Verrucomicrobiota Hedlund, 2021
- Dataset
- English Wikipedia - Species Pages
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- PHYLUM
Classification
- phylum
- Verrucomicrobiota
Abstract
Verrucomicrobiota is a phylum of Gram-negative bacteria that contains only a few described species. The species identified have been isolated from fresh water, marine 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. Verrucomicrobiota are abundant within the environment, though relatively inactive. This phylum is considered to have two sister phyla: Chlamydiota (formerly Chlamydiae) and Lentisphaerota (formerly Lentisphaerae) within the PVC superphylum. The Verrucomicrobiota phylum can be distinguished from neighbouring phyla within the PVC group by the presence of several conserved signature indels (CSIs). These CSIs represent unique, synapomorphic characteristics that suggest common ancestry within Verrucomicrobiota and an independent lineage amidst other bacteria. CSIs have also been found that are shared by Verrucomicrobiota and Chlamydiota exclusively of all other bacteria. These CSIs provide evidence that Chlamydiota is the closest relative to Verrucomicrobiota, and that they are more closely related to one another than to the Planctomycetales. Verrucomicrobiota might belong in the clade Planctobacteria in the larger clade Gracilicutes. 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 Pseudomonadota.
Phylogeny
The phylogeny based on the work of the All-Species Living Tree Project.
Taxonomy
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN) and the National Center for Biotechnology Information (NCBI).
Phylum Verrucomicrobiota Hedlund 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 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 Terrimicrobia García-López et al. 2020 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 Geminisphaera Wertz et al. 2018 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 Genus ?Lentimonas ♠ Choo & Cho 2006 Species "Lentimonas marisflavi" ♠ Choo & Cho 2006 Genus ?"Candidatus Epixenosoma" ♠ Bauer et al. 2005 Species "Candidatus Epixenosoma ejectans" ♠ Bauer et al. 2005 Class Verrucomicrobiae Hedlund et al. 1998 Order Verrucomicrobiales Ward-Rainey et al. 1996 Family Verrucomicrobia subdivision 3 [Pedosphaeraceae] Genus ?"Pedosphaera" ♠ Ozyurt 2008 Species "Pedosphaera parvula" ♠ Ozyurt 2008 Genus Limisphaera 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 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 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 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:
Phylum Verrucomicrobiota Hedlund 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 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 Terrimicrobia García-López et al. 2020 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 Geminisphaera Wertz et al. 2018 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 Genus ?Lentimonas ♠ Choo & Cho 2006 Species "Lentimonas marisflavi" ♠ Choo & Cho 2006 Genus ?"Candidatus Epixenosoma" ♠ Bauer et al. 2005 Species "Candidatus Epixenosoma ejectans" ♠ Bauer et al. 2005 Class Verrucomicrobiae Hedlund et al. 1998 Order Verrucomicrobiales Ward-Rainey et al. 1996 Family Verrucomicrobia subdivision 3 [Pedosphaeraceae] Genus ?"Pedosphaera" ♠ Ozyurt 2008 Species "Pedosphaera parvula" ♠ Ozyurt 2008 Genus Limisphaera 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 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 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 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: