Saccharibacteria

Saccharibacteria, formerly known as TM7,[1] is a major bacterial lineage. It was discovered through 16S rRNA sequencing . [2]

Saccharibacteria
Scientific classification
Domain: Bacteria
Infrakingdom: Candidate phyla radiation
Phylum: Saccharibacteria
Synonyms
  • Ca. Saccharibacteria
  • Candidate division TM7


TM7x from the human oral cavity was cultivated and revealed that TM7x is an extremely small coccus (200-300 nm) and has a distinctive lifestyle not previously observed in human-associated microbes.[3] It is an obligate epibiont of various hosts, including Actinomyces odontolyticus strain (XH001) yet also has a parasitic phase thereby killing its host. The full genome sequence revealed a highly reduced genome (705kB) [4] 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.[5]

Along with Candidate Phylum TM6,[6] 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).[7] It has been found in several environments since such as from activated sludges,[8][9] water treatment plant sludge[10] rainforest soil,[11] human saliva,[12][13] in association with sponges,[14] cockroaches,[15] gold mines,[16] acetate-amended aquifer sediment,[17] and other environments (bar thermophilic), making it an abundant and widespread phylum. Recently, TM7 rDNA and whole-cells were detected in activated sludge with >99.7% identity to a human skin TM7 and 98.6% identity to the human oral TM7a,[18] suggesting metabolically active TM7 isolates in environmental sites may serve as model organisms to investigate the role TM7 species play in human health.

Properties
 

Chloroflexi

 
 
 
 
 

ABY1
(OD1-ABY1 of Parcubacteria)

 
 

BD1-5 group (Gracilibacteria)

 
 
 
 

OP11 group (Microgenomates)

 
 

WS6
(Dojkabacteria)

 
 
 
 
 

TM7
(Saccharibacteria)

 
 
 

SC3

 
 
 

WS5

 
 

Guaymas1 (Thermodesulfobacteria-related)[19]

 
 
 
 
 
Relationship of phylum TM7 and its closest relatives, including the Chloroflexi as an outgroup[20] Clear names have been added, see list of bacterial phyla.

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).[10] The majority of bacterial phyla are Gram-negative diderms, whereas only the Firmicutes, the Actinobacteria and Chloroflexi are monoderms.[20]

Using a polycarbonate membrane as a growth support and soil extract as the substrate, microcolonies of this clade were grown consisting of long filamentous rods up to 15 μm long with less than 50 cells or short rods with several hundred cells per colony, after 10 days incubation.[21]

Thanks to a microfluidic chip allowing the isolation and amplification of the genome of a single cell, the genome of 3 long filament morphology cells with identical 16S rRNA were sequenced to create a draft sequence of the genome confirming some previously ascertained properties, elucidating some of its metabolic capabilities, revealing novel genes and hinting to potential pathogenic abilities.[22]

Over 50 different phylotypes have been identified[20] and it has a relatively modest intradivision 16S rDNA sequence divergence of 17%, which ranges from 13 to 33%.[10] An interactive phylogenetic tree of TM7,[18] built using jsPhyloSVG,[23] 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.[24][25]

Subgroups
TM7 Candidate Division neighbor-joining phylogenetic tree[18]

Named subgroups are according to Dinis et ql. (2011) as follows:[18]

  • Saccharibacteria I
  • Saccharibacteria II
  • TM7a
  • Saccharibacteria III
  • Sachharibacteria IV
Saccharibacteria
 

Saccharibacteria I

 
 
 

Saccharibacteria II

 
 
 
 

TM7a group

 
 

Saccharibacteria III

 
 
 

Saccharibacteria IV

 
 
 
 
Simplified phylogenetic tree of named subgroups.[18]

References
  1. "Candidatus Saccharibacteria". NCBI Taxonomy Browser. NCBI. Retrieved 18 September 2015.
  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. 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.
  4. "Candidatus Saccharibacteria oral taxon TM7x (ID 241438) - BioProject - NCBI".
  5. 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. doi:10.1128/AEM.01827-14. PMC 4178647. PMID 25107981.
  6. 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.
  7. 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.
  8. 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. doi:10.1128/AEM.61.5.1910-1916.1995. PMC 167453. PMID 7544094.
  9. Godon, JJ; Zumstein, E; Dabert, P; Habouzit, F; Moletta, R (1997). "Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis". Applied and Environmental Microbiology. 63 (7): 2802–13. doi:10.1128/AEM.63.7.2802-2813.1997. PMC 168577. PMID 9212428.
  10. Hugenholtz, P.; Tyson, G. W.; Webb, R. I.; Wagner, A. M.; Blackall, L. L. (2001). "Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives". Applied and Environmental Microbiology. 67 (1): 411–419. doi:10.1128/AEM.67.1.411-419.2001. PMC 92593. PMID 11133473.
  11. Borneman, J; Triplett, EW (1997). "Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation". Applied and Environmental Microbiology. 63 (7): 2647–53. doi:10.1128/AEM.63.7.2647-2653.1997. PMC 168563. PMID 9212415.
  12. 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: 523. doi:10.1186/1471-2164-11-523. PMC 2997015. PMID 20920195.
  13. 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.
  14. 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. doi:10.1007/s00248-006-9177-y. PMID 17364249. S2CID 34564973.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. Fredrik Bäckhed, Ruth Ley, Justin L Sonnenburg, Daniel A. Peterson: Host‐Bacterial Mutualism in the Human Intestine. In: Science 307(5717): 1915-1920. April 2005. doi:10.1126/science.1104816. PMID 15790844
  20. 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.
  21. Ferrari, B. C.; Binnerup, S. J.; Gillings, M. (2005). "Microcolony Cultivation on a Soil Substrate Membrane System Selects for Previously Uncultured Soil Bacteria". Applied and Environmental Microbiology. 71 (12): 8714–8720. doi:10.1128/AEM.71.12.8714-8720.2005. PMC 1317317. PMID 16332866.
  22. Marcy, Y.; Ouverney, C.; Bik, E. M.; Losekann, T.; Ivanova, N.; Martin, H. G.; Szeto, E.; Platt, D.; Hugenholtz, P.; Relman, D. A.; Quake, S. R. (2007). "Inaugural Article: Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth". Proceedings of the National Academy of Sciences. 104 (29): 11889–11894. Bibcode:2007PNAS..10411889M. doi:10.1073/pnas.0704662104. PMC 1924555. PMID 17620602.
  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. doi:10.1128/AEM.00283-09. PMC 2704817. PMID 19447956.
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