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Verrucomicrobia is a phylum of bacteria. This phylum contains only a few described species (Verrucomicrobium spinosum, is an example, the phylum is named after this). The species identified have been isolated from fresh water and soil environments and human faeces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes residing in their gametes. While verrucae is another name for the warts often found on hands and feet, this phylum is so called not because it is a causative agent thereof, but because of its wart-like morphology. Evidence suggests that verrucomicrobia are abundant within the environment, and important (especially to soil cultures). This phylum is considered to have two sister phyla: Chlamydiae
Chlamydiae
and Lentisphaerae within the PVC group.[1] The Verrucomicrobia phylum can be distinguished from neighbouring phyla within the PVC group
PVC group
by the presence of several conserved signature indels (CSIs).[2] These CSIs represent unique, synapomorphic characteristics that suggest common ancestry within Verrucomicrobia and an independent lineage amidst other bacteria.[3] CSIs have also been found that are shared by Verrucomicrobia and Chlamydiae
Chlamydiae
exclusively of all other bacteria.[4] These CSIs provide evidence that Chlamydiae
Chlamydiae
is the closest relative to Verrucomicrobia, and that they are more closely related to one another than to the Planctomycetales. Cavalier-Smith
Cavalier-Smith
has postulated that the Verrucomicrobia belong in the clade Planctobacteria
Planctobacteria
in the larger clade Gracilicutes. 16S rRNA data corroborate that view.[5] In 2008, the whole genome of Methylacidiphilum infernorum (2.3 Mbp) was published. On the single circular chromosome, 2473 predicted proteins were found, 731 of which had no detectable homologs. These analyses also revealed many possible homologies with Proteobacteria.[6][7] Phylogeny[edit] See also: Bacterial taxonomy The phylogeny based on the work of the All-Species Living Tree Project.[8]

Opitutae

Puniceicoccaceae

Coraliomargarita akajimensis

Puniceicoccus vermicola

Cerasicoccus arenae

Opitutaceae

Opitutus terrae

Alterococcus agarolyticus

Pelagicoccus

P. croceus

P. mobilis (type sp.)

P. albus

P. litoralis

Verrucomicrobiales

Limisphaera ngatamarikiensis

Verrucomicrobiaceae

Terrimicrobium sacchariphilum

Verrucomicrobium spinosum

Roseimicrobium gellanilyticum

Prosthecobacter

P. fluviatilis

P. vanneervenii

Brevifollis gellanilyticus

P. algae

P. dejongeii

P. debontii

P. fusiformis (type sp.)

Akkermansia muciniphila

Luteolibacter

L. cuticulihirudinis

L. pohnpeiensis (type sp.)

L. algae

L. luojiensis

L. yonseiensis

Haloferula

H. luteola

H. sargassicola

H. helveola

H. phyci

H. harenae

H. chungangensis

H. rosea (type sp.)

Roseibacillus

R. persicicus

R. ishigakijimensis (type sp.)

R. ponti

Persicirhabdus sediminis

Rubritalea

R. sabuli

R. halochordaticola

R. squalenifaciens

R. marina (type sp.)

R. spongiae

R. tangerina

Taxonomy[edit] The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[9] and the National Center for Biotechnology Information (NCBI).[10]

Phylum Verrucomicrobia Hedlund 2012 [Verrucomicrobaeota Oren et al. 2015]

Genus ?"Candidatus Epixenosoma" ♠ Bauer et al. 2005

Species "Candidatus Epixenosoma
Epixenosoma
ejectans" ♠ Bauer et al. 2005

Genus ?Lentimonas ♠ Choo & Cho 2006

Species "Lentimonas marisflavi" ♠ Choo & Cho 2006

Genus? "Methyloacida" ♠ Islam et al. 2008 Genus ?"Methylacidimicrobium" ♠ van Teeseling et al. 2014

Species "M. cyclopophantes" ♠ van Teeseling et al. 2014 Species "M. fagopyrum" ♠ van Teeseling et al. 2014 Species "M. tartarophylax" ♠ van Teeseling et al. 2014

Order ?"Methylacidiphilales" ♠ Op den Camp 2009

Family "Methylacidiphilaceae" ♠ Op den Camp 2009

Genus "Methylacidiphilum" ♠ Hou et al. 2008 emend. Op den Camp et al. 2009

Species "M. fumariolicum" ♠ (Pol et al. 2007) Op den Camp et al. 2009 Species "M. infernorum" ♠ (Dunfield et al. 2007) Hou et al. 2008 Species "M. kamchatkense" ♠ Islam et al. 2008

Class ?"Spartobacteria" Sangwan et al. 2004

Genus "Candidatus Xiphinematobacter" ♠ Vandekerckhove et al. 2000

Species "Ca. X. americani" ♠ Vandekerckhove et al. 2000 Species "Ca. X. brevicolli" ♠ Vandekerckhove et al. 2000 Species "Ca. X. rivesi" ♠ Vandekerckhove et al. 2000

Order "Chthoniobacterales" Sangwan et al. 2004

Family "Chthoniobacteraceae" Sangwan et al. 2004

Genus "Chthoniobacter" ♠ Sangwan et al. 2004

Species "Chthoniobacter flavus" ♠ Sangwan et al. 2004

Class Opitutae Choo et al. 2007

Order Opitutales Choo et al. 2007

Family Opitutaceae Choo et al. 2007

Genus ?"Diplosphaera" ♠ Wertz et al. 2012 non Bialosuknia 1909

Species " Diplosphaera colitermitum" ♠ Wertz et al. 2012

Genus Alterococcus Shieh and Jean 1999

Species Alterococcus agarolyticus Shieh and Jean 1999

Genus Opitutus Chin et al. 2001

Species Opitutus terrae Chin et al. 2001

Genus Cephaloticoccus Lin et al. 2016

Species C. capnophilus Lin et al. 2016 Species C. primus Lin et al. 2016

Order Puniceicoccales Choo et al. 2007

Family Puniceicoccaceae Choo et al. 2007

Genus Cerasicoccus Yoon et al. 2007

Species C. arenae Yoon et al. 2007 (type sp.) Species "C. frondis" ♠ Yoon et al. 2010 Species "C. maritimus" ♠ Yoon et al. 2010

Genus Coraliomargarita Yoon et al. 2007

Species Coraliomargarita akajimensis Yoon et al. 2007

Genus Pelagicoccus Yoon et al. 2007

Species P. albus Yoon et al. 2007 Species P. croceus Yoon et al. 2007 Species P. litoralis Yoon et al. 2007 Species P. mobilis Yoon et al. 2007 (type sp.)

Genus Puniceicoccus Choo et al. 2007

Species Puniceicoccus vermicola Choo et al. 2007

Class Verrucomicrobiae Hedlund et al. 1998 emend. Yoon et al. 2008

Order Verrucomicrobiales Ward-Rainey et al. 1996 emend. Yoon et al. 2008

Family Verrucomicrobia subdivision 3 [Pedosphaeraceae]

Genus ?"Pedosphaera" ♠ Ozyurt 2008

Species "Pedosphaera parvula" ♠ Ozyurt 2008

Genus Limisphaera ngatamarikiensis Anders et al. 2015

Species Limisphaera ngatamarikiensis Anders et al. 2015

Family Akkermansiaceae Hedlund & Derrien 2012

Genus Akkermansia Derrien et al. 2004

Species Akkermansia muciniphila Derrien et al. 2004

Family Rubritaleaceae Hedlund 2012

Genus Rubritalea Scheuermayer et al. 2006

Species R. halochordaticola Yoon et al. 2011 Species R. marina Scheuermayer et al. 2006 (type sp.) Species R. sabuli Yoon et al. 2008 Species R. spongiae Yoon et al. 2007 Species R. squalenifaciens Kasai et al. 2007 Species R. tangerina Yoon et al. 2007

Family Verrucomicrobiaceae Ward-Rainey et al. 1996 emend. Takeda et al. 2008

Genus ?Fucophilus ♠ Sakai et al. 2001b

Species Fucophilus fucoidanolyticus ♠ Sakai et al. 2001b

Genus Brevifollis Otsuka et al. 2013

Species Brevifollis gellanilyticus Otsuka et al. 2013

Genus Haloferula Yoon et al. 2008 emend. Bibi et al. 2011

Species H. chungangensis Kang et al. 2013 Species H. harenae Yoon et al. 2008 Species H. helveola Yoon et al. 2008 Species H. luteola Bibi et al. 2011 Species H. phyci Yoon et al. 2008 Species H. rosea Yoon et al. 2008 (type sp.) Species H. sargassicola Yoon et al. 2008

Genus Persicirhabdus Yoon et al. 2008

Species Persicirhabdus sediminis Yoon et al. 2008

Genus Luteolibacter Yoon et al. 2008

Species L. algae Yoon et al. 2008 Species L. cuticulihirudinis Glaeser et al. 2012 Species L. luojiensis Jiang et al. 2012 Species L. pohnpeiensis Yoon et al. 2008 (type sp.) Species L. yonseiensis Park et al. 2013

Genus Roseibacillus Yoon et al. 2008

Species R. persicicus Yoon et al. 2008 Species R. ishigakijimensis Yoon et al. 2008 (type sp.) Species R. ponti Yoon et al. 2008

Genus Roseimicrobium Otsuka et al. 2013

Species Roseimicrobium gellanilyticum Otsuka et al. 2013

Genus Prosthecobacter (ex Staley et al. 1976) Staley et al. 1980 emend. Takeda et al. 2008

Species P. algae Lee et al. 2014 Species P. dejongeii Hedlund et al. 1998 Species P. debontii Hedlund et al. 1998 Species P. fluviatilis Takeda et al. 2008 Species P. fusiformis (ex Staley et al. 1976) Staley et al. 1980 (type sp.) Species P. vanneervenii Hedlund et al. 1998

Genus Terrimicrobium Qiu et al. 2014

Species Terrimicrobium sacchariphilum Qiu et al. 2014

Genus Verrucomicrobium Schlesner 1988

Species Verrucomicrobium spinosum Schlesner 1988

Notes: ♠ Strain found at the National Center for Biotechnology Information (NCBI) but has no standing with the Bacteriological Code (1990 and subsequent Revision) as detailed by List of Prokaryotic names with Standing in Nomenclature (LPSN) as a result of the following reasons: References[edit]

^ Cho J, Vergin K, Morris R, Giovannoni S (2004). "Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae". Environ Microbiol. 6 (6): 611–21. doi:10.1111/j.1462-2920.2004.00614.x. PMID 15142250.  ^ Gupta RS, Bhandari V, Naushad HS (2012). "Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria
Bacteria
Provide Insights into Their Evolutionary Relationships". Front Microbiol. 3: 327. doi:10.3389/fmicb.2012.00327. PMC 3444138 . PMID 23060863.  ^ Gupta RS (2016). "Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification". FEMS Microbiol Rev. 40 (4): 520–53. doi:10.1093/femsre/fuw011. PMID 27279642.  ^ Griffiths E, Gupta RS (2007). "Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae". Microbiology. 153 (Pt 8): 2648–54. doi:10.1099/mic.0.2007/009118-0. PMID 17660429.  ^ Wagner, M; Horn, M (2006). "The Planctomycetes, Verrucomicrobia, Chlamydiae
Chlamydiae
and sister phyla comprise a superphylum with biotechnological and medical relevance". Current Opinion in Biotechnology. 17 (3): 241–9. doi:10.1016/j.copbio.2006.05.005. PMID 16704931.  ^ Hou, S; Makarova, KS; Saw, JH; Senin, P; Ly, BV; Zhou, Z; Ren, Y; Wang, J; Galperin, MY; Omelchenko, Marina V; Wolf, Yuri I; Yutin, Natalya; Koonin, Eugene V; Stott, Matthew B; Mountain, Bruce W; Crowe, Michelle A; Smirnova, Angela V; Dunfield, Peter F; Feng, Lu; Wang, Lei; Alam, Maqsudul (2008). "Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia". Biology direct. 3: 26. doi:10.1186/1745-6150-3-26. PMC 2474590 . PMID 18593465.  ^ Ludwig, W., Euzéby, J., & Whitman W.B. (2008). "Bergey's Taxonomic Outlines: Volume 4 - Draft Taxonomic Outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes" (PDF). Bergey's Manual Trust: 15 CS1 maint: Multiple names: authors list (link) ^ "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.  ^ J.P. Euzéby. "Verrucomicrobia". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.  ^ Sayers; et al. "Verrucomicrobia". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20. 

v t e

Prokaryotes: Bacteria
Bacteria
classification (phyla and orders)

Domain Archaea Bacteria Eukaryota (Supergroup Plant Hacrobia Heterokont Alveolata Rhizaria Excavata Amoebozoa Opisthokonta

Animal Fungi)

G-/ OM

Terra-/ Glidobacteria (BV1)

Eobacteria

Deinococcus–Thermus

Deinococcales Thermales

Chloroflexi

Anaerolineales Caldilineales Chloroflexales Herpetosiphonales Dehalococcoidales Ktedonobacterales Thermogemmatisporales Thermomicrobiales Sphaerobacterales

other glidobacteria

Thermodesulfobacteria thermophiles

Aquificae Thermotogae

Cyanobacteria

Proteobacteria (BV2)

Alpha

Caulobacterales Kiloniellales Kordiimonadales Magnetococcales Parvularculales Rhizobiales Rhodobacterales Rhodospirillales Rickettsiales Sneathiellales Sphingomonadales

Beta

Burkholderiales Hydrogenophilales Methylophilales Neisseriales Nitrosomonadales Procabacteriales Rhodocyclales

Gamma

Acidithiobacillales Aeromonadales Alteromonadales Cardiobacteriales Chromatiales Enterobacteriales Legionellales Methylococcales Oceanospirillales Orbales Pasteurellales Pseudomonadales Salinisphaerales Thiotrichales Vibrionales Xanthomonadales

Delta

Bdellovibrionales Desulfarculales Desulfobacterales Desulfovibrionales Desulfurellales Desulfuromonadales Myxococcales Syntrophobacterales Syntrophorhabdales

Epsilon

Campylobacterales Nautiliales

Zeta

Mariprofundales

BV4

Spirochaetes

Spirochaetes

Sphingobacteria (FCB group)

Fibrobacteres Chlorobi

Chlorobiales Ignavibacteriales

Bacteroidetes

Bacteroidales Cytophagales Flavobacteriales Sphingobacteriales

Planctobacteria/ (PVC group)

Chlamydiae Lentisphaerae

Lentisphaerales Oligosphaerales Victivallales

Planctomycetes

Phycisphaerales Planctomycetales

Verrucomicrobia

Puniceicoccales Opitutales Chthoniobacterales Verrucomicrobiales

"Poribacteria"

Other GN

Acidobacteria

Acidobacteriales Acanthopleuribacterales Holophagales Solibacterales

Armatimonadetes

Armatimonadales Chthonomonadales Fimbriimonadales

Caldiserica Chrysiogenetes Deferribacteres Dictyoglomi Elusimicrobia Fusobacteria Gemmatimonadetes Nitrospirae Synergistetes

G+/ no OM

Firmicutes (BV3)

Bacilli

Bacillales Lactobacillales

Clostridia

Clostridiales Halanaerobiales Thermoanaerobacteriales Natranaerobiales

Erysipelotrichia

Erysipelotrichiales

Thermolithobacteria

Thermolithobacterales

Tenericutes/ Mollicutes

Mycoplasmatales Entomoplasmatales Anaeroplasmatales Acholeplasmatales Haloplasmatales

Negativicutes

Selenomonadales

Actinobacteria (BV5)

Actinobacteria

Actinomycetales Bifidobacteriales

Acidimicrobiia

Acidimicrobiales

Coriobacteriidae

Coriobacteriales

Nitriliruptoria

Euzebyales Nitriliruptorales

Rubrobacteria

Gaiellales Rubrobacterales Thermoleophilales Solirubrobacterales

Incertae sedis

†Archaeosphaeroides †Eobacterium †Leptotrichites

Source: Bergey's Manual (2001–2012). Alternative views: Wikispecies.

Taxon identifiers

Wd: Q18667425 EoL: 289 iNaturalist: 151863 ITIS: 956126

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