Saccharibacteria

Saccharibacteria
Ca. Nanosynbacter lyticus (aka TM7x, green) and bacterial hosts (red).
Scale bars are 5 μm.
Scientific classification
(Candidatus)
Domain:
Bacteria
(unranked):
CPR group
Phylum:
Saccharibacteria

Albertsen et al. 2013
Class:
"Saccharimonadia"

corrig. McLean et al. 2020
Order:
"Saccharimonadales"

corrig. McLean et al. 2020
Families
  • "Nanogingivalaceae"
  • "Nanoperiodontomorbaceae"
  • "Nanosynbacteraceae"
  • "Nanosyncoccaceae"
  • "Saccharimonadaceae"
Synonyms
  • Candidate division TM7

Saccharibacteria, formerly known as TM7, is a major bacterial lineage. It was discovered through 16S rRNA sequencing.

A few Saccharibacteria species have been cultured. All of them are obligate parasites of bacterial hosts with small cell and genome sizes. The first species to be isolated, TM7x, is an epibiont of Schaalia odontolytica strain XH001 (formerly known as Actinomyces odontolyticus) with the ability to kill its host. The full genome sequence revealed a highly reduced genome (705kB) and a complete lack of amino acid biosynthetic capacity. An axenic culture of TM7 from the oral cavity was reported in 2014 but no sequence or culture was made available.

Along with Candidate Phylum TM6, it was named after sequences obtained in 1994 in an environmental study of a soil sample of peat bog in Germany where 262 PCR amplified 16S rDNA fragments were cloned into a plasmid vector, named TM clones for Torf, Mittlere Schicht (lit. peat, middle layer). It has been found in several environments since such as from activated sludges, water treatment plant sludge rainforest soil, human saliva, in association with sponges, cockroaches, gold mines, acetate-amended aquifer sediment, and other environments (bar thermophilic), making it an abundant and widespread phylum.

Properties

TM7 specific FISH probes identified species from a bioreactor sludge revealed the presence of a gram-positive cell envelopes and several morphotypes: a sheathed filament (abundant), a rod occurring in short chains, a thick filament and cocci; the former may be the cause of Eikelboom type 0041 (bulking problems of activated sludges). The majority of bacterial phyla are Gram-negative diderms, whereas only the Bacillota, the Actinomycetota and Chloroflexota are monoderms.

Saccharibacteria are part of the human oral microbiota, but their role in human health is unclear.

A characteristic feature of known Saccharibacteria is the inability to synthesize some amino acids, vitamins, and other important molecules. They are thus believed to be parasites or symbionts that obtain nutrients from a bacterial host. A small number of species have been successfully cultured by placing them into cultures of host bacteria.

Over 50 different phylotypes have been identified and it has a relatively modest intradivision 16S rDNA sequence divergence of 17%, which ranges from 13 to 33%.[needs update] An interactive phylogenetic tree of TM7, built using jsPhyloSVG, allows for quick access to GenBank sequences and distance matrix calculations between tree branches.

Stable-isotope probing studies have found that some members of this phylum can degrade toluene.

Taxonomy

120 marker proteins based GTDB 10-RS226
Saccharimonadales
Rappe & Giovannoni 2003
Patescibacteria
Parcubacteria group

ABY1 (OD1-ABY1)

Gracilibacteria (BD1-5 group)

(OD1)

Microgenomates (OP11 group)

Dojkabacteria (WS6)

Saccharibacteria (TM7)

(CPR)
Dinis et al. 2011
Saccharibacteria

Saccharibacteria I

Saccharibacteria II

Saccharibacteria IV

TM7a group

Saccharibacteria III

TM7 Candidate Division neighbor-joining phylogenetic tree

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

References

  1. 1 2 Schoch CL; et al. "Saccharimonadota". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2025-06-05.
  2. ↑ Pace, N. R. (2009). "Mapping the Tree of Life: Progress and Prospects". Microbiology and Molecular Biology Reviews. 73 (4): 565–576. doi:10.1128/MMBR.00033-09. PMC 2786576. PMID 19946133.
  3. 1 2 He, Wenxin; Liang, Hewei; Li, Wenxi; Gao, Xiaowei; Hu, Tongyuan; Lin, Xiaoqian; Wu, Zhinan; Sun, Jingxi; Li, Xiaofang; Wang, Mengmeng; Hou, Xiaoxue; Jie, Zhuye; Tong, Xin; Jin, Xin; Xiao, Liang (2024-12-19). "Revealing an unprecedented diversity of episymbiotic Saccharibacteria in a high-quality genome collection". npj Biofilms and Microbiomes. 10 (1): 153. doi:10.1038/s41522-024-00617-2. ISSN 2055-5008. PMC 11659515. PMID 39702451.
  4. ↑ He, Xuesong; McLean, Jeffrey S.; Edlund, Anna; Yooseph, Shibu; Hall, Adam P.; Liu, Su-Yang; Dorrestein, Pieter C.; Esquenazi, Eduardo; Hunter, Ryan C. (2015-01-06). "Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle". Proceedings of the National Academy of Sciences. 112 (1): 244–249. Bibcode:2015PNAS..112..244H. doi:10.1073/pnas.1419038112. ISSN 0027-8424. PMC 4291631. PMID 25535390.
  5. ↑ "Candidatus Saccharibacteria oral taxon TM7x (ID 241438) - BioProject - NCBI".
  6. 1 2 Soro, V. (2014). "Axenic Culture of a Candidate Division TM7 Bacterium from the Human Oral Cavity and Biofilm Interactions with Other Oral Bacteria". Applied and Environmental Microbiology. 80 (20): 6480–6489. Bibcode:2014ApEnM..80.6480S. doi:10.1128/AEM.01827-14. PMC 4178647. PMID 25107981.
  7. ↑ McLean, Jeffrey S.; Lombardo, Mary-Jane; Badger, Jonathan H.; Edlund, Anna; Novotny, Mark; Yee-Greenbaum, Joyclyn; Vyahhi, Nikolay; Hall, Adam P.; Yang, Youngik (2013-06-25). "Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum". Proceedings of the National Academy of Sciences. 110 (26): E2390–E2399. Bibcode:2013PNAS..110E2390M. doi:10.1073/pnas.1219809110. ISSN 0027-8424. PMC 3696752. PMID 23754396.
  8. ↑ Rheims, H.; Rainey, F. A.; Stackebrandt, E. (1996). "A molecular approach to search for diversity among bacteria in the environment". Journal of Industrial Microbiology & Biotechnology. 17 (3–4): 159–169. doi:10.1007/BF01574689. S2CID 31868442.
  9. ↑ Bond, PL; Hugenholtz, P; Keller, J; Blackall, LL (1995). "Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors". Applied and Environmental Microbiology. 61 (5): 1910–6. Bibcode:1995ApEnM..61.1910B. doi:10.1128/AEM.61.5.1910-1916.1995. PMC 167453. PMID 7544094.
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  13. ↑ Lazarevic, V.; Whiteson, K.; Hernandez, D.; Francois, P.; Schrenzel, J. (2010). "Study of inter- and intra-individual variations in the salivary microbiota". BMC Genomics. 11 (1): 523. Bibcode:2010BMCG...11..523L. doi:10.1186/1471-2164-11-523. PMC 2997015. PMID 20920195.
  14. ↑ Dewhirst, F. E.; Chen, T.; Izard, J.; Paster, B. J.; Tanner, A. C. R.; Yu, W. -H.; Lakshmanan, A.; Wade, W. G. (2010). "The Human Oral Microbiome". Journal of Bacteriology. 192 (19): 5002–5017. doi:10.1128/JB.00542-10. PMC 2944498. PMID 20656903.
  15. ↑ Thiel, V.; Leininger, S.; Schmaljohann, R.; Brümmer, F.; Imhoff, J. F. (2007). "Sponge-specific Bacterial Associations of the Mediterranean Sponge Chondrilla nucula (Demospongiae, Tetractinomorpha)". Microbial Ecology. 54 (1): 101–111. Bibcode:2007MicEc..54..101T. doi:10.1007/s00248-006-9177-y. PMID 17364249. S2CID 34564973.
  16. ↑ Berlanga, M; Paster, BJ; Guerrero, R (2009). "The taxophysiological paradox: changes in the intestinal microbiota of the xylophagous cockroach Cryptocercus punctulatus depending on the physiological state of the host". International Microbiology. 12 (4): 227–36. PMID 20112227.
  17. ↑ Rastogi, G.; Stetler, L. D.; Peyton, B. M.; Sani, R. K. (2009). "Molecular analysis of prokaryotic diversity in the deep subsurface of the former Homestake gold mine, South Dakota, USA". The Journal of Microbiology. 47 (4): 371–384. doi:10.1007/s12275-008-0249-1. PMID 19763410. S2CID 7972151.
  18. ↑ Kantor, Rose S.; Wrighton, Kelly C.; Handley, Kim M.; Sharon, Itai; Hug, Laura A.; Castelle, Cindy J.; Thomas, Brian C.; Banfield, Jillian F. (2013-01-01). "Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla". mBio. 4 (5): e00708–00713. doi:10.1128/mBio.00708-13. ISSN 2150-7511. PMC 3812714. PMID 24149512.
  19. 1 2 3 Rappe, M. S.; Giovannoni, S. J. (2003). "The Uncultured Microbial Majority". Annual Review of Microbiology. 57: 369–394. doi:10.1146/annurev.micro.57.030502.090759. PMID 14527284.
  20. 1 2 Bor, B.; Collins, A.J.; Murugkar, P.P.; Balasubramanian, S.; To, T.T.; Hendrickson, E.L.; Bedree, J.K.; Bidlack, F.B.; Johnston, C.D.; Shi, W.; McLean, J.S.; He, X.; Dewhirst, F.E. (2020). "Insights Obtained by Culturing Saccharibacteria with Their Bacterial Hosts". Journal of Dental Research. 99 (6): 685–694. doi:10.1177/0022034520905792. PMC 7243422. PMID 32075512.
  21. ↑ McLean, Jeffrey S.; Bor, Batbileg; Kerns, Kristopher A.; Liu, Quanhui; To, Thao T.; Solden, Lindsey; Hendrickson, Erik L.; Wrighton, Kelly; Shi, Wenyuan; He, Xuesong (2020-07-21). "Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts". Cell Reports. 32 (3) 107939. doi:10.1016/j.celrep.2020.107939. ISSN 2211-1247. PMC 7427843. PMID 32698001.
  22. 1 2 3 Dinis, J. M.; Barton, D. E.; Ghadiri, J.; Surendar, D.; Reddy, K.; Velasquez, F.; Chaffee, C. L.; Lee, M. C. W.; Gavrilova, H.; Ozuna, H.; Smits, S. A.; Ouverney, C. C. (2011). Yang, Ching-Hong (ed.). "In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment". PLOS ONE. 6 (6) e21280. Bibcode:2011PLoSO...621280D. doi:10.1371/journal.pone.0021280. PMC 3118805. PMID 21701585.
  23. ↑ Smits, S. A.; Ouverney, C. C. (2010). Poon, Art F. Y. (ed.). "JsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web". PLOS ONE. 5 (8) e12267. Bibcode:2010PLoSO...512267S. doi:10.1371/journal.pone.0012267. PMC 2923619. PMID 20805892.
  24. ↑ Xie, S.; Sun, W.; Luo, C.; Cupples, A. M. (2010). "Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing". Biodegradation. 22 (1): 71–81. doi:10.1007/s10532-010-9377-5. PMID 20549308. S2CID 9840162.
  25. ↑ Luo, C.; Xie, S.; Sun, W.; Li, X.; Cupples, A. M. (2009). "Identification of a Novel Toluene-Degrading Bacterium from the Candidate Phylum TM7, as Determined by DNA Stable Isotope Probing". Applied and Environmental Microbiology. 75 (13): 4644–4647. Bibcode:2009ApEnM..75.4644L. doi:10.1128/AEM.00283-09. PMC 2704817. PMID 19447956.
  26. ↑ "GTDB release 10-RS226". Genome Taxonomy Database. Retrieved 1 May 2025.
  27. ↑ "bac120_r226.sp_label". Genome Taxonomy Database. Retrieved 1 May 2025.
  28. ↑ "Taxon History". Genome Taxonomy Database. Retrieved 1 May 2025.
  29. 1 2 C. L. Schoch, Sayers et al.: Parcubacteria group, Parcubacteria group (clade/superphylum, syn. candidate division OD1); National Center for Biotechnology Information (NCBI)
  30. ↑ Damien M. de Vienne: Parcubacteria group, NCBI Lifemap, University of Lyon. Lifemap is an interactive tool to explore NCBI taxonomy.
  31. ↑ Dojka, M. A.; Hugenholtz, P.; Haack, S. K.; Pace, N. R. (October 1998). "Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation". Applied and Environmental Microbiology. 64 (10): 3869–3877. Bibcode:1998ApEnM..64.3869D. doi:10.1128/AEM.64.10.3869-3877.1998. ISSN 0099-2240. PMC 106571. PMID 9758812.
  32. ↑ C. L. Schoch, Sayers et al.: candidate division WS5, candidate division WS5 (clade, syn. candidate division Wurtsmith 5); National Center for Biotechnology Information (NCBI)
  33. ↑ Damien M. de Vienne: environmental samples - candidate division WS5, NCBI Lifemap, University of Lyon. Lifemap is an interactive tool to explore NCBI taxonomy.
  34. ↑ Bäckhed, Fredrik; Ley, Ruth E.; Sonnenburg, Justin L.; Peterson, Daniel A.; Gordon, Jeffrey I. (2005-03-25). "Host-Bacterial Mutualism in the Human Intestine". Science. 307 (5717): 1915–1920. Bibcode:2005Sci...307.1915B. doi:10.1126/science.1104816. ISSN 0036-8075. PMID 15790844.
  35. ↑ Saccharimonadia in LPSN; Freese, H. M.; Meier-Kolthoff, J. P.; Sardà Carbasse, J.; Afolayan, A. O.; Göker, M. (2026). "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. 54 (D1): D884–D891. doi:10.1093/nar/gkaf1110.