Bacterial phyla: Difference between revisions

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* '''[[Thermotogae]]''' (''[[Thermotoga maritima]]'')
* '''[[Thermotogae]]''' (''[[Thermotoga maritima]]'')


== <!-- If adding a newly proposed phylum, if the phylum was detected through 16S rRNA gene sequences alone, citation should be the study that found the first sequences as well as the first study to confirm that the phylum exists through more rigorous analyses (e.g.: first genome) --> ==
== List of bacterial phyla ==
The following is a list of bacterial phyla that have been proposed.
The following is a list of bacterial phyla that have been proposed.
{| class="wikitable sortable"
{| class="wikitable sortable"
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|[[Aerophobota]]
|[[Aerophobota]] / Aerophobetes
|CD12, BHI80-139
|CD12, BHI80-139
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|[[Balneolaeota]]<ref>{{Cite journal|last=Hahnke|first=Richard L.|last2=Meier-Kolthoff|first2=Jan P.|last3=García-López|first3=Marina|last4=Mukherjee|first4=Supratim|last5=Huntemann|first5=Marcel|last6=Ivanova|first6=Natalia N.|last7=Woyke|first7=Tanja|last8=Kyrpides|first8=Nikos C.|last9=Klenk|first9=Hans-Peter|last10=Göker|first10=Markus|date=2016|title=Genome-Based Taxonomic Classification of Bacteroidetes|url=https://www.ncbi.nlm.nih.gov/pubmed/28066339|journal=Frontiers in Microbiology|volume=7|pages=2003|doi=10.3389/fmicb.2016.02003|issn=1664-302X|pmc=5167729|pmid=28066339}}</ref>
|[[Balneolaeota]]
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|[[Caldisericum|Caldiserica]]<ref name=":8" />
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|BRC1
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|[[Caldisericum|Caldiserica]]
|OP5<ref name=":9">{{Cite journal|last=Dunfield|first=Peter F.|last2=Tamas|first2=Ivica|last3=Lee|first3=Kevin C.|last4=Morgan|first4=Xochitl C.|last5=McDonald|first5=Ian R.|last6=Stott|first6=Matthew B.|date=2012|title=Electing a candidate: a speculative history of the bacterial phylum OP10|url=https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.1462-2920.2012.02742.x|journal=Environmental Microbiology|language=en|volume=14|issue=12|pages=3069–3080|doi=10.1111/j.1462-2920.2012.02742.x|issn=1462-2920}}</ref>
|OP5<ref name=":9">{{Cite journal|last=Dunfield|first=Peter F.|last2=Tamas|first2=Ivica|last3=Lee|first3=Kevin C.|last4=Morgan|first4=Xochitl C.|last5=McDonald|first5=Ian R.|last6=Stott|first6=Matthew B.|date=2012|title=Electing a candidate: a speculative history of the bacterial phylum OP10|url=https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/j.1462-2920.2012.02742.x|journal=Environmental Microbiology|language=en|volume=14|issue=12|pages=3069–3080|doi=10.1111/j.1462-2920.2012.02742.x|issn=1462-2920}}</ref>
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|[[Calditrichaeota]]<ref>{{Cite journal|last=Kublanov|first=Ilya V.|last2=Sigalova|first2=Olga M.|last3=Gavrilov|first3=Sergey N.|last4=Lebedinsky|first4=Alexander V.|last5=Rinke|first5=Christian|last6=Kovaleva|first6=Olga|last7=Chernyh|first7=Nikolai A.|last8=Ivanova|first8=Natalia|last9=Daum|first9=Chris|last10=Reddy|first10=T.B.K.|last11=Klenk|first11=Hans-Peter|date=2017-02-20|title=Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota|url=http://dx.doi.org/10.3389/fmicb.2017.00195|journal=Frontiers in Microbiology|volume=8|doi=10.3389/fmicb.2017.00195|issn=1664-302X}}</ref>
|[[Calditrichaeota]]<ref>{{Cite journal|last=Kublanov|first=Ilya V.|last2=Sigalova|first2=Olga M.|last3=Gavrilov|first3=Sergey N.|last4=Lebedinsky|first4=Alexander V.|last5=Rinke|first5=Christian|last6=Kovaleva|first6=Olga|last7=Chernyh|first7=Nikolai A.|last8=Ivanova|first8=Natalia|last9=Daum|first9=Chris|last10=Reddy|first10=T.B.K.|last11=Klenk|first11=Hans-Peter|date=2017-02-20|title=Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota|url=http://dx.doi.org/10.3389/fmicb.2017.00195|journal=Frontiers in Microbiology|volume=8|doi=10.3389/fmicb.2017.00195|issn=1664-302X}}</ref>
|Caldithrix
|Caldithrix
|FCB group
|FCB group<ref name="MDM" />
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|[[Chlamydiae]]<ref>{{Cite journal|date=2001|editor-last=Boone|editor-first=David R.|editor2-last=Castenholz|editor2-first=Richard W.|editor3-last=Garrity|editor3-first=George M.|title=Bergey’s Manual® of Systematic Bacteriology|url=http://dx.doi.org/10.1007/978-0-387-21609-6|doi=10.1007/978-0-387-21609-6}}</ref>
|[[Chlamydiae]]
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|[[Cloacimonetes]]<ref>{{Cite journal|last=Chouari|first=Rakia|last2=Le Paslier|first2=Denis|last3=Dauga|first3=Catherine|last4=Daegelen|first4=Patrick|last5=Weissenbach|first5=Jean|last6=Sghir|first6=Abdelghani|date=2005-04|title=Novel Major Bacterial Candidate Division within a Municipal Anaerobic Sludge Digester|url=http://dx.doi.org/10.1128/aem.71.4.2145-2153.2005|journal=Applied and Environmental Microbiology|volume=71|issue=4|pages=2145–2153|doi=10.1128/aem.71.4.2145-2153.2005|issn=0099-2240}}</ref>
|[[Cloacimonetes]]<ref>{{Cite journal|last=Chouari|first=Rakia|last2=Le Paslier|first2=Denis|last3=Dauga|first3=Catherine|last4=Daegelen|first4=Patrick|last5=Weissenbach|first5=Jean|last6=Sghir|first6=Abdelghani|date=2005-04|title=Novel Major Bacterial Candidate Division within a Municipal Anaerobic Sludge Digester|url=http://dx.doi.org/10.1128/aem.71.4.2145-2153.2005|journal=Applied and Environmental Microbiology|volume=71|issue=4|pages=2145–2153|doi=10.1128/aem.71.4.2145-2153.2005|issn=0099-2240}}</ref>
|WWE1
|WWE1
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|FCB group<ref name="MDM" />
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|[[Delongbacteria]]<ref name=":1" />
|[[Delongbacteria]]<ref name=":1" />
|RIF26
|RIF26, H-178
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|No
|No
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|Dictyoglomi<ref>{{Citation|last=Patel|first=Bharat K. C.|title=Phylum XX. Dictyoglomi phyl. nov.|date=2010|url=http://dx.doi.org/10.1007/978-0-387-68572-4_9|work=Bergey’s Manual® of Systematic Bacteriology|pages=775–780|publisher=Springer New York|isbn=978-0-387-95042-6|access-date=2020-05-15}}</ref>
|Dictyoglomi
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|[[Dormibacteraeota]]<ref>{{Cite journal|last=Ji|first=Mukan|last2=Greening|first2=Chris|last3=Vanwonterghem|first3=Inka|last4=Carere|first4=Carlo R.|last5=Bay|first5=Sean K.|last6=Steen|first6=Jason A.|last7=Montgomery|first7=Kate|last8=Lines|first8=Thomas|last9=Beardall|first9=John|last10=van Dorst|first10=Josie|last11=Snape|first11=Ian|date=2017-12|title=Atmospheric trace gases support primary production in Antarctic desert surface soil|url=https://www.nature.com/articles/nature25014|journal=Nature|language=en|volume=552|issue=7685|pages=400–403|doi=10.1038/nature25014|issn=1476-4687}}</ref>
|[[Dormibacteraeota]]<ref name=":13">{{Cite journal|last=Ji|first=Mukan|last2=Greening|first2=Chris|last3=Vanwonterghem|first3=Inka|last4=Carere|first4=Carlo R.|last5=Bay|first5=Sean K.|last6=Steen|first6=Jason A.|last7=Montgomery|first7=Kate|last8=Lines|first8=Thomas|last9=Beardall|first9=John|last10=van Dorst|first10=Josie|last11=Snape|first11=Ian|date=2017-12|title=Atmospheric trace gases support primary production in Antarctic desert surface soil|url=https://www.nature.com/articles/nature25014|journal=Nature|language=en|volume=552|issue=7685|pages=400–403|doi=10.1038/nature25014|issn=1476-4687}}</ref>
|AD3
|AD3
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|[[Edwardsbacteria]]<ref name=":1" />
|[[Edwardsbacteria]]<ref name=":12" /><ref name=":1" />
|RIF29, UBP-2 <ref name=":14">{{Cite journal|last=Youssef|first=Noha H.|last2=Farag|first2=Ibrahim F.|last3=Hahn|first3=C. Ryan|last4=Premathilake|first4=Hasitha|last5=Fry|first5=Emily|last6=Hart|first6=Matthew|last7=Huffaker|first7=Krystal|last8=Bird|first8=Edward|last9=Hambright|first9=Jimmre|last10=Hoff|first10=Wouter D.|last11=Elshahed|first11=Mostafa S.|date=2019-01-01|title=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|url=http://www.sciencedirect.com/science/article/pii/S072320201830331X|journal=Systematic and Applied Microbiology|series=Taxonomy of uncultivated Bacteria and Archaea|language=en|volume=42|issue=1|pages=85–93|doi=10.1016/j.syapm.2018.11.002|issn=0723-2020}}</ref>
|RIF29
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|No
|No
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|[[Elusimicrobia]]
|[[Elusimicrobia]]<ref name=":8" />
|Termite Group 1, OP7<ref name=":9" />
|OP7, Termite Group 1 (TG1)<ref name=":9" />
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|Yes<ref>{{Cite journal|last=Herlemann|first=D. P. R.|last2=Geissinger|first2=O.|last3=Ikeda-Ohtsubo|first3=W.|last4=Kunin|first4=V.|last5=Sun|first5=H.|last6=Lapidus|first6=A.|last7=Hugenholtz|first7=P.|last8=Brune|first8=A.|date=2009-05-01|title=Genomic Analysis of “Elusimicrobium minutum,” the First Cultivated Representative of the Phylum “Elusimicrobia” (Formerly Termite Group 1)|url=https://aem.asm.org/content/75/9/2841|journal=Applied and Environmental Microbiology|language=en|volume=75|issue=9|pages=2841–2849|doi=10.1128/AEM.02698-08|issn=0099-2240|pmid=19270133}}</ref>
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|[[Eremiobacteraeota]]<ref>{{Cite journal|last=Nogales|first=Balbina|last2=Moore|first2=Edward R. B.|last3=Llobet-Brossa|first3=Enrique|last4=Rossello-Mora|first4=Ramon|last5=Amann|first5=Rudolf|last6=Timmis|first6=Kenneth N.|date=2001-04-01|title=Combined Use of 16S Ribosomal DNA and 16S rRNA To Study the Bacterial Community of Polychlorinated Biphenyl-Polluted Soil|url=https://aem.asm.org/content/67/4/1874|journal=Applied and Environmental Microbiology|language=en|volume=67|issue=4|pages=1874–1884|doi=10.1128/AEM.67.4.1874-1884.2001|issn=0099-2240|pmid=11282645}}</ref><ref name=":13" />
|[[Eremiobacteraeota]]
|WPS-2, Palusbacterota<ref>{{Cite web|title=Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Palusbacterota (WPS-2)|url=http://dx.doi.org/10.1101/534180|last=Ward|first=Lewis M.|last2=Cardona|first2=Tanai|date=2019-01-29|website=dx.doi.org|access-date=2020-05-15|last3=Holland-Moritz|first3=Hannah}}</ref>
|WPS-2
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|No
|No
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|[[Gemmatimonadetes]]<ref name=":11">{{Cite journal|last=Zhang|first=Hui|last2=Sekiguchi|first2=Yuji|last3=Hanada|first3=Satoshi|last4=Hugenholtz|first4=Philip|last5=Kim|first5=Hongik|last6=Kamagata|first6=Yoichi|last7=Nakamura|first7=Kazunori|date=2003|title=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.|url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.02520-0|journal=International Journal of Systematic and Evolutionary Microbiology,|volume=53|issue=4|pages=1155–1163|doi=10.1099/ijs.0.02520-0|issn=1466-5026}}</ref>
|[[Gemmatimonadetes]]<ref name=":11">{{Cite journal|last=Zhang|first=Hui|last2=Sekiguchi|first2=Yuji|last3=Hanada|first3=Satoshi|last4=Hugenholtz|first4=Philip|last5=Kim|first5=Hongik|last6=Kamagata|first6=Yoichi|last7=Nakamura|first7=Kazunori|date=2003|title=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.|url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.02520-0|journal=International Journal of Systematic and Evolutionary Microbiology,|volume=53|issue=4|pages=1155–1163|doi=10.1099/ijs.0.02520-0|issn=1466-5026}}</ref>
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|FCB group<ref name="MDM" />
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|Yes<ref name=":11" />
|Yes<ref name=":11" />
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|[[Gracilibacteria]]<ref name=":15">{{Cite journal|last=Ley|first=Ruth E.|last2=Harris|first2=J. Kirk|last3=Wilcox|first3=Joshua|last4=Spear|first4=John R.|last5=Miller|first5=Scott R.|last6=Bebout|first6=Brad M.|last7=Maresca|first7=Julia A.|last8=Bryant|first8=Donald A.|last9=Sogin|first9=Mitchell L.|last10=Pace|first10=Norman R.|date=2006-05-01|title=Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat|url=https://aem.asm.org/content/72/5/3685|journal=Applied and Environmental Microbiology|language=en|volume=72|issue=5|pages=3685–3695|doi=10.1128/AEM.72.5.3685-3695.2006|issn=0099-2240|pmid=16672518}}</ref>
|[[Gracilibacteria]]
|GN02, BD1-5
|GN02, BD1-5
|CPR
|CPR
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|CPR
|CPR
|No
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|KD3-62
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|No
|No
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|No
|No
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|[[Krumholzibacteriota]]<ref name=":14" />
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|[[Latescibacteria]]
|[[Latescibacteria]]
|WS3
|WS3
|FCB group
|FCB group<ref name="MDM" />
|No
|No
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|LCP-89<ref>{{Cite journal|last=Youssef|first=Noha H.|last2=Farag|first2=Ibrahim F.|last3=Hahn|first3=C. Ryan|last4=Jarett|first4=Jessica|last5=Becraft|first5=Eric|last6=Eloe-Fadrosh|first6=Emiley|last7=Lightfoot|first7=Jorge|last8=Bourgeois|first8=Austin|last9=Cole|first9=Tanner|last10=Ferrante|first10=Stephanie|last11=Truelock|first11=Mandy|date=2019-05-15|title=Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities|url=https://aem.asm.org/content/85/10/e00110-19|journal=Applied and Environmental Microbiology|language=en|volume=85|issue=10|doi=10.1128/AEM.00110-19|issn=0099-2240|pmid=30902854}}</ref>
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|Marinimicrobia
|Marinimicrobia
|SAR406, Marine Group A
|SAR406, Marine Group A
|FCB group<ref name="MDM" />
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|Yes
|Yes
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|Superphylum
|Superphylum
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|[[Modulibacteria]]<ref name=":15" /><ref>{{Cite journal|last=Sekiguchi|first=Yuji|last2=Ohashi|first2=Akiko|last3=Parks|first3=Donovan H.|last4=Yamauchi|first4=Toshihiro|last5=Tyson|first5=Gene W.|last6=Hugenholtz|first6=Philip|date=2015-01-27|title=First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312070/|journal=PeerJ|volume=3|doi=10.7717/peerj.740|issn=2167-8359|pmc=4312070|pmid=25650158}}</ref>
|[[Modulibacteria]]
|KSB3
|KSB3, GN06
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|No
|No
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|NC10<ref>{{Cite journal|last=Holmes|first=Andrew J.|last2=Tujula|first2=Niina A.|last3=Holley|first3=Marita|last4=Contos|first4=Annalisa|last5=James|first5=Julia M.|last6=Rogers|first6=Peter|last7=Gillings|first7=Michael R.|date=2001|title=Phylogenetic structure of unusual aquatic microbial formations in Nullarbor caves, Australia|url=https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1046/j.1462-2920.2001.00187.x|journal=Environmental Microbiology|language=en|volume=3|issue=4|pages=256–264|doi=10.1046/j.1462-2920.2001.00187.x|issn=1462-2920}}</ref><ref name="Rappe" />
|NC10
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|Nitrospinae<ref>{{Cite journal|last=Luecker|first=Sebastian|last2=Nowka|first2=Boris|last3=Rattei|first3=Thomas|last4=Spieck|first4=Eva|last5=Daims|first5=Holger|date=2013|title=The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer|url=https://www.frontiersin.org/articles/10.3389/fmicb.2013.00027/full|journal=Frontiers in Microbiology|language=English|volume=4|doi=10.3389/fmicb.2013.00027|issn=1664-302X}}</ref>
|Nitrospinae
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|No
|No
|Superphylum
|Superphylum
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|[[PAUC34f]]<ref>{{Cite journal|last=Astudillo‐García|first=Carmen|last2=Slaby|first2=Beate M.|last3=Waite|first3=David W.|last4=Bayer|first4=Kristina|last5=Hentschel|first5=Ute|last6=Taylor|first6=Michael W.|date=2018|title=Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges|url=https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.13965|journal=Environmental Microbiology|language=en|volume=20|issue=2|pages=561–576|doi=10.1111/1462-2920.13965|issn=1462-2920}}</ref>
|sponge‐associated unclassified lineage (SAUL)
|FCB group
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|[[Perigrinibacteria]]<ref>{{Cite journal|last=Wrighton|first=K. C.|last2=Thomas|first2=B. C.|last3=Sharon|first3=I.|last4=Miller|first4=C. S.|last5=Castelle|first5=C. J.|last6=VerBerkmoes|first6=N. C.|last7=Wilkins|first7=M. J.|last8=Hettich|first8=R. L.|last9=Lipton|first9=M. S.|last10=Williams|first10=K. H.|last11=Long|first11=P. E.|date=2012-09-27|title=Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla|url=http://dx.doi.org/10.1126/science.1224041|journal=Science|volume=337|issue=6102|pages=1661–1665|doi=10.1126/science.1224041|issn=0036-8075}}</ref>
|[[Perigrinibacteria]]<ref>{{Cite journal|last=Wrighton|first=K. C.|last2=Thomas|first2=B. C.|last3=Sharon|first3=I.|last4=Miller|first4=C. S.|last5=Castelle|first5=C. J.|last6=VerBerkmoes|first6=N. C.|last7=Wilkins|first7=M. J.|last8=Hettich|first8=R. L.|last9=Lipton|first9=M. S.|last10=Williams|first10=K. H.|last11=Long|first11=P. E.|date=2012-09-27|title=Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla|url=http://dx.doi.org/10.1126/science.1224041|journal=Science|volume=337|issue=6102|pages=1661–1665|doi=10.1126/science.1224041|issn=0036-8075}}</ref>
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|[[Poribacteria]]<ref>{{Cite journal|last=Fieseler|first=Lars|last2=Horn|first2=Matthias|last3=Wagner|first3=Michael|last4=Hentschel|first4=Ute|date=2004-6|title=Discovery of the Novel Candidate Phylum “Poribacteria” in Marine Sponges|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC427773/|journal=Applied and Environmental Microbiology|volume=70|issue=6|pages=3724–3732|doi=10.1128/AEM.70.6.3724-3732.2004|issn=0099-2240|pmid=15184179}}</ref>
|[[Poribacteria]]
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|CPR
|CPR
|No
|No
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|[[Sumerlaeota]]<ref>{{Cite journal|last=Derakshani|first=Manigee|last2=Lukow|first2=Thomas|last3=Liesack|first3=Werner|date=2001-02-01|title=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|url=http://dx.doi.org/10.1128/aem.67.2.623-631.2001|journal=Applied and Environmental Microbiology|volume=67|issue=2|pages=623–631|doi=10.1128/aem.67.2.623-631.2001|issn=1098-5336}}</ref><ref>{{Cite journal|last=Kadnikov|first=Vitaly V.|last2=Mardanov|first2=Andrey V.|last3=Beletsky|first3=Alexey V.|last4=Rakitin|first4=Andrey L.|last5=Frank|first5=Yulia A.|last6=Karnachuk|first6=Olga V.|last7=Ravin|first7=Nikolai V.|date=2019-01|title=Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer|url=https://www.ncbi.nlm.nih.gov/pubmed/30201528|journal=Systematic and Applied Microbiology|volume=42|issue=1|pages=67–76|doi=10.1016/j.syapm.2018.08.013|issn=1618-0984|pmid=30201528}}</ref>
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|BRC1
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|UBP-1<ref name=":12">{{Cite journal|last=Parks|first=Donovan H.|last2=Rinke|first2=Christian|last3=Chuvochina|first3=Maria|last4=Chaumeil|first4=Pierre-Alain|last5=Woodcroft|first5=Ben J.|last6=Evans|first6=Paul N.|last7=Hugenholtz|first7=Philip|last8=Tyson|first8=Gene W.|date=2017-11|title=Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life|url=https://www.nature.com/articles/s41564-017-0012-7|journal=Nature Microbiology|language=en|volume=2|issue=11|pages=1533–1542|doi=10.1038/s41564-017-0012-7|issn=2058-5276}}</ref>
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Revision as of 00:04, 16 May 2020

EuryarchaeotaNanoarchaeotaThermoproteotaProtozoaAlgaePlantSlime moldsAnimalFungusGram-positive bacteriaChlamydiotaChloroflexotaActinomycetotaPlanctomycetotaSpirochaetotaFusobacteriotaCyanobacteriaThermophilesAcidobacteriotaPseudomonadota
Phylogenetic tree showing the diversity of bacteria, compared to other organisms.[1] Eukaryotes are colored red, archaea green and bacteria blue.

The bacterial phyla are the major lineages of the domain Bacteria. 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.

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.[2]

It has been estimated that ~1,300 bacterial phyla exist.[2] As of May 2020, only 41 bacterial phyla are formally accepted by the LPSN[3] while 89 bacterial phyla are recognized on the Silva database although many more have been proposed [4][5] and many more undoubtedly remain to be discovered. As of 2017, approximately 72% of widely recognized bacterial phyla were candidate phyla.[6]

There are no fixed rules to the nomenclature of bacterial phyla. It was proposed that the suffix "-bacteria" be used for phyla.

Molecular phylogenetics

For historical classifications of bacteria, see Bacterial taxonomy.

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.[7] 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".[8]

Initial sub-division

For branching order, see Branching order of bacterial phyla (Woese, 1987).
Atomic structure of the 30S ribosomal Subunit from Thermus thermophilus of which 16S makes up a part. Proteins are shown in blue and the single RNA strand in tan.[9]

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[8][10] . Many new phyla have been proposed since then.

The following is a list of bacterial phyla that have been proposed.

Phylum Alternative names Group Cultured representative Notes
10bav-F6[21] No
Abawacabacteria[4] RIF46 CPR No
Abditibacteriota[22] FBP Yes[22]
Absconditabacteria[23] SR1 CPR No
Acetothermia[24] OP1
Acidobacteria Yes[25]
Actinobacteria Yes[26]
Adlerbacteria[27] CPR; Parcubacteria No
Aerophobota / Aerophobetes CD12, BHI80-139
Amesbacteria[27] CPR; Microgenomates No
Andersenbacteria[4] RIF9 CPR No
Armatimonadetes[24] OP10 Yes[28]
Aminicenantes[24] OP8
AncK6[21]
Apal-E12[21]
Atribacteria[24] OP9, JS1 No
Aquificae
Azambacteria[27] CPR; Parcubacteria No
Bacteroidetes FCB group Yes
Balneolaeota[29] Yes
Bdellovibrionota
Beckwithbacteria[27] CPR; Microgenomates No
BHI80-139[21]
Berkelbacteria ACD58 CPR No
Blackburnbacteria[4] RIF35 CPR No
Brennerbacteria[4] RIF18 CPR No
Buchananbacteria[4] RIF37 CPR No
Caldiserica[24] OP5[30] Yes[31]
Calditrichaeota[32] Caldithrix FCB group[33]
Calescamantes EM19, OP1
Campbellbacteria[27] CPR; Parcubacteria No
Chlamydiae[34]
Chlorobi FCB group
Chloroflexi
Chisholmbacteria[4] RIF36 CPR No
Chrysiogenetes
Cloacimonetes[35] WWE1 FCB group[33]
Coatesbacteria[4] RIF8 No
Collierbacteria[27] CPR; Microgenomates No
Colwellbacteria[4] RIF41 CPR No
Curtisbacteria[27] CPR; Microgenomates No
CPR-1
CPR-2 CPR No
Cyanobacteria
Dadabacteria[36] No
Daviesbacteria[27] CPR; Microgenomates No
Delphibacteria[6] FCB group No
Delongbacteria[4] RIF26, H-178 No
Deferribacteres
Deinococcus–Thermus
Dependentiae[37] TM6
Dictyoglomi[38]
Dojkabacteria CPR3
Dormibacteraeota[39] AD3 No
Doudnabacteria[27][4] SM2F11 CPR No
Edwardsbacteria[40][4] RIF29, UBP-2 [41] No
Eisenbacteria[4] RIF28 FCB group No
Elusimicrobia[24] OP7, Termite Group 1 (TG1)[30] Yes[42]
Eremiobacteraeota[43][39] WPS-2, Palusbacterota[44] No
Falkowbacteria[27] CPR; Parcubacteria No
Fermentibacteria Hyd24-12 No
Fertabacteria[6] No
Fibrobacteres FCB group
Firestonebacteria[4] RIF1 No
Fervidibacteria OctSpa1-106
Fischerbacteria[4] RIF25 No
Firmicutes
Fraserbacteria[4] RIF31 No
Fusobacteria
Gemmatimonadetes[45] FCB group[33] Yes[45]
Glassbacteria[4] RIF5 No
Giovannonibacteria[27] CPR; Parcubacteria No
Gottesmanbacteria[27] CPR; Microgenomates No
Gracilibacteria[46] GN02, BD1-5 CPR No
Handelsmanbacteria[4] RIF27 No
Harrisonbacteria[4] RIF43 CPR No
Hydrogenedentes NKB19 No
Ignavibacteria ZB1
Jacksonbacteria[4] RIF38 CPR No
Jorgensenbacteria[27] CPR; Parcubacteria No
Kaiserbacteria[27] CPR; Parcubacteria No
Katanobacteria[47] WWE3 No
Kazan CPR No
Kerfeldbacteria[4] RIF4 CPR No
Komeilibacteria[4] RIF6 CPR No
Kryptonia[48] No
KSB1 No
Krumholzibacteriota[41]
Kuenenbacteria[27] CPR; Parcubacteria No
Lambdaproteobacteria[4] RIF24 No
Latescibacteria WS3 FCB group[33] No
LCP-89[49]
Lentisphaerae vadinBE97
Levybacteria[27] CPR; Microgenomates No
Lindowbacteria[4] RIF2 No
Liptonbacteria[4] RIF42 CPR No
Lloydbacteria[4] RIF45 CPR No
Magasanikbacteria[27] CPR; Parcubacteria No
Margulisbacteria[4] RIF30 No
Marinimicrobia SAR406, Marine Group A FCB group[33] Yes
Melainabacteria[50] No
Microgenomates[51] OP11 CPR No Superphylum
Modulibacteria[46][52] KSB3, GN06 No
Moranbacteria[27] CPR; Parcubacteria No
Muproteobacteria[4] RIF23 No
NC10[53][54] No
Nealsonbacteria[4] RIF40 CPR No
Niyogibacteria[4] RIF11 CPR No
Nitrospinae[55]
Nitrospirae
Nomurabacteria[27] CPR; Parcubacteria No
Omnitrophica[24] OP3 No
Pacebacteria[27] CPR; Microgenomates No
Parcubacteria[23] OD1 CPR No Superphylum
PAUC34f[56] sponge‐associated unclassified lineage (SAUL) FCB group
Perigrinibacteria[57] PER No
Planctomycetes
Poribacteria[58]
Portnoybacteria[4] RIF22 CPR No
Proteobacteria
Raymondbacteria[4] RIF7 No
Riflebacteria[4] RIF32 No
Roizmanbacteria[27] CPR; Microgenomates No
Rokubacteria[36] No
Ryanbacteria[4] RIF10 CPR No
Saccharibacteria[37] TM7 Yes
Schekmanbacteria[4] RIF3 CPR No
Shapirobacteria[27] CPR; Microgenomates No
Spechtbacteria[4] RIF19 CPR No
Spirochaetes
Staskawiczbacteria[4] RIF20 CPR No
Sumerlaeota[59][60] BRC1
Sungbacteria[4] RIF17 CPR No
Synergistetes
TA06[61] No
Tagabacteria[4] RIF12 CPR No
Taylorbacteria[4] RIF16 CPR No
Tectomicrobia[62]
Tenericutes
Terrybacteria[4] RIF13 CPR No
Thermodesulfobacteria
Thermomicrobia
Thermotogae OP2, EM3[30] Yes[63]
UBP-1[40] No
UBP-3[40] No
UBP-4[40] No
UBP-5[40] No
UBP-6[40] No
UBP-7[40] No
UBP-8[40] No
UBP-9[40] No
UBP-10[40] No
UBP-11[40] No
UBP-12[40] No
UBP-13[40] No
UBP-14[40] No
UBP-15[40] No
UBP-16[40] No
UBP-17[40] No
Uhrbacteria[27] CPR; Parcubacteria No
Veblenbacteria[4] RIF39 CPR No
Verrucomicrobia
Vogelbacteria[4] RIF14 CPR No
Wallbacteria[4] RIF33 No
Wildermuthbacteria[4] RIF21 CPR No
Woesebacteria[27] CPR; Microgenomates No
Wolfebacteria[27] CPR; Parcubacteria No
Woykebacteria[4] RIF34 CPR No
WOR-1[61] No
WOR-2[61] No
WOR-3[61] No
WS6 No
Yanofskybacteria[27] CPR; Parcubacteria No
Yonathbacteria[4] RIF44 CPR No
Zambryskibacteria[4] RIF15 CPR No
Zixibacteria[64] RBG-1 No

Uncultivated phyla and metagenomics

For a list of such phyla, see List of taxa with candidatus status § Phyla.

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.[54] 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.[65][66] When the species are members of a whole phylum it is called a candidate division (or candidate phylum)[67] and in 2003 there were 26 candidate phyla out of 52.[54] 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.[24] More recently an even lower threshold of 75% was proposed.[68] 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:[54])

Since then a candidate phylum called Poribacteria was discovered, living in symbiosis with sponges and extensively studied.[71] (Note: the divergence of the major bacterial lineages predates sponges) Another candidate phylum, called Tectomicrobia, was also found living in symbiosis with sponges.[72] And Nitrospina gracilis, which had long eluded phylogenetic placement, was proposed to belong to a new phylum, Nitrospinae.[73]

Other candidate phyla that have been the center of some studies are TM7,[67] the genomes of organisms of which have even been sequenced (draft),[74] WS6[75] and Marine Group A.[54]

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[76] and Chthonomonas calidirosea from an isolate from geothermally heated soil at Hell's Gate, Tikitere, New Zealand.[77]

One species, Caldisericum exile, of the candidate phylum OP5 was cultured, leading to it being named Caldiserica.[78]

The candidate phylum VadinBE97 is now known as Lentisphaerae after Lentisphaera araneosa and Victivallis vadensis were cultured.[79]

More recently several candidate phyla have been given provisional names despite the fact that they have no cultured representatives:[33]

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),[85] 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),[21] 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),[86] 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),[85] 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).[87]

Many phyla of this type forms a larger clade distinct from other bacteria called the candidate phyla radiation.[88]

Superphyla

Despite the unclear branching order for most bacterial phyla, several groups of phyla consistently cluster together and are referred to as superphyla.

The FCB Group

Main article: Sphingobacteria

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.[33][81]

The PVC Group

Main article: Planctobacteria

The PVC group (now called Planctobacteria) includes Chlamydiae, Lentisphaerae, candidate phylum Omnitrophica, Planctomycetes, candidate phylum Poribacteria, and Verrucomicrobia.[33][81]

Patescibacteria

The superphylum Patescibacteria was originally proposed to encompass the phyla Microgenomates (OP11), Parcubacteria (OD1), and Gracilibacteria (GNO2 / BD1-5)[33]. Unfortunately, the meaning of the term 'Patescibacteria' has become confused and is sometimes erroneously used interchangeably with the term Candidate Phyla Radiation (CPR)[89] . To complicate matters, it has been suggested that the Microgenomates and Parcubacteria groups within the Patescibacteria are themselves actually superphyla (see the section on cryptic superphyla below).

Terrabacteria

The proposed superphylum, Terrabacteria,[90] includes Actinobacteria, Cyanobacteria, Deinococcus–Thermus, Chloroflexi, Firmicutes, and candidate phylum OP10.[90][91][33][81]

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.[68] For example, the Deltaproteobacteria group does not consistently form a monophyletic lineage with the other Proteobacteria classes [70].

Candidate Phyla Radiation (CPR)

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[88]. It includes the Patescibacteria group as well as dozens of additional phyla and superphyla.

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.[68]

Overview of phyla

For the origin of each phylum name, see Bacterial taxonomy § Phyla endings.

As of January  2016, there are 30 phyla in the domain "Bacteria" accepted by LPSN.[3] There are no fixed rules to the nomenclature of bacterial phyla. It was proposed that the suffix "-bacteria" be used for phyla,[92] 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

Main article: Acidobacteria

The Acidobacteria (diderm Gram negative) is the 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.[93] Generally its members divide slowly, exhibit slow metabolic rates under low-nutrient conditions and can tolerate fluctuations in soil hydration.[94]

Actinobacteria

Main article: Actinobacteria

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), Cutibacterium acnes (odorous skin commensal) and Propionibacterium freudenreichii (holes in Emmental)

Aquificae

Main article: 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, this may be one of the most deep branching phyla.

Armatimonadetes

Main article: Armatimonadetes

Bacteroidetes

Main article: 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 of a bacterial weight loss powder.[95]

Caldiserica

Main article: Caldiserica

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

Chlamydiae

Main article: 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

Main article: 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).[96]

Chloroflexi

Main article: Chloroflexi (phylum)

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

Chrysiogenetes

Main article: Chrysiogenetes

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

Cyanobacteria

Main article: Cyanobacteria

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

Deferribacteres

Main article: Deferribacteres

Deferribacteres

Deinococcus–Thermus

Main article: Deinococcus–Thermus

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

Dictyoglomi

Main article: Dictyoglomi

Dictyoglomi

Elusimicrobia

Main article: Elusimicrobia

Elusimicrobia, formerly candidate phylum Termite Group 1

Fibrobacteres

Main article: Fibrobacteres

Fibrobacteres, member of the FBC superphylum.

Firmicutes

Main article: 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

Main article: Fusobacteria

Fusobacteria

Gemmatimonadetes

Main article: Gemmatimonadetes

Gemmatimonadetes, member of the FBC superphylum.

Lentisphaerae

Main article: Lentisphaerae

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

Nitrospirae

Main article: Nitrospirae

Nitrospirae

Planctomycetes

Main article: Planctomycetes

Planctomycetes, member of the PVC superphylum.

Proteobacteria

Main article: Proteobacteria

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

Spirochaetes

Main article: Spirochaetes

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

Synergistetes

Main article: Synergistetes

The Synergistetes is a phylum whose members are diderm Gram negative, rod-shaped obligate anaerobes, some of which are human commensals.[97]

Tenericutes

Main article: 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

Main article: 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

Main article: Thermomicrobia

The Thermomicrobia is a group of thermophilic green non-sulfur bacteria.

Thermotogae

Main article: 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

Main article: 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.[98]

Branching order

The branching order of the phyla of bacteria is unclear.[99] 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.

See also

Footnotes

  1. ^ Until recently, it was believed than only Firmicutes and Actinobacteria were Gram-positive. However, the candidate phylum TM7 may also be Gram positive.[12] Chloroflexi however possess a single bilayer, but stain negative (with some exceptions[13]).[14]
  2. ^ Pasteuria is now assigned to phylum Bacilli, not to phylum Planctomycetes.
  3. ^ It has been proposed to call the clade Xenobacteria[17] or Hadobacteria[18] (the latter is considered an illegitimate name[19]).
Cite error: A list-defined reference named "official" is not used in the content (see the help page).

[91][90]

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