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 from genus Xiphinema, residing in their gametes.[2][3] The verrucomicrobial bacterium Akkermansia muciniphila is a human intestinal symbiotic bacterium that is considered as a promising probiotic.[4]
| Verrucomicrobiota | |
|---|---|
| |
| Transmission electron micrograph of stage II epixenosomes. | |
Scientific classification 
| |
| Domain: | Bacteria |
| Superphylum: | PVC superphylum |
| Phylum: | Verrucomicrobiota Hedlund 2021[1] |
| Classes | |
| Synonyms | |
| |
Verrucomicrobiota are abundant within the environment, though relatively inactive.[5] This phylum is considered to have two sister phyla: Chlamydiota (formerly Chlamydiae) and Lentisphaerota (formerly Lentisphaerae) within the PVC superphylum.[6] The Verrucomicrobiota phylum can be distinguished from neighbouring phyla within the PVC group by the presence of several conserved signature indels (CSIs).[7] These CSIs represent unique, synapomorphic characteristics that suggest common ancestry within Verrucomicrobiota and an independent lineage amidst other bacteria.[8] CSIs have also been found that are shared by Verrucomicrobiota and Chlamydiota exclusively of all other bacteria.[9] 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.[10]
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.[11][12]
Phylogeny
edit| 16S rRNA based LTP_01_2022[13][14][15] | 120 single copy marker proteins based GTDB 08-RS214[16][17][18] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
Taxonomy
editThe currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[19] and National Center for Biotechnology Information (NCBI)[20]
- Genus ?"Ca. Epixenosoma" Bauer et al. 2005
- Genus ?"Ca. Nucleicoccus" corrig. Sato et al. 2014
- Genus ?"Ca. Organicella" Williams et al. 2021
- Genus ?"Ca. Rhizospheria" Nunes da Rocha 2010
- Class Opitutae Choo et al. 2007
- Order Opitutales Choo et al. 2007
- Family "Cerasicoccaceae" Pallen, Rodriguez-R & Alikhan 2022 [KCTC-12870]
- Genus Ruficoccus Lin et al. 2017
- Genus Cerasicoccus Yoon et al. 2007
- Family "Coraliomargaritaceae" Pallen, Rodriguez-R & Alikhan 2022 [DSM-45221]
- Genus "Lentimonas" Choo & Cho 2006
- Genus Coraliomargarita Yoon et al. 2007
- Family "Merdousiaceae" Pallen, Rodriguez-R & Alikhan 2022 [CAG-312]
- Genus "Ca. Merdousia" Gilroy et al. 2021
- Family "Moanibacteraceae" Pallen, Rodriguez-R & Alikhan 2022 [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
- Family Puniceicoccaceae Choo et al. 2007
- Genus "Ca. Fucivorax" Orellana et al. 2022
- Genus "Ca. Marcellius" Nixon et al. 2019
- Genus "Ca. Pelagisphaera" Bar-Shalom et al. 2023
- Genus "Ca. Pinguicoccus" Serra et al. 2020
- Genus Puniceicoccus Choo et al. 2007
- Family "Spyradosomataceae" Pallen, Rodriguez-R & Alikhan 2022 [UBA953]
- Genus "Ca. Spyradosoma" Gilroy et al. 2021
- Family Verruco-01
- Genus Oceanipulchritudo Feng et al. 2020
- Family "Cerasicoccaceae" Pallen, Rodriguez-R & Alikhan 2022 [KCTC-12870]
- Order Opitutales Choo et al. 2007
- Class "Methylacidiphilae"
- Order "Methylacidiphilales" Op den Camp 2009 ["Limisphaerales" Podosokorskaya et al. 2022]
- Family "Methylacidiphilaceae" Op den Camp 2009
- Genus "Methylacidimicrobium" van Teeseling et al. 2014
- Genus "Ca. Methylacidiphilum" Hou et al. 2008
- Genus "Ca. Methylacidithermus" Picone et al. 2021
- Family "Limisphaeraceae" Pallen, Rodriguez-R & Alikhan 2022 [NGM72-4]
- Genus Limisphaera Anders et al. 2015
- Family "Pedosphaeraceae"
- Genus "Pedosphaera" Ozyurt 2008
- Family "Methylacidiphilaceae" Op den Camp 2009
- Order "Methylacidiphilales" Op den Camp 2009 ["Limisphaerales" Podosokorskaya et al. 2022]
- Class Terrimicrobia García-López et al. 2020
- Order Terrimicrobiales García-López et al. 2020 ["Chthoniobacterales" Sangwan et al. 2004]
- 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 "Udaeobacteraceae" Pallen, Rodriguez-R & Alikhan 2022 [UBA10450]
- Genus "Ca. Udaeobacter" Brewer et al. 2016
- Family "Xiphinematobacteraceae"
- Genus "Ca. Xiphinematobacter" Vandekerckhove et al. 2000
- Family "Chthoniobacteraceae" Sangwan et al. 2004
- Order Terrimicrobiales García-López et al. 2020 ["Chthoniobacterales" Sangwan et al. 2004]
- Class Verrucomicrobiae Hedlund et al. 1998
- Order Verrucomicrobiales Ward-Rainey et al. 1996
- Family Akkermansiaceae Hedlund & Derrien 2012
- Genus Akkermansia Derrien et al. 2004
- Genus Haloferula Yoon et al. 2008
- Genus Luteolibacter Yoon et al. 2008
- Genus "Ca. Mariakkermansia" Orellana et al. 2022
- Genus Oceaniferula Jin et al. 2022
- Genus Persicirhabdus Yoon et al. 2008
- Genus Roseibacillus Yoon et al. 2008
- Genus Rubritalea Scheuermayer et al. 2006
- Family SLCJ01
- Genus "Sulfuriroseicoccus" Feng et al. 2022
- Family Verrucomicrobiaceae Ward-Rainey et al. 1996
- Genus "Fucophilus" Sakai et al. 2001b
- Genus Brevifollis Otsuka et al. 2013
- Genus Phragmitibacter Szuróczki et al. 2021
- Genus Prosthecobacter Staley et al. 1976 ex Staley et al. 1980
- Genus Roseimicrobium Otsuka et al. 2013
- Genus Verrucomicrobium Schlesner 1988
- Family Akkermansiaceae Hedlund & Derrien 2012
- Order Verrucomicrobiales Ward-Rainey et al. 1996
See also
editReferences
edit- ^ Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987. S2CID 239887308.
- ^ Coomans A, Vandekerckhove TT, Claeys M (1 January 2000). "Transovarial transmission of symbionts in Xiphinema brevicollum (Nematoda: Longidoridae)". Nematology. 2 (4). Brill: 443–449. doi:10.1163/156854100509303. eISSN 1568-5411. ISSN 1388-5545.
- ^ Vandekerckhove TT, Willems A, Gillis M, Coomans A (2000). "Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, Longidoridae)". International Journal of Systematic and Evolutionary Microbiology. 50 (6). Microbiology Society: 2197–2205. doi:10.1099/00207713-50-6-2197. ISSN 1466-5034. PMID 11155997.
- ^ Zhang, Ting; Li, Qianqian; Cheng, Lei; Buch, Heena; Zhang, Faming (November 2019). "Akkermansia muciniphila is a promising probiotic". Microbial Biotechnology. 12 (6): 1109–1125. doi:10.1111/1751-7915.13410. ISSN 1751-7915. PMC 6801136. PMID 31006995.
- ^ White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya; Zucker, Jeremy D.; Brislawn, Colin J.; Nicora, Carrie D.; Fansler, Sarah J.; Glaesemann, Kurt R.; Glass, Kevin; Jansson, Janet K. (2016-06-28). Langille, Morgan (ed.). "Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes". mSystems. 1 (3): e00045–16. doi:10.1128/mSystems.00045-16. ISSN 2379-5077. PMC 5069762. PMID 27822530.
- ^ 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. Bibcode:2004EnvMi...6..611C. 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 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. S2CID 2094762.
- ^ Wagner, M; Horn, M (2006). "The Planctomycetes, Verrucomicrobia, 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 WB (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. Archived from the original (PDF) on 2016-11-08. Retrieved 2011-06-22.
- ^ "The LTP". Retrieved 23 February 2022.
- ^ "LTP_all tree in newick format". Archived from the original on 4 September 2022. Retrieved 23 February 2022.
- ^ "LTP_01_2022 Release Notes" (PDF). Retrieved 23 February 2022.
- ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
- ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
- ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
- ^ J.P. Euzéby. "Verrucomicrobiota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2022-09-09.
- ^ Sayers; et al. "Verrucomicrobia". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-09-09.