Bacterial phyla explained

Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.[1]

It has been estimated that ~1,300 bacterial phyla exist. As of May 2020, 41 bacterial phyla are formally accepted by the LPSN, 89 bacterial phyla are recognized on the Silva database, dozens more have been proposed,[2] and hundreds likely remain to be discovered. As of 2017, approximately 72% of widely recognized bacterial phyla were candidate phyla[3] (i.e. have no cultured representatives).

The rank of phylum has been included in the rules of the International Code of Nomenclature of Prokaryotes, using the ending –ota for phylum names that must be based on the name of a genus as its nomenclatural type.[4] [5]

List of bacterial phyla

The following is a list of bacterial phyla that have been validly published (not current).

!Phylum!Alternative names!Group!Cultured representative!Notes
10bav-F6[6] No
"Abawacabacteria"RIF46CPR; Gracilibacteria-related CPRNo
"Abditibacteriota"[7] FBPYes
"Absconditabacteria"[8] SR1CPR; Gracilibacteria-related CPRNo
ABY1OD1-ABY1[9] CPR; ParcubacteriaNo
"Bipolaricaulota"[10] OP1, "Acetothermia"
Acidobacteriota"Acidobacteria"Yes
Actinomycetota"Actinobacteria"TerrabacteriaYes[11]
"Adlerbacteria"[12] CPR; Patescibacteria; Parcubacteria; Parcubacteria 4No
"Aerophobota" / "Aerophobetes"CD12, BHI80-139
"Amesbacteria"CPR; Patescibacteria; MicrogenomatesNo
"Andersenbacteria"RIF9CPR; Parcubacteria; Parcubacteria 4-relatedNo
Armatimonadota"Armatimonadetes", OP10TerrabacteriaYes[13]
"Aminicenantes"OP8
AncK6
Apal-E12
AtribacterotaOP9, JS1No
Aquificota"Aquificae"
"Azambacteria" iCPR; Patescibacteria; Parcubacteria; unclassified ParcubacteriaNosplit by Anantharaman et al. …
"Azambacteria" iiCPR; Patescibacteria; Parcubacteria; unclassified ParcubacteriaNo… (Oct 2016) as being polyphyletic
Bacteroidota"Bacteroidetes"FCB groupYes
Balneolota[14] Yes
Bdellovibrionota
"Beckwithbacteria"CPR; Patescibacteria; MicrogenomatesNo
"Berkelbacteria"[15] ACD58CPR; Saccharibacteria-related CPRNo
BHI80-139
"Blackburnbacteria"RIF35CPR; MicrogenomatesNo
"Brennerbacteria"RIF18CPR; Parcubacteria; Parcubacteria 3No
"Brownbacteria"CPR; Parcubacteria; unclassified ParcubacteriaNo
"Buchananbacteria"RIF37CPR; Parcubacteria; Parcubacteria 1No
CaldisericotaOP5,[16] "Caldiserica"FCB groupYes[17]
Calditrichota[18] FCB group[19]
"Calescamantes"EM19
"Campbellbacteria"CPR; Patescibacteria; Parcubacteria; Parcubacteria 4Noseem to be polyphyletic: two clades
Campylobacterota
Chlamydiota"Chlamydiae"[20] PVC group
Chlorobiota"Chlorobi"FCB group
Chloroflexota"Chloroflexi""Terrabacteria"
ChisholmbacteriaRIF36CPR; "Microgenomates"No
Chrysiogenota"Chrysiogenetes"
"Cloacimonetes"[21] WWE1FCB group
"Coatesbacteria"RIF8No
"Collierbacteria"CPR; Patescibacteria; MicrogenomatesNo
"Colwellbacteria"RIF41CPR; Parcubacteria; Parcubacteria 3No
Coprothermobacterota
"Curtissbacteria"CPR; Patescibacteria; MicrogenomatesNo
CPR-1CPRNo
CPR-3CPRNo
"Cyanobacteria"Terrabacteria
"Dadabacteria"[22] No
"Daviesbacteria"CPR; Patescibacteria; MicrogenomatesNo
"Delphibacteria"FCB groupNo
"Delongbacteria"RIF26, H-178No
DeferribacterotaDeferribacteres
DeinococcotaDeinococcus–ThermusTerrabacteria
"Dependentiae"[23] TM6
DictyoglomotaDictyoglomi[24]
"Dojkabacteria"WS6CPR; Microgenomates-related CPR
"Dormibacteraeota"[25] AD3No
"Doudnabacteria"SM2F11CPR; Parcubacteria; Parcubacteria 1-relatedNo
"Edwardsbacteria"RIF29, UBP-2 [26] No
"Eisenbacteria"RIF28FCB groupNo
ElusimicrobiotaElusimicrobia, OP7, Termite Group 1 (TG1)Yes[27]
"Eremiobacteraeota"[28] WPS-2, Palusbacterota[29] No
"Falkowbacteria"CPR; Patescibacteria; Parcubacteria; Parcubacteria 1No
"Fermentibacteria"[30] Hyd24-12No
"Fertabacteria"CPR; Gracilibacteria-related CPRNo
Fibrobacterota"Fibrobacteres"FCB group
"Firestonebacteria"RIF1No
"Fervidibacteria"OctSpa1-106
"Fischerbacteria"RIF25No
Bacillota"Firmicutes"Terrabacteria
"Fraserbacteria"RIF31No
Fusobacteriota"Fusobacteria"
GemmatimonadotaGemmatimonadetes[31] FCB groupYes
"Glassbacteria"RIF5No
"Giovannonibacteria"CPR; Patescibacteria; Parcubacteria; Parcubacteria 4-relatedNo
"Gottesmanbacteria"CPR; Patescibacteria; MicrogenomatesNo
"Gracilibacteria"[32] GN02, BD1-5, SN-2CPR; Patescibacteria; Gracilibacteria-related CPRNo
"Gribaldobacteria"CPR; Parcubacteria; Parcubacteria 2No
"Handelsmanbacteria"RIF27No
"Harrisonbacteria"RIF43CPR; Parcubacteria; Parcubacteria 3No
"Howlettbacteria"CPR; Saccharibacteria-related CPRNo
"Hugbacteria"CPR; Parcubacteria; unclassified ParcubacteriaNo
"Hydrogenedentes"NKB19No
Ignavibacteriota"Ignavibacteria", ZB1FCB group
"Jacksonbacteria"RIF38CPR; Parcubacteria; Parcubacteria 1No
"Jorgensenbacteria"CPR; Patescibacteria; Parcubacteria; Parcubacteria 3No
"Kaiserbacteria"CPR; Patescibacteria; Parcubacteria; Parcubacteria 4No
"Katanobacteria"[33] [34] WWE3CPR; Microgenomates-relatedNo
"Kazanbacteria"KazanCPR; Saccharibacteria-related CPRNo
"Kerfeldbacteria"RIF4CPR; Parcubacteria; Parcubacteria 1No
Kiritimatiellota
"Komeilibacteria"RIF6CPR; Parcubacteria; Parcubacteria 1Nosometimes misspelled as "Komelilbacteria"
"Kryptonia"[35] No
KSB1No
"Krumholzibacteriota"
"Kuenenbacteria"CPR; Patescibacteria; Parcubacteria; Parcubacteria 1No
"Lambdaproteobacteria"RIF24ProteobacteriaNo
"Latescibacteria"WS3FCB groupNo
LCP-89[36]
Lentisphaerota"Lentisphaerae", vadinBE97PVC group
"Levybacteria"CPR; Patescibacteria; MicrogenomatesNo
"Lindowbacteria"RIF2CPR; Saccharibacteria-related CPRNo
"Liptonbacteria"RIF42CPR; Parcubacteria; Parcubacteria 3No
"Lloydbacteria"RIF45CPR; Parcubacteria; Parcubacteria 4No
"Magasanikbacteria"[37] CPR; Patescibacteria; Parcubacteria; Parcubacteria 1No
"Margulisbacteria"RIF30No
"Marinimicrobia"SAR406, Marine Group AFCB groupYes
"Melainabacteria"[38] No
"Microgenomates"[39] OP11CPR; PatescibacteriaNoSuperphylum
"Modulibacteria"[40] KSB3, GN06No
"Moranbacteria"OD1-iCPR; Patescibacteria; Parcubacteria; unclassified ParcubacteriaNo
"Muproteobacteria"RIF23ProteobacteriaNo
Myxococcota
NC10[41] [42] No
"Nealsonbacteria"RIF40CPR; Parcubacteria; Parcubacteria 2No
"Niyogibacteria"RIF11CPR; Parcubacteria; Parcubacteria 4-relatedNo
Nitrospinota"Nitrospinae"[43] Yes[44] [45]
Nitrospirota"Nitrospirae"Yes
"Nomurabacteria"CPR; Patescibacteria; Parcubacteria; Parcubacteria 1No
"Omnitrophica"OP3PVC groupNo
"Pacebacteria"CPR; Patescibacteria; MicrogenomatesNo
"Parcubacteria"OD1CPRNoSuperphylum
"Parcubacteria" 1CPR; ParcubacteriaNo
"Parcubacteria" 2CPR; ParcubacteriaNo
"Parcubacteria" 3CPR; ParcubacteriaNo
"Parcubacteria" 4CPR; ParcubacteriaNo
"Parcunitrobacteria"[46] CPR; Parcubacteria; unclassified ParcubacteriaNoSuperphylum
PAUC34f[47] sponge‐associated unclassified lineage (SAUL)FCB group
"Peregrinibacteria"[48] [49] [50] [51] PERCPR; Gracilibacteria-related CPRNo
"Peribacteria"CPR; Gracilibacteria-related CPRNo
Planctomycetota"Planctomycetes"PVC group
"Poribacteria"[52] PVC group
"Portnoybacteria"RIF22CPR; Parcubacteria; Parcubacteria 4-relatedNo
Pseudomonadota"Proteobacteria"
"Raymondbacteria"RIF7No
RiflebacteriaRIF32No
Rhodothermota
"Roizmanbacteria"CPR; Patescibacteria; MicrogenomatesNo
"Rokubacteria"No
"Ryanbacteria"RIF10CPR; Parcubacteria; Parcubacteri 4-relatedNo
"Saccharibacteria"TM7CPR; Saccharibacteria-related CPRYes
"Saltatorellota"[53]
"Schekmanbacteria"RIF3ProteobacteriaNo
"Shapirobacteria"CPR; Patescibacteria; MicrogenomatesNo
"Spechtbacteria"RIF19CPR; Parcubacteria; Parcubacteria 2No
Spirochaetota"Spirochaetes"
"Staskawiczbacteria"RIF20CPR; Parcubacteria; Parcubacteria 2No
"Sumerlaeota"[54] [55] BRC1
"Sungbacteria"RIF17CPR; Parcubacteria; Parcubacteria 4-relatedNo
Synergistota"Synergistetes"
TA06No
"Tagabacteria"RIF12CPR; Parcubacteria; Parcubacteria 4-relatedNo
"Taylorbacteria"RIF16CPR; Parcubacteria; Parcubacteria 4No
"Tectomicrobia"[56]
Mycoplasmatota"Tenericutes"
"Terrybacteria"RIF13CPR; Parcubacteria; Parcubacteria 2No
Thermodesulfobacteriota"Thermodesulfobacteria"
Thermomicrobiota"Thermomicrobia"
Thermotogota"Thermotogae", OP2, EM3Yes
"Torokbacteria"CPR; Parcubacteria; unclssified ParcubacteriaNo
UBP-1[57] No
UBP-3No
UBP-4No
UBP-5No
UBP-6No
UBP-7No
UBP-8No
UBP-9No
UBP-10No
UBP-11No
UBP-12No
UBP-13No
UBP-14No
UBP-15No
UBP-16No
UBP-17No
"Uhrbacteria"CPR; Patescibacteria; Parcubacteria; Parcubacteria 1Noseem to be polyphyletic: two clades
"Veblenbacteria"RIF39CPR; Parcubacteria; Parcubacteria 1-relatedNo
Verrucomicrobiota"Verrucomicrobia"PVC group
"Vogelbacteria"RIF14CPR; Parcubacteria; Parcubacteria 4No
"Wallbacteria"RIF33No
"Wildermuthbacteria"RIF21CPR; Parcubacteria; Parcubacteria 2No
"Wirthbacteria"[58] CPR-related bacteriaNo
"Woesebacteria"CPR; Patescibacteria; MicrogenomatesNo
"Wolfebacteria"CPR; Patescibacteria; Parcubacteria; Parcubacteria 3No
"Woykebacteria"RIF34CPR; MicrogenomatesNo
WOR-1[59] No
WOR-2No
WOR-3No
"Yanofskybacteria"CPR; Patescibacteria; Parcubacteria; unclassified ParcubacteriaNo
"Yonathbacteria"RIF44CPR; Parcubacteria; Parcubacteria 4No
"Zambryskibacteria"RIF15CPR; Parcubacteria; Parcubacteria 4No
ZB2OD1-ZB2CPR; ParcubacteriaNo
"Zixibacteria"[60] FCB groupNo

Supergroups

Despite the unclear branching order for most bacterial phyla, several groups of phyla consistently cluster together and are referred to as supergroups or superphyla. In some instances, bacterial clades clearly consistently cluster together but it is unclear what to call the group. For example, the Candidate Phyla Radiation includes the Patescibacteria group which includes Microgenomates group which includes over 11 bacterial phyla.

Candidate phyla radiation (CPR)

See main article: Candidate phyla radiation. The CPR is a descriptive term referring to a massive monophyletic radiation of candidate phyla that exists within the Bacterial domain.[61] It includes two main clades, the Microgenomates and Parcubacteria groups, each containing the eponymous superphyla and a few other phyla.

Patescibacteria

The superphylum Patescibacteria was originally proposed to encompass the phyla Microgenomates (OP11), Parcubacteria (OD1), and Gracilibacteria (GNO2 / BD1-5). More recent phylogenetic analyses show that the last common ancestor of these taxa is the same node as that of CPR.[62]

Sphingobacteria

See main article: Sphingobacteria. The Sphingobacteria (FCB group) includes Bacteroidota, Calditrichota, Chlorobiota, candidate phylum "Cloacimonetes", Fibrobacterota, Gemmatimonadota, Ignavibacteriota, candidate phylum "Latescibacteria", candidate phylum "Marinimicrobia", and candidate phylum "Zixibacteria".[63]

Microgenomates

Microgenomates was originally thought to be a single phylum although evidence suggests it actually encompasses over 11 bacterial phyla, including Curtisbacteria, Daviesbacteria, Levybacteria, Gottesmanbacteria, Woesebacteria, Amesbacteria, Shapirobacteria, Roizmanbacteria, Beckwithbacteria, Collierbacteria, Pacebacteria.

Parcubacteria

Parcubacteria was originally described as a single phylum using fewer than 100 16S rRNA sequences. With a greater diversity of 16S rRNA sequences from uncultured organisms now available, it is estimated it may consist of up to 28 bacterial phyla. In line with this, over 14 phyla have now been described within the Parcubacteria group, including Kaiserbacteria, Adlerbacteria, Campbellbacteria, Nomurabacteria, Giovannonibacteria, Wolfebacteria, Jorgensenbacteria, Yanofskybacteria, Azambacteria, Moranbacteria, Uhrbacteria, and Magasanikbacteria.

Proteobacteria

It has been proposed that some classes of the phylum Proteobacteria may be phyla in their own right, which would make Proteobacteria a superphylum.[64] For example, the Deltaproteobacteria group does not consistently form a monophyletic lineage with the other Proteobacteria classes.[65]

Planctobacteria

See main article: Planctobacteria. The Planctobacteria (PVC group) includes Chlamydiota, Lentisphaerota, candidate phylum "Omnitrophica", Planctomycetota, candidate phylum "Poribacteria", and Verrucomicrobiota.

Terrabacteria

See main article: Terrabacteria. The proposed superphylum, Terrabacteria, includes Actinomycetota, "Cyanobacteria"/"Melainabacteria"-group, Deinococcota, Chloroflexota, Bacillota, and candidate phylum OP10.

Cryptic superphyla

Several candidate phyla (Microgenomates, Omnitrophica, Parcubacteria, and Saccharibacteria) and several accepted phyla (Elusimicrobiota, Caldisericota, and Armatimonadota) have been suggested to actually be superphyla that were incorrectly described as phyla because rules for defining a bacterial phylum are lacking or due to a lack of sequence diversity in databases when the phylum was first established. For example, it is suggested that candidate phylum Parcubacteria is actually a superphylum that encompasses 28 subordinate phyla and that phylum Elusimicrobia is actually a superphylum that encompasses 7 subordinate phyla.[64]

Historical perspective

Given the rich history of the field of bacterial taxonomy and the rapidity of changes therein in modern times, it is often useful to have a historical perspective on how the field has progressed in order to understand references to antiquated definitions or concepts.

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 1987, Carl Woese, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, listed below.[66]

Traditionally, phylogeny was inferred and taxonomy established based on studies of morphology. The advent of molecular phylogenetics has allowed for improved elucidation of the evolutionary relationship of species by analyzing their DNA and protein sequences, for example their ribosomal DNA.[71] 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". Many bacterial taxa were re-classified or re-defined using molecular phylogenetics.

The advent of molecular sequencing technologies has allowed for the recovery of genomes directly from environmental samples (i.e. bypassing culturing), leading to rapid expansion of our knowledge of the diversity of bacterial phyla. These techniques are genome-resolved metagenomics and single-cell genomics.

See also

Notes and References

  1. Yarza. Pablo. Yilmaz. Pelin. Pruesse. Elmar. Glöckner. Frank Oliver. Ludwig. Wolfgang. Schleifer. Karl-Heinz. Whitman. William B.. Euzéby. Jean. Amann. Rudolf. Rosselló-Móra. Ramon. 21895693. September 2014. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Reviews Microbiology. en. 12. 9. 635–645. 10.1038/nrmicro3330. 25118885. 1740-1534.
  2. Anantharaman. Karthik. Brown. Christopher T.. Hug. Laura A.. Sharon. Itai. Castelle. Cindy J.. Probst. Alexander J.. Thomas. Brian C.. Singh. Andrea. Wilkins. Michael J.. Karaoz. Ulas. Brodie. Eoin L.. 2016-10-24. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nature Communications. en. 7. 1. 13219. 10.1038/ncomms13219. 27774985. 5079060. 2041-1723. 2016NatCo...713219A.
  3. Dudek. Natasha K.. Sun. Christine L.. Burstein. David. Kantor. Rose S.. Aliaga Goltsman. Daniela S.. Bik. Elisabeth M.. Thomas. Brian C.. Banfield. Jillian F.. Relman. David A.. 2017-12-18. Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome. Current Biology. 27. 24. 3752–3762.e6. 10.1016/j.cub.2017.10.040. 1879-0445. 29153320. free.
  4. Oren . Aharon . Arahal . David R. . Rosselló-Móra . Ramon . Sutcliffe . Iain C. . Moore . Edward R. B. . Emendation of Rules 5b, 8, 15 and 22 of the International Code of Nomenclature of Prokaryotes to include the rank of phylum . International Journal of Systematic and Evolutionary Microbiology . 23 June 2021 . 71 . 6 . 10.1099/ijsem.0.004851. 34161220 . 235625014 . free .
  5. Oren . Aharon . Garrity . George M. . Valid publication of the names of forty-two phyla of prokaryotes . International Journal of Systematic and Evolutionary Microbiology . 20 October 2021 . 71 . 10 . 10.1099/ijsem.0.005056. 34694987 . 239887308 . free .
  6. Web site: ARB-Silva: comprehensive ribosomal RNA database. The ARB development Team. 2 January 2016.
  7. Tahon. Guillaume. Tytgat. Bjorn. Lebbe. Liesbeth. Carlier. Aurélien. Willems. Anne. 2018-07-01. Abditibacterium utsteinense sp. nov., the first cultivated member of candidate phylum FBP, isolated from ice-free Antarctic soil samples. Systematic and Applied Microbiology. en. 41. 4. 279–290. 10.1016/j.syapm.2018.01.009. 29475572. 3515091 . 0723-2020.
  8. Harris. J. Kirk. Kelley. Scott T.. Pace. Norman R.. February 2004. New Perspective on Uncultured Bacterial Phylogenetic Division OP11. Applied and Environmental Microbiology. 70. 2. 845–849. 10.1128/AEM.70.2.845-849.2004. 0099-2240. 14766563. 348892. 2004ApEnM..70..845H .
  9. Kenly A. Hiller, Kenneth H. Foreman, David Weisman, Jennifer L. Bowen: Permeable Reactive Barriers Designed To Mitigate Eutrophication Alter Bacterial Community Composition and Aquifer Redox Conditions. In: Appl Environ Microbiol v.81(20); 2015 Oct; pp.7114–7124. . . .
  10. Hugenholtz P. etal. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology. 180. 2. 366–76. 10.1128/JB.180.2.366-376.1998. 106892. 9440526.
  11. Book: Goodfellow, Michael. Phylum XXVI. Actinobacteria phyl. Nov.. 2012. Bergey's Manual® of Systematic Bacteriology. 33–2028. Springer New York. 10.1007/978-0-387-68233-4_3. 978-0-387-95043-3.
  12. Christopher T. Brown, Laura A. Hug, Brian C. Thomas et al.. 4397558. etal. 2015. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature. 523. 7559. 208–11. 2015Natur.523..208B. 10.1038/nature14486. 26083755. 1512215.
  13. Tamaki. Hideyuki. Tanaka. Yasuhiro. Matsuzawa. Hiroaki. Muramatsu. Mizuho. Meng. Xian-Ying. Hanada. Satoshi. Mori. Kazuhiro. Kamagata. Yoichi. June 2011. Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. International Journal of Systematic and Evolutionary Microbiology. 61. Pt 6. 1442–1447. 10.1099/ijs.0.025643-0. 1466-5034. 20622056. free.
  14. Hahnke. Richard L.. Meier-Kolthoff. Jan P.. García-López. Marina. Mukherjee. Supratim. Huntemann. Marcel. Ivanova. Natalia N.. Woyke. Tanja. Kyrpides. Nikos C.. Klenk. Hans-Peter. Göker. Markus. 2016. Genome-Based Taxonomic Classification of Bacteroidetes. Frontiers in Microbiology. 7. 2003. 10.3389/fmicb.2016.02003. 1664-302X. 5167729. 28066339. free.
  15. Wrighton. Kelly C.. Castelle. Cindy J.. Wilkins. Michael J.. Hug. Laura A.. Sharon. Itai. Thomas. Brian C.. Handley. Kim M.. Mullin. Sean W.. Nicora. Carrie D.. Singh. Andrea. Lipton. Mary S.. July 2014. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. The ISME Journal. en. 8. 7. 1452–1463. 10.1038/ismej.2013.249. 24621521. 4069391. 1751-7370.
  16. Dunfield. Peter F.. Tamas. Ivica. Lee. Kevin C.. Morgan. Xochitl C.. McDonald. Ian R.. Stott. Matthew B.. 2012. Electing a candidate: a speculative history of the bacterial phylum OP10. Environmental Microbiology. en. 14. 12. 3069–3080. 10.1111/j.1462-2920.2012.02742.x. 22497633. 1462-2920. free.
  17. Mori. K.. Yamaguchi. K.. Sakiyama. Y.. Urabe. T.. Suzuki. K.-i.. 2009-07-23. 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. 11. 2894–2898. 10.1099/ijs.0.010033-0. 19628600. 1466-5026. free.
  18. Kublanov. Ilya V.. Sigalova. Olga M.. Gavrilov. Sergey N.. Lebedinsky. Alexander V.. Rinke. Christian. Kovaleva. Olga. Chernyh. Nikolai A.. Ivanova. Natalia. Daum. Chris. Reddy. T.B.K.. Klenk. Hans-Peter. 2017-02-20. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. Frontiers in Microbiology. 8. 10.3389/fmicb.2017.00195. 28265262. 1664-302X. 5317091. 195. free.
  19. Rinke C. etal. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 499. 7459. 431–7. 2013Natur.499..431R. 10.1038/nature12352. 23851394. free. 10453/27467. free.
  20. Book: 2001. Boone. David R.. Castenholz. Richard W.. Garrity. George M.. Bergey's Manual® of Systematic Bacteriology. 10.1007/978-0-387-21609-6. 978-1-4419-3159-7. 41426624.
  21. Chouari. Rakia. Le Paslier. Denis. Dauga. Catherine. Daegelen. Patrick. Weissenbach. Jean. Sghir. Abdelghani. April 2005. Novel Major Bacterial Candidate Division within a Municipal Anaerobic Sludge Digester. Applied and Environmental Microbiology. 71. 4. 2145–2153. 10.1128/aem.71.4.2145-2153.2005. 15812049. 1082523. 2005ApEnM..71.2145C . 0099-2240.
  22. Hug. Laura A.. Thomas. Brian C.. Sharon. Itai. Brown. Christopher T.. Sharma. Ritin. Hettich. Robert L.. Wilkins. Michael J.. Williams. Kenneth H.. Singh. Andrea. Banfield. Jillian F.. 2016. Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. Environmental Microbiology. en. 18. 1. 159–173. 10.1111/1462-2920.12930. 26033198. 1328276. 43160538 . 1462-2920.
  23. Rheims. H. Rainey. F A. Stackebrandt. E. 31868442. September 1996. A molecular approach to search for diversity among bacteria in the environment. Journal of Industrial Microbiology & Biotechnology. 17. 3–4. 159–169. 10.1007/bf01574689. 0169-4146. free.
  24. Book: Patel, Bharat K. C.. Phylum XX. Dictyoglomi phyl. Nov.. 2010. Bergey's Manual® of Systematic Bacteriology. 775–780. Springer New York. 10.1007/978-0-387-68572-4_9. 978-0-387-95042-6.
  25. Ji. Mukan. Greening. Chris. Vanwonterghem. Inka. Carere. Carlo R.. Bay. Sean K.. Steen. Jason A.. Montgomery. Kate. Lines. Thomas. Beardall. John. van Dorst. Josie. Snape. Ian. December 2017. Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature. en. 552. 7685. 400–403. 10.1038/nature25014. 29211716. 2017Natur.552..400J. 1476-4687. free. 2440/124244. free.
  26. Youssef. Noha H.. Farag. Ibrahim F.. Hahn. C. Ryan. Premathilake. Hasitha. Fry. Emily. Hart. Matthew. Huffaker. Krystal. Bird. Edward. Hambright. Jimmre. Hoff. Wouter D.. Elshahed. Mostafa S.. 2019-01-01. Candidatus Krumholzibacterium zodletonense gen. nov., sp nov, the first representative of the candidate phylum Krumholzibacteriota phyl. nov. recovered from an anoxic sulfidic spring using genome resolved metagenomics. Systematic and Applied Microbiology. Taxonomy of uncultivated Bacteria and Archaea. en. 42. 1. 85–93. 10.1016/j.syapm.2018.11.002. 30477901. 0723-2020.
  27. Herlemann. D. P. R.. Geissinger. O.. Ikeda-Ohtsubo. W.. Kunin. V.. Sun. H.. Lapidus. A.. Hugenholtz. P.. Brune. A.. 2009-05-01. Genomic Analysis of "Elusimicrobium minutum," the First Cultivated Representative of the Phylum "Elusimicrobia" (Formerly Termite Group 1). Applied and Environmental Microbiology. en. 75. 9. 2841–2849. 10.1128/AEM.02698-08. 0099-2240. 19270133. 2681670. 2009ApEnM..75.2841H .
  28. Nogales. Balbina. Moore. Edward R. B.. Llobet-Brossa. Enrique. Rossello-Mora. Ramon. Amann. Rudolf. Timmis. Kenneth N.. 2001-04-01. Combined Use of 16S Ribosomal DNA and 16S rRNA To Study the Bacterial Community of Polychlorinated Biphenyl-Polluted Soil. Applied and Environmental Microbiology. en. 67. 4. 1874–1884. 10.1128/AEM.67.4.1874-1884.2001. 0099-2240. 11282645. 92809. 2001ApEnM..67.1874N .
  29. Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Palusbacterota (WPS-2). Ward. Lewis M.. Cardona. Tanai. 2019-01-29. Holland-Moritz. Hannah. 92796436. 10.1101/534180. free.
  30. Knittel. Katrin. Boetius. Antje. Lemke. Andreas. Eilers. Heike. Lochte. Karin. Pfannkuche. Olaf. Linke. Peter. Amann. Rudolf. 140639772. July 2003. Activity, Distribution, and Diversity of Sulfate Reducers and Other Bacteria in Sediments above Gas Hydrate (Cascadia Margin, Oregon). Geomicrobiology Journal. 20. 4. 269–294. 10.1080/01490450303896. 2003GmbJ...20..269K . 0149-0451. 21.11116/0000-0001-D20F-2. free.
  31. Zhang. Hui. Sekiguchi. Yuji. Hanada. Satoshi. Hugenholtz. Philip. Kim. Hongik. Kamagata. Yoichi. Nakamura. Kazunori. 2003. Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov.. International Journal of Systematic and Evolutionary Microbiology. 53. 4. 1155–1163. 10.1099/ijs.0.02520-0. 12892144. 1466-5026. free.
  32. Ley. Ruth E.. Harris. J. Kirk. Wilcox. Joshua. Spear. John R.. Miller. Scott R.. Bebout. Brad M.. Maresca. Julia A.. Bryant. Donald A.. Sogin. Mitchell L.. Pace. Norman R.. 2006-05-01. Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat. Applied and Environmental Microbiology. en. 72. 5. 3685–3695. 10.1128/AEM.72.5.3685-3695.2006. 0099-2240. 16672518. 1472358. 2006ApEnM..72.3685L .
  33. Guermazi. Sonda. Daegelen. Patrick. Dauga. Catherine. Rivière. Delphine. Bouchez. Théodore. Godon. Jean Jacques. Gyapay. Gábor. Sghir. Abdelghani. Pelletier. Eric. Weissenbach. Jean. Le Paslier. Denis. August 2008. Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach. Environmental Microbiology. 10. 8. 2111–2123. 10.1111/j.1462-2920.2008.01632.x. 1462-2912. 2702496. 18459975.
  34. Alexander L. Jaffe, Cindy J. Castelle, Paula B. Matheus Carnevali, Simonetta Gribaldo, Jillian F. Banfield: The rise of diversity in metabolic platforms across the Candidate Phyla Radiation. In: BMC Biology Vol. 18, Nr. 69; June 2020);
  35. Eloe-Fadrosh. Emiley A.. Paez-Espino. David. Jarett. Jessica. Dunfield. Peter F.. Hedlund. Brian P.. Dekas. Anne E.. Grasby. Stephen E.. Brady. Allyson L.. Dong. Hailiang. Briggs. Brandon R.. Li. Wen-Jun. 2016-01-27. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nature Communications. en. 7. 1. 10476. 10.1038/ncomms10476. 26814032. 4737851. 2016NatCo...710476E. 2041-1723.
  36. Youssef. Noha H.. Farag. Ibrahim F.. Hahn. C. Ryan. Jarett. Jessica. Becraft. Eric. Eloe-Fadrosh. Emiley. Lightfoot. Jorge. Bourgeois. Austin. Cole. Tanner. Ferrante. Stephanie. Truelock. Mandy. 2019-05-15. Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities. Applied and Environmental Microbiology. en. 85. 10. 10.1128/AEM.00110-19. 0099-2240. 30902854. 6498177. 2019ApEnM..85E.110Y .
  37. NCBI: Candidatus Magasanikbacteria (phylum)
  38. Di Rienzi. Sara C. Sharon. Itai. Wrighton. Kelly C. Koren. Omry. Hug. Laura A. Thomas. Brian C. Goodrich. Julia K. Bell. Jordana T. Spector. Timothy D. Banfield. Jillian F. Ley. Ruth E. 2013-10-01. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife. 2. e01102. 10.7554/eLife.01102. 2050-084X. 3787301. 24137540 . free .
  39. Hugenholtz. Philip. Goebel. Brett M.. Pace. Norman R.. 1998-12-15. Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity. Journal of Bacteriology. 180. 24. 4765–74. 10.1128/jb.180.24.6793-6793.1998. 9733676. 107498. 1098-5530. free.
  40. Sekiguchi. Yuji. Ohashi. Akiko. Parks. Donovan H.. Yamauchi. Toshihiro. Tyson. Gene W.. Hugenholtz. Philip. 2015-01-27. First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ. 3. e740. 10.7717/peerj.740. 2167-8359. 4312070. 25650158 . free .
  41. Holmes. Andrew J.. Tujula. Niina A.. Holley. Marita. Contos. Annalisa. James. Julia M.. Rogers. Peter. Gillings. Michael R.. 2001. Phylogenetic structure of unusual aquatic microbial formations in Nullarbor caves, Australia. Environmental Microbiology. en. 3. 4. 256–264. 10.1046/j.1462-2920.2001.00187.x. 11359511. 1462-2920.
  42. Rappé. Michael S.. Giovannoni. Stephen J.. 2003. The Uncultured Microbial Majority. Annual Review of Microbiology. 57. 369–94. 10.1146/annurev.micro.57.030502.090759. 14527284.
  43. Luecker. Sebastian. Nowka. Boris. Rattei. Thomas. Spieck. Eva. Daims. Holger. 2013. The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer. Frontiers in Microbiology. en. 4. 27. 10.3389/fmicb.2013.00027. 23439773. 3578206. 1664-302X. free.
  44. Mueller. Anna J.. Jung. Man-Young. Strachan. Cameron R.. Herbold. Craig W.. Kirkegaard. Rasmus H.. Wagner. Michael. Daims. Holger. March 2021. Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting. The ISME Journal. en. 15. 3. 732–745. 10.1038/s41396-020-00809-6 . 8026999. 33067588. 1751-7362. free.
  45. Spieck. Eva. Keuter. Sabine. Wenzel. Thilo. Bock. Eberhard. Ludwig. Wolfgang. May 2014. Characterization of a new marine nitrite oxidizing bacterium, Nitrospina watsonii sp. nov., a member of the newly proposed phylum "Nitrospinae". Systematic and Applied Microbiology. en. 37. 3. 170–176. 10.1016/j.syapm.2013.12.005. 24581679.
  46. LPSN: Phylum "Candidatus Parcunitrobacteria"
  47. Astudillo‐García. Carmen. Slaby. Beate M.. Waite. David W.. Bayer. Kristina. Hentschel. Ute. Taylor. Michael W.. 23892350. 2018. Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges. Environmental Microbiology. en. 20. 2. 561–576. 10.1111/1462-2920.13965. 29098761. 1462-2920.
  48. Wrighton. K. C.. Thomas. B. C.. Sharon. I.. Miller. C. S.. Castelle. C. J.. VerBerkmoes. N. C.. Wilkins. M. J.. Hettich. R. L.. Lipton. M. S.. Williams. K. H.. Long. P. E.. 10362580. 2012-09-27. Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla. Science. 337. 6102. 1661–1665. 10.1126/science.1224041. 23019650. 2012Sci...337.1661W. 0036-8075.
  49. NCBI: Candidatus Peregrinibacteria (phylum)
  50. UniProt: Taxonomy - Candidatus Peregrinibacteria (PHYLUM)
  51. Karthik Anantharaman, Christopher T. Brown, David Burstein, Cindy Castelle: Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. In: PeerJ 4(8):e1607; Jan 2016;
  52. Fieseler. Lars. Horn. Matthias. Wagner. Michael. Hentschel. Ute. June 2004. Discovery of the Novel Candidate Phylum "Poribacteria" in Marine Sponges. Applied and Environmental Microbiology. 70. 6. 3724–3732. 10.1128/AEM.70.6.3724-3732.2004. 0099-2240. 15184179. 427773. 2004ApEnM..70.3724F .
  53. The novel shapeshifting bacterial phylum Saltatorellota. Wiegand. Sandra. Jogler. Mareike. 2019-10-24. Kohn. Timo. Awal. Ram Prasad. Oberbeckmann. Sonja. Kesy. Katharina. Jeske. Olga. Schumann. Peter. Peeters. Stijn H.. 208566371. 10.1101/817700.
  54. Derakshani. Manigee. Lukow. Thomas. Liesack. Werner. 2001-02-01. Novel Bacterial Lineages at the (Sub)Division Level as Detected by Signature Nucleotide-Targeted Recovery of 16S rRNA Genes from Bulk Soil and Rice Roots of Flooded Rice Microcosms. Applied and Environmental Microbiology. 67. 2. 623–631. 10.1128/aem.67.2.623-631.2001. 11157225. 92629. 2001ApEnM..67..623D . 1098-5336.
  55. Kadnikov. Vitaly V.. Mardanov. Andrey V.. Beletsky. Alexey V.. Rakitin. Andrey L.. Frank. Yulia A.. Karnachuk. Olga V.. Ravin. Nikolai V.. January 2019. Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer. Systematic and Applied Microbiology. 42. 1. 67–76. 10.1016/j.syapm.2018.08.013. 1618-0984. 30201528. 52183718.
  56. Wilson. Micheal C.. Mori. Tetsushi. Rückert. Christian. Uria. Agustinus R.. Helf. Maximilian J.. Takada. Kentaro. Gernert. Christine. Steffens. Ursula A. E.. Heycke. Nina. Schmitt. Susanne. Rinke. Christian. February 2014. An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature. en. 506. 7486. 58–62. 10.1038/nature12959. 24476823. 1476-4687. 2014Natur.506...58W. free.
  57. Parks. Donovan H.. Rinke. Christian. Chuvochina. Maria. Chaumeil. Pierre-Alain. Woodcroft. Ben J.. Evans. Paul N.. Hugenholtz. Philip. Tyson. Gene W.. November 2017. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology. en. 2. 11. 1533–1542. 10.1038/s41564-017-0012-7. 28894102. 2058-5276. free.
  58. Probst . AJ . Castelle . CJ . Singh . A . Brown . CT . Anantharaman . K . Sharon . I . Hug . LA . Burstein . D . Emerson . JB . Thomas . BC . Banfield . JF . Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. . Environmental Microbiology . February 2017 . 19 . 2 . 459–474 . 10.1111/1462-2920.13362 . 27112493. 1567074 . 21126011 .
  59. Baker. Brett J.. Lazar. Cassandre Sara. Teske. Andreas P.. Dick. Gregory J.. 2015-04-13. Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome. 3. 1. 14. 10.1186/s40168-015-0077-6. 2049-2618. 4411801. 25922666 . free .
  60. Castelle. Cindy J.. Hug. Laura A.. Wrighton. Kelly C.. Thomas. Brian C.. Williams. Kenneth H.. Wu. Dongying. Tringe. Susannah G.. Singer. Steven W.. Eisen. Jonathan A.. Banfield. Jillian F.. 2013-08-27. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications. en. 4. 1. 2120. 10.1038/ncomms3120. 23979677. 2041-1723. 3903129. 2013NatCo...4.2120C.
  61. Castelle CJ, Banfield JF. March 2018. Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life. Cell. 172. 6. 1181–1197. 10.1016/j.cell.2018.02.016. 29522741. free.
  62. Castelle. Cindy J.. Banfield. Jillian F.. 2018-03-08. Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life. Cell. en. 172. 6. 1181–1197. 10.1016/j.cell.2018.02.016. 29522741. 0092-8674. free.
  63. Sekiguchi Y. etal. 2015. First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ. 3. e740. 10.7717/peerj.740. 4312070. 25650158 . free .
  64. Yarza P. 21895693. etal. 2014. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Reviews Microbiology. 12. 9. 635–645. 10.1038/nrmicro3330. 25118885. 10261/123763.
  65. Hug LA. et al.. 2016. A new view of the tree of life. Nature Microbiology. Article 16048. 5. 16048. 10.1038/nmicrobiol.2016.48. 27572647. free.
  66. Holland L. 22 May 1990. Carl Woese in forefront of bacterial evolution revolution. The Scientist. 3. 10.
  67. Stackebrandt. etal. 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. 10.1099/00207713-38-3-321. free.
  68. 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. 10.1099/00207713-47-2-479. free.
  69. Web site: List of Prokaryotic names with Standing in Nomenclature: classification of Deinococcus–Thermus. J.P. Euzéby. dead. https://web.archive.org/web/20130127030659/http://www.bacterio.cict.fr/classifphyla.html. 27 January 2013. 30 December 2010.
  70. Book: Boone DR. The Archaea and the Deeply Branching and Phototrophic Bacteria. Castenholz RW. 18 May 2001. Springer. 978-0-387-98771-2. Garrity GM. 2nd. Bergey's Manual of Systematic Bacteriology. 1. New York. 721. British Library no. GBA561951. 1984 (Williams & Wilkins). registration.
  71. Olsen GJ, Woese CR, Overbeek R. 1994. The winds of (evolutionary) change: breathing new life into microbiology. Journal of Bacteriology. 176. 1. 1–6. 10.2172/205047. 205007. 8282683.

This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Bacterial phyla".

Except where otherwise indicated, Everything.Explained.Today is © Copyright 2009-2024, A B Cryer, All Rights Reserved. Cookie policy.