Verrucomicrobiota is a phylum of
Gram-negative bacteria
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...
that contains only a few described species. The species identified have been isolated from
fresh water
Fresh water or freshwater is any naturally occurring liquid or frozen water containing low concentrations of dissolved salts and other total dissolved solids. Although the term specifically excludes seawater and brackish water, it does include ...
, marine and
soil
Soil, also commonly referred to as earth or dirt, is a mixture of organic matter, minerals, gases, liquids, and organisms that together support life. Some scientific definitions distinguish ''dirt'' from ''soil'' by restricting the former te ...
environments and human
faeces
Feces ( or faeces), known colloquially and in slang as poo and poop, are the solid or semi-solid remains of food that was not digested in the small intestine, and has been broken down by bacteria in the large intestine. Feces contain a relati ...
. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive
ectosymbionts of
protist
A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the exc ...
s and
endosymbiont
An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship.
(The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within" ...
s of
nematode
The nematodes ( or grc-gre, Νηματώδη; la, Nematoda) or roundworms constitute the phylum Nematoda (also called Nemathelminthes), with plant-Parasitism, parasitic nematodes also known as eelworms. They are a diverse animal phylum inhab ...
s residing in their
gamete
A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce t ...
s.
Verrucomicrobiota are abundant within the environment, though relatively inactive. This phylum is considered to have two sister phyla:
Chlamydiota (formerly Chlamydiae) and
Lentisphaerota
Lentisphaerota is a phylum of bacteria closely related to Chlamydiota and Verrucomicrobiota.
It includes two monotypic orders Lentisphaerales and Victivallales. Phylum members can be aerobic or anaerobic and fall under two distinct phenotyp ...
(formerly Lentisphaerae) within the
PVC superphylum
The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota. Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wal ...
. The Verrucomicrobiota phylum can be distinguished from neighbouring phyla within the PVC group by the presence of several
conserved signature indels Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers ...
(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
A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, ...
Planctobacteria
The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota. Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wall ...
in the larger clade
Gracilicutes
Gracilicutes (Latin: ''gracilis'', slender, and ''cutis'', skin, referring to the cell wall) is a clade in bacterial phylogeny.
Traditionally gram staining results were most commonly used as a classification tool, consequently until the advent o ...
.
In 2008, the whole
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
of ''
Methylacidiphilum infernorum
''Methylacidiphilum infernorum '' is an extremely acidophilic methanotrophic aerobic bacteria first isolated and described in 2007 growing on soil and sediment on Hell's Gate, New Zealand. Similar organisms have also been isolated from geotherm ...
'' (2.3
Mbp) was published. On the single circular
chromosome
A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
, 2473 predicted proteins were found, 731 of which had no detectable homologs. These analyses also revealed many possible
homologies with
Pseudomonadota
Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria. The renaming of phyla in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. The ...
.
Phylogeny
Taxonomy
The currently accepted taxonomy is based on the
List of Prokaryotic names with Standing in Nomenclature
List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclature ...
(LPSN)
and
National Center for Biotechnology Information
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...
(NCBI)
* Genus ?"''Ca.''
Epixenosoma"
Bauer et al. 2005
* Genus ?"''
Methyloacida''"
Islam et al. 2008
* Genus ?"''
Nucleococcus''"
Sato et al. 2014
* Class
Opitutae
The Opitutales is an order in the phylum Verrucomicrobiota
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 enviro ...
Choo et al. 2007
** Order
Opitutales Choo et al. 2007
*** Family CAG-312
**** Genus "''Ca.''
Merdousia"
Gilroy et al. 2021
*** Family UBA953
**** Genus "''Ca.''
Spyradosoma"
Gilroy et al. 2021
*** Family KCTC-12870
**** Genus ''
Ruficoccus''
Lin et al. 2017
**** Genus ''
Cerasicoccus''
Yoon et al. 2007
*** Family DSM-45221
**** Genus "''
Lentimonas
''Lentimonas'' is a bacterial genus from the family of Puniceicoccaceae with one known species ('' Lentimonas marisflavi'').
See also
* List of bacterial orders
* List of bacteria genera This article lists the genera of the bacteria. The curr ...
''"
Choo & Cho 2006
**** Genus ''
Coraliomargarita''
Yoon et al. 2007
*** Family
Puniceicoccaceae Choo et al. 2007
**** Genus "''Ca.''
Fucivorax"
Orellana et al. 2022
**** Genus "''Ca.''
Marcellius"
Nixon et al. 2019
**** Genus ''
Oceanipulchritudo''
Feng et al. 2020
**** Genus "''Ca.''
Pinguicoccus"
Serra et al. 2020
**** Genus ''
Puniceicoccus''
Choo et al. 2007
*** Family UBA2987
**** Genus "''Ca.''
Moanibacter"
corrig. Vosseberg, Martijn & Ettema 2018
*** Family
Opitutaceae Choo et al. 2007
**** Genus ''
Alterococcus''
Shieh and Jean 1999
**** Genus ''
Cephaloticoccus''
Lin et al. 2016
**** Genus "''Ca.''
Didemniditutus"
corrig. Lopera et al. 2017
**** Genus ''
Ereboglobus''
Tegtmeier et al. 2018
**** Genus "''
Geminisphaera''"
Wertz et al. 2018
**** Genus "''
Lacunisphaera''"
Rast et al. 2017
**** Genus ''
Nibricoccus''
Baek et al. 2019
**** Genus ''
Oleiharenicola''
Rochman et al. 2018
**** Genus ''
Opitutus''
Chin et al. 2001
**** Genus ''
Pelagicoccus''
Yoon et al. 2007
**** Genus ''
Rariglobus''
Pitt et al. 2020
**** Genus "''Ca.''
Synoicihabitans"
Murray et al. 2021
* Class "
Methylacidiphilae"
** Order "
Methylacidiphilales"
Op den Camp 2009
*** Family "
Methylacidiphilaceae"
Op den Camp 2009
**** Genus "''
Methylacidimicrobium''"
van Teeseling et al. 2014
**** Genus "''
Methylacidiphilum''"
Hou et al. 2008
**** Genus "''Ca.''
Methylacidithermus"
Picone et al. 2021
*** Family NGM72-4
**** Genus ''
Limisphaera''
Anders et al. 2015
*** Family "
Pedosphaeraceae"
**** Genus "''
Pedosphaera''"
Ozyurt 2008
* Class
Terrimicrobia García-López et al. 2020
** Order
Terrimicrobiales García-López et al. 2020
*** Family "
Chthoniobacteraceae"
Sangwan et al. 2004
**** Genus "''
Chthoniobacter''"
Sangwan et al. 2004
*** Family
Terrimicrobiaceae García-López et al. 2020
**** Genus ''
Terrimicrobium''
Qiu et al. 2014
*** Family UBA10450
**** Genus "''Ca.''
Udaeobacter"
Brewer et al. 2016
*** Family "
Xiphinematobacteraceae"
**** Genus "''Ca.''
Xiphinematobacter"
Vandekerckhove et al. 2000
* Class
Verrucomicrobiae Hedlund et al. 1998
** Order
Verrucomicrobiales Ward-Rainey et al. 1996
*** Family
Akkermansiaceae Hedlund & Derrien 2012
**** Genus ''
Akkermansia
''Akkermansia'' is a genus in the phylum Verrucomicrobiota (Bacteria). The genus was first proposed by Derrien '' et al.'' (2004), with the type species ''Akkermansia muciniphila'' (gen. nov., sp. nov).
Etymology
The name ''Akkermansia'' der ...
''
Derrien et al. 2004
**** Genus ''
Haloferula''
Yoon et al. 2008
**** Genus ''
Luteolibacter''
Yoon et al. 2008
**** Genus ''
Persicirhabdus''
Yoon et al. 2008
**** Genus ''
Rubritalea''
Scheuermayer et al. 2006
**** Genus ''
Roseibacillus''
Yoon et al. 2008
*** Family
Verrucomicrobiaceae Ward-Rainey et al. 1996
**** Genus "''
Fucophilus''"
Sakai et al. 2001b
**** Genus ''
Brevifollis''
Otsuka et al. 2013
**** Genus ''
Oceaniferula''
Jin et al. 2022
**** Genus ''
Phragmitibacter''
Szuróczki et al. 2021
**** Genus ''
Prosthecobacter
''Prosthecobacter'' is a genus of bacteria from the phylum Verrucomicrobiota with a distinctive characteristic; the presence of tubulin-like genes.
Tubulins, which are components of the microtubule, have never been observed in Gracilicutes bef ...
''
Staley et al. 1976 ex Staley et al. 1980
**** Genus ''
Roseimicrobium''
Otsuka et al. 2013
**** Genus "''
Sulfuriroseicoccus''" Feng et al. 2022
**** Genus ''
Terrimicrobium''
Qiu et al. 2014
**** Genus ''
Verrucomicrobium''
Schlesner 1988
See also
*
List of bacterial orders
This article lists the orders of the Bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI)
and the phylogeny is based on 16S ...
*
List of bacteria genera This article lists the genera of the bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI). However many taxonomic names are ...
References
{{Taxonbar, from=Q18667425
Bacteria phyla