Gracilibacteria

Gracilibacteria
Scientific classification
Domain:	Bacteria
(unranked):	CPR group
Phylum:	"Gracilibacteria"; Rinke et al. 2013
Genus:	"Ca. Altimarinus"
Type species
	"Ca. A. pacificus"; Rinke et al. 2013

Gracilibacteria is a bacterial candidate phylum formerly known as GN02, BD1-5, or SN-2. It is part of the Candidate Phyla Radiation and the Patescibacteria group.

The first representative of the Gracilibacteria phylum was reported in 1999 after being recovered from a deep-sea sediment sample. The representative 16S rRNA sequence was referred to as "BD1-5" (sample BD1, sequence 5) and while it was noted that it displayed low sequence identity to any known 16S rRNA gene, it was not proposed as a new phylum at this time.¹ In 2006, representatives of Gracilibacteria were recovered from a hypersaline microbial mat from Guerrero Negro, Baja California Sur, Mexico and proposed as a new phylum "GN02".² The name "Gracilibacteria" was proposed for the BD1-5/GN02 lineage in 2013, based on a substantial expansion of the genomic representation of this phylum.³⁴

The first Gracilibacteria genome was recovered from an acetate-amended aquifer (Rifle, CO, USA) using culture-independent, genome-resolved metagenomic techniques in 2012.⁵ Genomic analyses suggest that members of the Gracilibacteria phylum have limited metabolisms and are likely symbionts or endosymbionts.³ Members of Gracilibacteria use an alternative genetic code in which UGA encodes the glycine amino acid instead of a stop codon⁶

Phylogeny

120 marker proteins based GTDB 10-RS226⁷⁸⁹

"Gracilibacteria" cluster

"Vampirococcia"

	"Ca. Altimarinus" {BD1-5: UBA6164}

	"Absconditicoccaceae" {"Absconditabacterales"}

"Gracilibacteria"

"Abawacabacteriales" (RBG-16-42-10)

"Peregrinibacterales" (UBA1369)

	"Fallacibacteriales" (UBA4473)

	"Peribacteraceae" {"Peribacterales"}

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)¹⁰ and National Center for Biotechnology Information (NCBI).¹¹

Clade "Gracilibacteria" cluster

Class "Vampirococcia" Pallen, Rodriguez-R & Alikhan 2022 (SR1; JAEDAM01)
- Order "Absconditibacterales" Yakimov et al. 2022 corrig. Kostovski, Oren & Göker 2025
  - Family "Absconditicoccaceae" Yakimov et al. 2022
    - ?Genus "Candidatus Strigamonas" Bouderka et al. 2024
      - Species "Ca. S. methylophilicida" Bouderka et al. 2024
    - Genus "Candidatus Absconditicoccus" Yakimov et al. 2022
      - Species "Ca. A. praedator" Yakimov et al. 2022
    - Genus "Candidatus Vampirococcus" Guerrero et al. 1986 non Kizina 2017
      - Species "Ca. V. lugosii" Moreira et al. 2021
- Order BD1-5
  - Family UBA6164
    - Genus "Candidatus' Altimarinus" Rinke et al. 2013
      - Species "Ca.' A. pacificus" Rinke et al. 2013
Class "Gracilibacteriia" Yakimov et al. 2022
- Order "Peribacterales" Anantharaman et al. 2016
  - Family "Peribacteraceae" Anantharaman et al. 2016
    - Genus "Candidatus Peribacter" Anantharaman et al. 2016
      - Species "Ca. P. riflensis" Anantharaman et al. 2016

References

Li, Lina; Kato, Chiaki; Horikoshi, Koki (1999-05-01). "Bacterial diversity in deep-sea sediments from different depths". Biodiversity & Conservation. 8 (5): 659–677. doi:10.1023/A:1008848203739. ISSN 1572-9710. S2CID 25820840.
Ley, Ruth E.; Harris, J. Kirk; Wilcox, Joshua; Spear, John R.; Miller, Scott R.; Bebout, Brad M.; Maresca, Julia A.; Bryant, Donald A.; Sogin, Mitchell L.; Pace, Norman R. (2006-05-01). "Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat". Applied and Environmental Microbiology. 72 (5): 3685–3695. Bibcode:2006ApEnM..72.3685L. doi:10.1128/AEM.72.5.3685-3695.2006. ISSN 0099-2240. PMC 1472358. PMID 16672518.
Sieber, Christian M. K.; Paul, Blair G.; Castelle, Cindy J.; Hu, Ping; Tringe, Susannah G.; Valentine, David L.; Andersen, Gary L.; Banfield, Jillian F. (2019-11-12). "Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community". mBio. 10 (6). doi:10.1128/mbio.02128-19. ISSN 2150-7511. PMC 6851277. PMID 31719174.
Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander; Ivanova, Natalia N.; Anderson, Iain J.; Cheng, Jan-Fang; Darling, Aaron; Malfatti, Stephanie; Swan, Brandon K.; Gies, Esther A.; Dodsworth, Jeremy A. (July 2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499 (7459): 431–437. Bibcode:2013Natur.499..431R. doi:10.1038/nature12352. hdl:10453/27467. ISSN 1476-4687. PMID 23851394.
Wrighton, K. C.; Thomas, B. C.; Sharon, I.; Miller, C. S.; Castelle, C. J.; VerBerkmoes, N. C.; Wilkins, M. J.; Hettich, R. L.; Lipton, M. S.; Williams, K. H.; Long, P. E. (2012-09-27). "Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla". Science. 337 (6102): 1661–1665. Bibcode:2012Sci...337.1661W. doi:10.1126/science.1224041. ISSN 0036-8075. PMID 23019650. S2CID 10362580.
Hanke, Anna; Hamann, Emmo; Sharma, Ritin; Geelhoed, Jeanine S.; Hargesheimer, Theresa; Kraft, Beate; Meyer, Volker; Lenk, Sabine; Osmers, Harald; Wu, Rong; Makinwa, Kofi (2014-05-16). "Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat". Frontiers in Microbiology. 5: 231. doi:10.3389/fmicb.2014.00231. ISSN 1664-302X. PMC 4032931. PMID 24904545.
"GTDB release 10-RS226". Genome Taxonomy Database. Retrieved 1 May 2025.
"bac120_r226.sp_label". Genome Taxonomy Database. Retrieved 1 May 2025.
"Taxon History". Genome Taxonomy Database. Retrieved 1 May 2025.
Desulfacinum in LPSN; Freese, H. M.; Meier-Kolthoff, J. P.; Sardà Carbasse, J.; Afolayan, A. O.; Göker, M. (29 October 2025). "TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity". Nucleic Acids Research. 53: D1–D12. doi:10.1093/nar/gkaf1110.
Schoch CL; et al. "Desulfacinum". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2025-06-05.

[1] Li, Lina; Kato, Chiaki; Horikoshi, Koki (1999-05-01). "Bacterial diversity in deep-sea sediments from different depths". Biodiversity & Conservation. 8 (5): 659–677. doi:10.1023/A:1008848203739. ISSN 1572-9710. S2CID 25820840.

[2] Ley, Ruth E.; Harris, J. Kirk; Wilcox, Joshua; Spear, John R.; Miller, Scott R.; Bebout, Brad M.; Maresca, Julia A.; Bryant, Donald A.; Sogin, Mitchell L.; Pace, Norman R. (2006-05-01). "Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat". Applied and Environmental Microbiology. 72 (5): 3685–3695. Bibcode:2006ApEnM..72.3685L. doi:10.1128/AEM.72.5.3685-3695.2006. ISSN 0099-2240. PMC 1472358. PMID 16672518.

[:0-3] Sieber, Christian M. K.; Paul, Blair G.; Castelle, Cindy J.; Hu, Ping; Tringe, Susannah G.; Valentine, David L.; Andersen, Gary L.; Banfield, Jillian F. (2019-11-12). "Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community". mBio. 10 (6). doi:10.1128/mbio.02128-19. ISSN 2150-7511. PMC 6851277. PMID 31719174.

[4] Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander; Ivanova, Natalia N.; Anderson, Iain J.; Cheng, Jan-Fang; Darling, Aaron; Malfatti, Stephanie; Swan, Brandon K.; Gies, Esther A.; Dodsworth, Jeremy A. (July 2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499 (7459): 431–437. Bibcode:2013Natur.499..431R. doi:10.1038/nature12352. hdl:10453/27467. ISSN 1476-4687. PMID 23851394.

[5] Wrighton, K. C.; Thomas, B. C.; Sharon, I.; Miller, C. S.; Castelle, C. J.; VerBerkmoes, N. C.; Wilkins, M. J.; Hettich, R. L.; Lipton, M. S.; Williams, K. H.; Long, P. E. (2012-09-27). "Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla". Science. 337 (6102): 1661–1665. Bibcode:2012Sci...337.1661W. doi:10.1126/science.1224041. ISSN 0036-8075. PMID 23019650. S2CID 10362580.

[6] Hanke, Anna; Hamann, Emmo; Sharma, Ritin; Geelhoed, Jeanine S.; Hargesheimer, Theresa; Kraft, Beate; Meyer, Volker; Lenk, Sabine; Osmers, Harald; Wu, Rong; Makinwa, Kofi (2014-05-16). "Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat". Frontiers in Microbiology. 5: 231. doi:10.3389/fmicb.2014.00231. ISSN 1664-302X. PMC 4032931. PMID 24904545.

[about-7] "GTDB release 10-RS226". Genome Taxonomy Database. Retrieved 1 May 2025.

[tree_bac-8] "bac120_r226.sp_label". Genome Taxonomy Database. Retrieved 1 May 2025.

[taxon_history-9] "Taxon History". Genome Taxonomy Database. Retrieved 1 May 2025.

[LPSN-10] Desulfacinum in LPSN; Freese, H. M.; Meier-Kolthoff, J. P.; Sardà Carbasse, J.; Afolayan, A. O.; Göker, M. (29 October 2025). "TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity". Nucleic Acids Research. 53: D1–D12. doi:10.1093/nar/gkaf1110.

[NCBI-11] Schoch CL; et al. "Desulfacinum". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2025-06-05.

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