces, Arthrobacter, Micrococcus, Bifidobacterium)
- Low-G+C species (later renamed Firmicutes) (Clostridium, Peptococcus, Bacillus, Mycoplasma)
- Photosynthetic species (Heliobacteria)
- Species with Gram-negative walls (Megasphaera, Sporomusa)
- Cyanobacteria and chloroplasts (Aphanocapsa, Oscillatoria, Nostoc, Synechococcus, Gloeobacter, Prochloron)
- Spirochetes and relatives
- Green sulfur bacteria (Chlorobium, Chloroherpeton)
- Bacteroides, Flavobacteria and relatives (later renamed Bacteroidetes
- Planctomyces and relatives (later renamed Planctomycetes)
- Chlamydiae (Chlamydia psittaci, Chlamydia trachomatis)
- Radioresistant micrococci and relatives (now commonly referred to as Deinococcus–Thermus or Thermi)[Note 5]
- Green non-sulfur bacteria and relatives (later renamed Chloroflexi)
- Thermotogae (Thermotoga maritima)
New cultured phylaEdit
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 metagenomicsEdit
This section needs additional citations for verification. (January 2018) (Learn how and when to remove this template message)
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:
- OS-K group (from Octopus spring, Yellowstone National Park)
- Marine Group A (from Pacific ocean)
- Termite Group 1 (from a Reticulitermes speratus termite gut, now Elusimicrobia)
Since then several other candidate phyla have been identified:)
- OP1, OP3, OP5 (now Caldiserica), OP8, OP9 (now Atribacteria), OP10 (now Armatimonadetes), OP11 (obsidian pool, Yellowstone National Park)
- WS2, WS3, WS5, WS6 (Wurtsmith contaminated aquifer)
- SC3 and SC4 (from arid soil)
- vadinBE97 (now Lentisphaerae)
- NC10 (from flooded caves)
- BRC1 (from bulk soil and rice roots)
- ABY1 (from sediment)
- Guyamas1 (from hydrothermal vents)
- GN01, GN02, GN04 (from a Guerrero Negro hypersaline microbial mat)
- NKB19 (from activated sludge)
- SBR1093 (from activated sludge)
- TM6 and TM7 (Torf, Mittlere Schicht lit. "peat, middle layer")
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.
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.
More recently several candidate phyla have been given provisional names despite the fact that they have no cultured representatives:
- Candidate phylum ACD58 was renamed Berkelbacteria
- Candidate phylum CD12 (also known as candidate phylum BHI80-139) was renamed Aerophobetes
- Candidate phylum EM19 was renamed Calescamantes
- Candidate phylum GN02 (also known as candidate phylum BD1-5) was renamed Gracilibacteria
- Candidate phylum KSB3 was renamed Modulibacteria
- Candidate phylum NKB19 was renamed Hydrogenedentes
- Candidate phylum OctSpa1-106 was renamed Fervidibacteria
- Candidate phylum OD1 was renamed Parcubacteria
- Candidate phylum OP1 was renamed Acetothermia
- Candidate phylum OP3 was renamed Omnitrophica
- Candidate phylum OP8 was renamed Aminicenantes
- Candidate phylum OP9 (also known as candidate phylum JS1) was renamed Atribacteria
- Candidate phylum OP11 was renamed Microgenomates
- Candidate phylum PER was renamed Perigrinibacteria
- Candidate phylum SAR406 (also known as candidate phylum Marine Group A) was renamed Marinimicrobia
- Candidate phylum SR1 was renamed Absconditabacteria
- Candidate phylum TM6 was renamed Dependentiae
- Candidate phylum TM7 was renamed Saccharibacteria
- Candidate phylum WS3 was renamed Latescibacteria
- Candidate phylum WWE1 was renamed Cloacimonetes
- Candidate phylum WWE3 was renamed Katanobacteria
- Candidate phylum ZB1 was renamed Ignavibacteriae
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).
Despite the unclear branching order for most bacterial phyla, several groups of phyla have clear clustering and are referred to as superphyla.
The FCB GroupEdit
The FCB group (now called Sphingobacteria) 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 GroupEdit
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).
Proteobacteria as superphylumEdit
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. It was recently proposed that the class Epsilonproteobacteria be combined with the order Desulfurellales to create the new phylum Epsilonbacteraeota.
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 phylaEdit
As of January 2016[update], 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).
The Acidobacteria (diderm Gram negative) is most abundant bacterial phylum in many soils, but its members are mostly uncultured. Additionally, they are 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 fluctuations in soil hydration.
The Actinobacteria is a phylum of monoderm Gram positive bacteria, many of which are 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)
The Aquificae (diderm Gram negative) contains only 14 genera (including Aquifex and Hydrogenobacter). The species are hyperthermophiles and chemolithotrophs (sulphur). According to some studies, this may be one of the most deep branching phyla.
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 of a bacterial weight loss powder.
This phylum was formerly known as candidate phylum OP5, Caldisericum exile is the sole representative.
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 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, a diverse phylum including thermophiles and halorespirers, are known colloquially as Green non-sulfur bacteria.
Chrysiogenetes, only 3 genera (Chrysiogenes arsenatis, Desulfurispira natronophila, Desulfurispirillum alkaliphilum)
Cyanobacteria, major photosynthetic clade believed to have caused Earth's oxygen atmosphere, also known as the blue-green algae
Deinococcus–Thermus, Deinococcus radiodurans and Thermus aquaticus are "commonly known" species of this phylum.
Elusimicrobia, formerly candidate phylum Termite Group 1
Fibrobacteres, member of the FBC superphylum.
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)
Gemmatimonadetes, member of the FBC superphylum.
Lentisphaerae, formerly clade VadinBE97, member of the PVC superphylum.
Planctomycetes, member of the PVC superphylum.
The Synergistetes is a phylum whose members are diderm Gram negative, rod-shaped obligate anaerobes, some of which are human commensals.
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.
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.
The Thermotogae is a phylum of whose members possess an unusual outer envelope called the toga and are mostly hyperthermophilic obligate anaerobic fermenters.
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.
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.
- Branching order of bacterial phyla (Woese, 1987)
- Branching order of bacterial phyla (Rappe and Giovanoni, 2004)
- Branching order of bacterial phyla after ARB Silva Living Tree
- Branching order of bacterial phyla (Ciccarelli et al., 2006)
- Branching order of bacterial phyla (Battistuzzi et al., 2004)
- Branching order of bacterial phyla (Gupta, 2001)
- Branching order of bacterial phyla (Cavalier-Smith, 2002)
- Past editions of Brock Biology of Microorganisms have referred to the phyla as kingdoms.
- For historical reasons, taxa above the rank of class are not covered by the Rules of the Bacteriological Code (1990 Revision), consequently there is no "official" nomenclature, but there are several authorities in the field, such as Bergey's Manual of Systematic Bacteriology, which contains a taxonomy outline and the journal International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM), on which the List of Prokaryotic names with Standing in Nomenclature (LPSN) repository is based.
- Until recently, it was believed than only Firmicutes and Actinobacteria were Gram-positive. However, the candidate phylum TM7 may also be Gram positive. Chloroflexi however possess a single bilayer, but stain negative (with some exceptions).
- Pasteuria is now assigned to phylum Bacilli, not to phylum Planctomycetes.
- It has been proposed to call the clade Xenobacteria or Hadobacteria (the latter is considered an illegitimate name).
- Ciccarelli FD; et al. (2006). "Toward automatic reconstruction of a highly resolved tree of life". Science. 311 (5765): 1283–7. Bibcode:2006Sci...311.1283C. CiteSeerX 10.1.1.381.9514. doi:10.1126/science.1123061. PMID 16513982.
- Carl Linnaeus (1735). Systemae Naturae, sive regna tria naturae, systematics proposita per classes, ordines, genera & species.
- Woese, C. R.; Kandler, O.; Wheelis, M. L. (1990). "Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences. 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
- Lapage, S. P.; Sneath PHA; Lessel, E. F.; Skerman VBD; Seeliger HPR; Clark, W. A. (1992). Lapage SP; Sneath PHA; Lessel EF; Skerman VBD; Seeliger HPR; Clark WA, eds. International Code of Nomenclature of Bacteria, 1990 Revision. Washington (DC): American Society for Microbiology. ISBN 978-1-55581-039-9. PMID 21089234.
- Madigan M (2009). Brock Biology of Microorganisms. San Francisco: Pearson/Benjamin Cummings. ISBN 978-0-13-232460-1.
- Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzéby J, Tindall BJ (2007). "Taxonomic Outline of the Bacteria and Archaea, Release 7.7". Taxonomic Outline of Bacteria and Archaea. doi:10.1601/TOBA7.7.
- Bacterial phyla entry in LPSN [Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int J Syst Bacteriol. 47 (2): 590–2. doi:10.1099/00207713-47-2-590. ISSN 0020-7713. PMID 9103655.]
- Rappe, M. S.; Giovannoni, S. J. (2003). "The Uncultured Microbial Majority". Annual Review of Microbiology. 57: 369–94. doi:10.1146/annurev.micro.57.030502.090759. PMID 14527284.
- Yarza P; et al. (2014). "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences". Nature Reviews Microbiology. 12 (9): 635–645. doi:10.1038/nrmicro3330. hdl:10261/123763. PMID 25118885.
- Pace, N. R. (2009). "Mapping the Tree of Life: Progress and Prospects". Microbiology and Molecular Biology Reviews. 73 (4): 565–576. doi:10.1128/MMBR.00033-09. PMC 2786576. PMID 19946133.
- Olsen GJ, Woese CR, Overbeek R (1994). "The winds of (evolutionary) change: breathing new life into microbiology". Journal of Bacteriology. 176 (1): 1–6. doi:10.2172/205047. PMC 205007. PMID 8282683.
- Woese, CR (1987). "Bacterial evolution". Microbiological Reviews. 51 (2): 221–71. PMC 373105. PMID 2439888.
- Schluenzen F; et al. (2000). "Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution". Cell. 102 (5): 615–23. doi:10.1016/S0092-8674(00)00084-2. PMID 11007480.
- Holland L (22 May 1990). "Carl Woese in forefront of bacterial evolution revolution". The Scientist. 3 (10).
- Stackebrandt; et al. (1988). "Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "purple bacteria and their relatives"". Int. J. Syst. Bacteriol. 38 (3): 321–325. doi:10.1099/00207713-38-3-321.
- Hugenholtz, P.; Tyson, G. W.; Webb, R. I.; Wagner, A. M.; Blackall, L. L. (2001). "Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives". Applied and Environmental Microbiology. 67 (1): 411–9. doi:10.1128/AEM.67.1.411-419.2001. PMC 92593. PMID 11133473.
- Yabe, S.; Aiba, Y.; Sakai, Y.; Hazaka, M.; Yokota, A. (2010). "Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria". International Journal of Systematic and Evolutionary Microbiology. 61 (4): 903–910. doi:10.1099/ijs.0.024877-0. PMID 20495028.
- Sutcliffe, I. C. (2011). "Cell envelope architecture in the Chloroflexi: A shifting frontline in a phylogenetic turf war". Environmental Microbiology. 13 (2): 279–282. doi:10.1111/j.1462-2920.2010.02339.x. PMID 20860732.
- Stackebrandt, E.; Rainey, F. A.; Ward-Rainey, N. L. (1997). "Proposal for a New Hierarchic Classification System, Actinobacteria classis nov". International Journal of Systematic Bacteriology. 47 (2): 479–491. doi:10.1099/00207713-47-2-479.
- J.P. Euzéby. "List of Prokaryotic names with Standing in Nomenclature: classification of Deinococcus–Thermus". Archived from the original on 27 January 2013. Retrieved 30 December 2010.
- Bergey's Manual of Systematic Bacteriology 1st Ed.
- Cavalier-Smith, T (2002). "The neomuran origin of Archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 1): 7–76. doi:10.1099/00207713-52-1-7. PMID 11837318.
- "List of Prokaryotic names with Standing in Nomenclature—Class Hadobacteria". LPSN. Archived from the original on 19 April 2012. Retrieved 30 December 2010. Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int J Syst Bacteriol. 47 (2): 590–2. doi:10.1099/00207713-47-2-590. ISSN 0020-7713. PMID 9103655.
- Boone DR; Castenholz RW (May 18, 2001) [1984 (Williams & Wilkins)]. Garrity GM, ed. The Archaea and the Deeply Branching and Phototrophic Bacteria. Bergey's Manual of Systematic Bacteriology. 1 (2nd ed.). New York: Springer. p. 721. ISBN 978-0-387-98771-2. British Library no. GBA561951.
- Miroshnichenko ML; et al. (2009). "Caldithrix palaeochoryensis sp. nov., a thermophilic, anaerobic, chemo-organotrophic bacterium from a geothermally heated sediment, and emended description of the genus Caldithrix". International Journal of Systematic and Evolutionary Microbiology. 60 (Pt 9): 2120–3. doi:10.1099/ijs.0.016667-0. PMID 19854873.
- Miroshnichenko ML; et al. (2003). "Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage". International Journal of Systematic and Evolutionary Microbiology. 53 (Pt 1): 323–9. doi:10.1099/ijs.0.02390-0. PMID 12656191.
- Euzéby JP. "List of Prokaryotic names with Standing in Nomenclature: Caldithrix". Archived from the original on 22 January 2011. Retrieved 30 December 2010.
- Euzéby JP. "List of Prokaryotic names with Standing in Nomenclature: Deferribacterales". Archived from the original on 5 April 2011. Retrieved 30 December 2010.
- Murray, R. G. E.; Schleifer, K. H. (1994). "Taxonomic Notes: A Proposal for Recording the Properties of Putative Taxa of Procaryotes". International Journal of Systematic Bacteriology. 44 (1): 174–6. doi:10.1099/00207713-44-1-174. PMID 8123559.
- Frederiksen, W (1995). "Judicial commission of the international committee on systematic bacteriology: Minutes of the meetings, 2 and 6 July 1994, Prague, Czech Republic" (PDF). Int. J. Syst. Bacteriol. 45 (1): 195–196. doi:10.1099/00207713-45-1-195.
- Hugenholtz P; et al. (1998). "Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity". Journal of Bacteriology. 180 (18): 4765–74. PMC 107498. PMID 9733676.
- Hugenholtz P; et al. (1998). "Novel division level bacterial diversity in a Yellowstone hot spring". Journal of Bacteriology. 180 (2): 366–76. PMC 106892. PMID 9440526.
- Geissinger O; et al. (2009). "The Ultramicrobacterium Elusimicrobium minutum gen. nov., sp. nov., the first cultivated representative of the Termite Group 1 Phylum". Applied and Environmental Microbiology. 75 (9): 2831–40. doi:10.1128/AEM.02697-08. PMC 2681718. PMID 19270135.
- Hug LA; et al. (2016). "A new view of the tree of life". Nature Microbiology. Article 16048 (5): 16048. doi:10.1038/nmicrobiol.2016.48. PMID 27572647.
- Fieseler L; et al. (2004). "Discovery of the Novel Candidate Phylum "Poribacteria" in Marine Sponges". Applied and Environmental Microbiology. 70 (6): 3724–32. doi:10.1128/AEM.70.6.3724-3732.2004. PMC 427773. PMID 15184179.
- Wilson MC; et al. (2014). "An environmental bacterial taxon with a large and distinct metabolic repertoire". Nature. 506 (7486): 58–62. Bibcode:2014Natur.506...58W. doi:10.1038/nature12959. PMID 24476823.
- Lucker S; et al. (2013). "The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer". Front. Microbiol. 4: 27. doi:10.3389/fmicb.2013.00027. PMC 3578206. PMID 23439773.
- Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR (July 2007). "Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth". Proceedings of the National Academy of Sciences of the United States of America. 104 (29): 11889–94. doi:10.1073/pnas.0704662104. PMC 1924555. PMID 17620602.
- Dojka MA; et al. (2000). "Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria". Applied and Environmental Microbiology. 66 (4): 1617–21. doi:10.1128/AEM.66.4.1617-1621.2000. PMC 92031. PMID 10742250.
- Tamaki H; et al. (2010). "Armatimonas rosea gen. nov., sp. nov., a Gram-negative, aerobic, chemoheterotrophic bacterium of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10". International Journal of Systematic and Evolutionary Microbiology. 61 (Pt 6): 1442–7. doi:10.1099/ijs.0.025643-0. PMID 20622056.
- Lee KCY; et al. (2010). "Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic microorganism of a novel bacterial class, Chthonomonadetes classis. nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10". International Journal of Systematic and Evolutionary Microbiology. 61 (Pt 10): 2482–90. doi:10.1099/ijs.0.027235-0. PMID 21097641.
- Mori K; et al. (2009). "Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov". International Journal of Systematic and Evolutionary Microbiology. 59 (Pt 11): 2894–8. doi:10.1099/ijs.0.010033-0. PMID 19628600.
- Cho JC; et al. (2004). "Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae". Environmental Microbiology. 6 (6): 611–21. doi:10.1111/j.1462-2920.2004.00614.x. PMID 15142250.
- Rinke C; et al. (2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499 (7459): 431–7. Bibcode:2013Natur.499..431R. doi:10.1038/nature12352. PMID 23851394.
- Wrighton KC; et al. (2014). "Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer". The ISME Journal. 8 (7): 1452–1463. doi:10.1038/ismej.2013.249. PMC 4069391. PMID 24621521.
- Sekiguchi Y; et al. (2015). "First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking". PeerJ. 3: e740. doi:10.7717/peerj.740. PMC 4312070. PMID 25650158.
- Brown CT; et al. (2015). "Unusual biology across a group comprising more than 15% of domain Bacteria". Nature. 523 (7559): 208–11. Bibcode:2015Natur.523..208B. doi:10.1038/nature14486. PMID 26083755.
- Yeoh YK; et al. (2015). "Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage". Mol Biol Evol. 33 (4): 915–927. doi:10.1093/molbev/msv281. PMC 4776705. PMID 26615204.
- Albertsen M; et al. (2013). "Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes". Nat. Biotechnol. 31 (6): 533–8. doi:10.1038/nbt.2579. PMID 23707974.
- Podosokorskaya OA; et al. (2013). "Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae". Environ. Microbiol. 15 (6): 1759–71. doi:10.1111/1462-2920.12067. PMID 23297868.
- Kirkegaard, Rasmus Hansen; Dueholm, Morten Simonsen; McIlroy, Simon Jon; Nierychlo, Marta; Karst, Søren Michael; Albertsen, Mads; Nielsen, Per Halkjær (2016-10-01). "Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters". The ISME Journal. 10 (10): 2352–2364. doi:10.1038/ismej.2016.43. ISSN 1751-7370. PMC 5030696. PMID 27058503.
- "ARB-Silva: comprehensive ribosomal RNA database". The ARB development Team. Retrieved January 2, 2016.
- "Hierarchy Browser". Ribosomal database project. Retrieved January 2, 2016.
- "Taxonomy Browser". NCBI. Retrieved January 2, 2016.
- Battistuzzi FU, Feijao A, Hedges SB (November 2004). "A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land". BMC Evolutionary Biology. 4: 44. doi:10.1186/1471-2148-4-44. PMC 533871. PMID 15535883.
- Battistuzzi, F. U.; Hedges, S. B. (6 November 2008). "A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land". Molecular Biology and Evolution. 26 (2): 335–343. doi:10.1093/molbev/msn247. PMID 18988685.
- Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P (2017). "Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)". Frontiers in Microbiology. 8: 682. doi:10.3389/fmicb.2017.00682. PMC 5401914. PMID 28484436.
- Murray, R. G. E. 1984. The higher taxa, or, a place for everything…?, p. 33. In N. R. Krieg and J. G. Holt (ed.), Bergey’s manual of systematic bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore.
- Kielak, A.; Pijl, A. S.; Van Veen, J. A.; Kowalchuk, G. A. (2008). "Phylogenetic diversity of Acidobacteria in a former agricultural soil". The ISME Journal. 3 (3): 378–382. doi:10.1038/ismej.2008.113. PMID 19020558.
- Ward NL; et al. (2009). "Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils". Applied and Environmental Microbiology. 75 (7): 2046–2056. doi:10.1128/AEM.02294-08. PMC 2663196. PMID 19201974.
- Duncan SH; et al. (2008). "Human colonic microbiota associated with diet, obesity and weight loss". International Journal of Obesity. 32 (11): 1720–1724. doi:10.1038/ijo.2008.155. PMID 18779823.
- Oostergetel GT, Amerongen H, Boekema EJ (2010). "The chlorosome: A prototype for efficient light harvesting in photosynthesis". Photosynthesis Research. 104 (2–3): 245–255. doi:10.1007/s11120-010-9533-0. PMC 2882566. PMID 20130996.
- Marchandin HLN; et al. (2010). "Phylogeny, diversity and host specialization in the phylum Synergistetes with emphasis on strains and clones of human origin". Research in Microbiology. 161 (2): 91–100. doi:10.1016/j.resmic.2009.12.008. PMID 20079831.
- Lee, K. C.; Webb, R. I.; Janssen, P. H.; Sangwan, P.; Romeo, T.; Staley, J. T.; Fuerst, J. A. (2009). "Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes". BMC Microbiology. 9: 5. doi:10.1186/1471-2180-9-5. PMC 2647929. PMID 19133117.
- Euzéby JP. "List of Prokaryotic names with Standing in Nomenclature". Archived from the original on 30 December 2010. Retrieved 30 December 2010.