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Saccharibacteria

(Redirected from Candidatus Saccharibacteria)

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

Saccharibacteria
Ca. Nanosynbacter lyticus (aka TM7x, green) and bacterial hosts (red).
Scale bars are 5 μm.
Scientific classification
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

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

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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.[19]

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.[20]

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.[21]

Over 50 different phylotypes have been identified[19] 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,[22] 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.[23][24]

Taxonomy

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120 marker proteins based GTDB 08-RS214[25][26][27]
Saccharimonadales
Rappe & Giovannoni 2003[19]
Patescibacteria

Saccharibacteria (TM7)

(CPR)
Dinis et al. 2011[18]
Saccharibacteria

Saccharibacteria I

Saccharibacteria II

Saccharibacteria IV

TM7a group

Saccharibacteria III

 
TM7 Candidate Division neighbor-joining phylogenetic tree[18]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[34] and National Center for Biotechnology Information (NCBI)[1]

  • Class "Saccharimonadia" corrig. McLean et al. 2020 ["Nanoperiodontomorbia" corrig. McLean et al. 2020; "Nanosyncoccia" corrig. McLean et al. 2020]
    • Order "Saccharimonadales" McLean et al. 2020 ["Nanogingivalales" corrig. McLean et al. 2020; "Nanoperiodontomorbales" corrig. McLean et al. 2020; "Nanosynbacterales" McLean et al. 2020; "Nanosyncoccales" McLean et al. 2020]
      • "Ca. Minimicrobia" Ibrahim et al. 2021
        • "Ca. M. naudis" Ibrahim et al. 2021
        • "Ca. M. vallesae" Ibrahim et al. 2021
      • "Ca. Mycolatisynbacter" corrig. Batinovic et al. 2021 ["Ca. Mycosynbacter" Batinovic et al. 2021] (JR1)
        • "Ca. M. amalyticus" corrig. Batinovic et al. 2021
      • "Ca. Nanosynsaccharibacterium" corrig. McLean et al. 2020
      • Family AMD01
        • "Ca. Chaera" corrig. Lemos et al. 2019
          • "Ca. C. renei" corrig. Lemos et al. 2019
      • Family "Nanogingivalaceae" McLean et al. 2020
        • "Ca. Nanogingivalis" McLean et al. 2020 (CMJM_G6_1_HOT_870; UMGS1907)
          • "Ca. N. gingivitcus" McLean et al. 2020
      • Family "Nanoperiodontomorbaceae" corrig. McLean et al. 2020
        • "Ca. Nanoperiodontomorbus" corrig. McLean et al. 2020 (EAM_G5_1_HOT_356; UBA1103)
          • "Ca. N. periodonticus" corrig. McLean et al. 2020
      • Family "Nanosynbacteraceae" McLean et al. 2020
        • "Ca. Nanosynbacter" McLean et al. 2020 (TM7x)
          • "Ca. N. featherlites" McLean et al. 2020
          • "Ca. N. lyticus" McLean et al. 2020
      • Family "Nanosyncoccaceae" McLean et al. 2020
        • "Ca. Nanosyncoccus" McLean et al. 2020 (G3_2_Rum_HOT_351B; UBA2866)
          • "Ca. N. alces" McLean et al. 2020
          • "Ca. N. nanoralicus" McLean et al. 2020
      • Family "Saccharimonadaceae" McLean et al. 2020
        • "Ca. Saccharimonas" Albertsen et al. 2013
          • "Ca. S. aalborgensis" Albertsen et al. 2013
      • Family UBA1547
        • "Ca. Microsaccharimonas" corrig. Lemos et al. 2019 ["Candidatus Saccharibacter" Lemos et al. 2019 non Jojima et al. 2004] (AMD02; UBA6175)
          • "Ca. M. sossegonensis" corrig. Lemos et al. 2019

See also

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References

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  1. ^ a b Sayers; et al. "Saccharibacteria". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  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. Bibcode:2014ApEnM..80.6480S. 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.
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  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. ^ a b c d 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. ^ a b c 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. ^ 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. Bibcode:2005ApEnM..71.8714F. doi:10.1128/AEM.71.12.8714-8720.2005. PMC 1317317. PMID 16332866.
  21. ^ 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.
  22. ^ 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.
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  26. ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
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  29. ^ Damien M. de Vienne: Parcubacteria group, NCBI Lifemap, University of Lyon. Lifemap is an interactive tool to explore NCBI taxonomy.
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  33. ^ Fredrik Bäckhed, Ruth Ley, Justin L Sonnenburg, Daniel A. Peterson, Jeffrey I. Gordon: Host‐Bacterial Mutualism in the Human Intestine. In: Science 307(5717): 1915-1920. April 2005. doi:10.1126/science.1104816. PMID 15790844
  34. ^ J.P. Euzéby. "Saccharibacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.
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