Biology:Gracilibacteria

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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.[3][4]

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 codon[6]

Phylogeny

120 marker proteins based GTDB 10-RS226[7][8][9]
"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

  1. ↑ Li, Lina; Kato, Chiaki; Horikoshi, Koki (1999-05-01). "Bacterial diversity in deep-sea sediments from different depths" (in en). Biodiversity & Conservation 8 (5): 659–677. doi:10.1023/A:1008848203739. ISSN 1572-9710. 
  2. ↑ Ley, Ruth E.; Harris, J. Kirk; Wilcox, Joshua; Spear, John R.; Miller, Scott R.; Bebout, Brad M.; Maresca, Julia A.; Bryant, Donald A. et al. (2006-05-01). "Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat" (in en). Applied and Environmental Microbiology 72 (5): 3685–3695. doi:10.1128/AEM.72.5.3685-3695.2006. ISSN 0099-2240. PMID 16672518. Bibcode: 2006ApEnM..72.3685L. 
  3. ↑ 3.0 3.1 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. PMID 31719174. 
  4. ↑ Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander; Ivanova, Natalia N.; Anderson, Iain J.; Cheng, Jan-Fang; Darling, Aaron; Malfatti, Stephanie et al. (July 2013). "Insights into the phylogeny and coding potential of microbial dark matter" (in en). Nature 499 (7459): 431–437. doi:10.1038/nature12352. ISSN 1476-4687. PMID 23851394. Bibcode: 2013Natur.499..431R. 
  5. ↑ Wrighton, K. C.; Thomas, B. C.; Sharon, I.; Miller, C. S.; Castelle, C. J.; VerBerkmoes, N. C.; Wilkins, M. J.; Hettich, R. L. et al. (2012-09-27). "Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla". Science 337 (6102): 1661–1665. doi:10.1126/science.1224041. ISSN 0036-8075. PMID 23019650. Bibcode: 2012Sci...337.1661W. 
  6. ↑ Hanke, Anna; Hamann, Emmo; Sharma, Ritin; Geelhoed, Jeanine S.; Hargesheimer, Theresa; Kraft, Beate; Meyer, Volker; Lenk, Sabine et al. (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. PMID 24904545. 
  7. ↑ "GTDB release 10-RS226". https://gtdb.ecogenomic.org/about#4%7C. 
  8. ↑ "bac120_r226.sp_label". https://data.gtdb.ecogenomic.org/releases/release226/226.0/auxillary_files/bac120_r226.sp_labels.tree. 
  9. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/. 
  10. ↑ Template:Lpsn3
  11. ↑ Schoch CL. "Desulfacinum". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?command=show&mode=tree&id=35836&lvl=3. Retrieved 2025-06-05. 

Wikidata ☰ Q26967716 entry



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