Saccharibacteria Explained

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

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 German: 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

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 Bacillota, the Actinomycetota and Chloroflexota are monoderms.

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.[19]

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.[20]

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%.[10] An interactive phylogenetic tree of TM7,[18] built using jsPhyloSVG,[21] 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.[22] [23]

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[24] and National Center for Biotechnology Information (NCBI)[1]

See also

References

  1. Web site: Sayers. etal. Saccharibacteria . 2021-03-20 . National Center for Biotechnology Information (NCBI) taxonomy database.
  2. 10.1128/MMBR.00033-09 . Pace . N. R. . Mapping the Tree of Life: Progress and Prospects . Microbiology and Molecular Biology Reviews . 73 . 4 . 565–576 . 2009 . 19946133 . 2786576.
  3. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proceedings of the National Academy of Sciences. 2015-01-06. 0027-8424. 4291631. 25535390. 244–249. 112. 1. 10.1073/pnas.1419038112. Xuesong. He. Jeffrey S.. McLean. Anna. Edlund. Shibu. Yooseph. Adam P.. Hall. Su-Yang. Liu. Pieter C.. Dorrestein. Eduardo. Esquenazi. Ryan C.. Hunter. 2015PNAS..112..244H. free.
  4. Web site: Candidatus Saccharibacteria oral taxon TM7x (ID 241438) - BioProject - NCBI.
  5. Soro. V.. Axenic Culture of a Candidate Division TM7 Bacterium from the Human Oral Cavity and Biofilm Interactions with Other Oral Bacteria. Applied and Environmental Microbiology. 2014. 80. 20. 6480–6489. 10.1128/AEM.01827-14. 25107981. 4178647. 2014ApEnM..80.6480S.
  6. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proceedings of the National Academy of Sciences. 2013-06-25. 0027-8424. 3696752. 23754396. E2390–E2399. 110. 26. 10.1073/pnas.1219809110. Jeffrey S.. McLean. Mary-Jane. Lombardo. Jonathan H.. Badger. Anna. Edlund. Mark. Novotny. Joyclyn. Yee-Greenbaum. Nikolay. Vyahhi. Adam P.. Hall. Youngik. Yang. 2013PNAS..110E2390M. free.
  7. 10.1007/BF01574689. Rheims . H. . Rainey . F. A. . Stackebrandt . E. . A molecular approach to search for diversity among bacteria in the environment . Journal of Industrial Microbiology & Biotechnology . 17 . 3–4 . 159–169 . 1996. 31868442 . free .
  8. Bond. PL. Hugenholtz. P. Keller. J. Blackall. LL. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Applied and Environmental Microbiology. 61. 5. 1910–6. 1995. 10.1128/AEM.61.5.1910-1916.1995. 7544094. 167453. 1995ApEnM..61.1910B.
  9. Godon. JJ. Zumstein. E. Dabert. P. Habouzit. F. Moletta. R. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Applied and Environmental Microbiology. 63. 7. 2802–13. 1997. 10.1128/AEM.63.7.2802-2813.1997. 9212428. 168577. 1997ApEnM..63.2802G.
  10. Hugenholtz . P.. Tyson . G. W.. Webb . R. I.. Wagner . A. M.. Blackall . L. L.. 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. 2001. 11133473. 92593. 10.1128/AEM.67.1.411-419.2001. 2001ApEnM..67..411H.
  11. Borneman. J. Triplett. EW. 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. 1997. 10.1128/AEM.63.7.2647-2653.1997. 9212415. 168563. 1997ApEnM..63.2647B.
  12. Lazarevic . V.. Whiteson . K.. Hernandez . D.. Francois . P.. Schrenzel . J.. Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics. 11. 523. 2010. 20920195. 2997015. 10.1186/1471-2164-11-523. free.
  13. Dewhirst . F. E.. Chen . T.. Izard . J.. Paster . B. J.. Tanner . A. C. R.. Yu . W. -H.. Lakshmanan . A.. Wade . W. G.. The Human Oral Microbiome. Journal of Bacteriology. 192. 19. 5002–5017. 2010. 20656903. 2944498. 10.1128/JB.00542-10.
  14. Thiel . V. . Leininger . S. . Schmaljohann . R. . Brümmer . F. . Imhoff . J. F. . Sponge-specific Bacterial Associations of the Mediterranean Sponge Chondrilla nucula (Demospongiae, Tetractinomorpha) . 10.1007/s00248-006-9177-y . Microbial Ecology . 54 . 1 . 101–111 . 2007 . 17364249 . 34564973 .
  15. Berlanga. M. Paster. BJ. Guerrero. R. 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. 2009. 20112227.
  16. Rastogi . G.. Stetler . L. D.. Peyton . B. M.. Sani . R. K.. 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. 2009. 19763410. 10.1007/s12275-008-0249-1. 7972151.
  17. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. mBio . 2013-01-01. 2150-7511. 3812714. 24149512. e00708–00713. 4. 5. 10.1128/mBio.00708-13. Rose S.. Kantor. Kelly C.. Wrighton. Kim M.. Handley. Itai. Sharon. Laura A.. Hug. Cindy J.. Castelle. Brian C.. Thomas. Jillian F.. Banfield.
  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. . Yang . Ching-Hong . In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment . 10.1371/journal.pone.0021280 . PLOS ONE . 6 . 6 . e21280 . 2011 . 21701585 . 3118805 . 2011PLoSO...621280D . free.
  19. Ferrari . B. C.. Binnerup . S. J.. Gillings . M.. Microcolony Cultivation on a Soil Substrate Membrane System Selects for Previously Uncultured Soil Bacteria. Applied and Environmental Microbiology. 71. 12. 8714–8720. 2005. 16332866. 1317317. 10.1128/AEM.71.12.8714-8720.2005. 2005ApEnM..71.8714F.
  20. 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.. 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. 2007. 10.1073/pnas.0704662104. 2007PNAS..10411889M . 17620602 . 1924555. free.
  21. Smits . S. A. . Ouverney . C. C. . Poon . Art F. Y. . 10.1371/journal.pone.0012267 . JsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web . PLOS ONE . 5 . 8 . e12267 . 2010 . 20805892 . 2923619 . 2010PLoSO...512267S . free .
  22. Xie . S.. Sun . W.. Luo . C.. Cupples . A. M.. Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing. Biodegradation. 22. 1. 71–81. 2010. 20549308. 10.1007/s10532-010-9377-5. 9840162.
  23. Luo . C.. Xie . S.. Sun . W.. Li . X.. Cupples . A. M.. 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. 2009. 19447956. 2704817. 10.1128/AEM.00283-09. 2009ApEnM..75.4644L.
  24. Web site: J.P. Euzéby . Saccharibacteria . List of Prokaryotic names with Standing in Nomenclature (LPSN). 2021-06-27.

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External links

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