Kontent qismiga oʻtish

Saccharibacteria

Vikipediya, ochiq ensiklopediya
Ca. Nanosynbacter lyticus (aka TM7x, green) and bacterial hosts (red).
Scale bars are 5 μm.
Biologik klassifikatsiya
Domen: Bacteria
(unranked) CPR group
Tip: Saccharibacteria
Albertsen et al. 2013
Sinf: "Saccharimonadia"
corrig. McLean et al. 2020
Turkum: "Saccharimonadales"
corrig. McLean et al. 2020
Famlies
  • "Nanogingivalaceae"
  • "Nanoperiodontomorbaceae"
  • "Nanosynbacteraceae"
  • "Nanosyncoccaceae"
  • "Saccharimonadaceae"
Sinonimlari
  • Candidate division TM7
Saccharibacteria
Ca. Nanosynbacter lyticus (TM7x, yashil) va bakterial xostlar (qizil).
Biologik tasnifi
Olam:
Bacteria
Tartibi:
CPR group
Tip:
Saccharibacteria


Albertsen et al. 2013
Sinf:
"Saccharimonadia"


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


corrig. McLean et al. 2020
Tipga mansub oilalar
  • „Nanogingivalaceae“
  • „Nanoperiodontomorbaceae“
  • „Nanosynbacteraceae“
  • „Nanosyncoccaceae“
  • „Saccharimonadaceae“
Sinonimlari
  • Candidate division TM7

Saccharibacteria— yumaloq bakteriyalar guruhiga mansub boʻlgan bakteriyalarning yirik guruhi boʻlib, ilgari TM7 nomi bilan tanilgan'[1] asosiy bakterial guruhidir. U 16S rRNK tanlash orqali kashf etilgan[2].

Uchrashi

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Odamning ogʻiz boʻshligʻidan TM7x uchraydi va TM7x juda kichik kokk o‘lchamiga ega bo‘lib (200-300 nm ekanligini aniqladi), insoniyatga maʼlum boʻlgan mikroblarda ilgari kuzatilmagan oʻziga xos hayot tarziga ega boʻlgan[3]. Bu bakteriyalar turli xildagi tuzilishga ega boʻlib, epibiontikligi, jumladan Actinomyces odontolyticus shtammi (XH001), shu bilan birga parazitar fazaga ega boʻlishi bilan farqlanadi. Toʻliq genom ketma-ketligi juda kamaygan (705 kB)[4] va aminokislotalarning biosintetik qobiliyatining toʻliq yetishmasligini aniqlangan. 2014-yilda ogʻiz boʻshligʻidan TM7x aksenik hayot sikli haqida xabar berilgan[5].

Candidate Phylum TM6[6] bilan bir qatorda, 1994-yilda Germaniyadagi torf botqogʻining tuproq namunasini atrof-muhitni oʻrganishda olingan namunalar ketma-ketliklari sharafiga nomlangan boʻlib, bu yerda 262 PCR kuchaytirilgan 16S rDNK fragmentlari Torf, Mittlere Schicht uchun TM klonlari deb nomlangan plazmid vektoriga klonlangan. Torf, Mittlere Schicht (lit. torf, oʻrta qatlam)[7]. U bir nechta muhitda topilgan, masalan, botqoqliklardan[8][9], suv tozalash inshootlaridan[10], tropik oʻrmon tuprogʻidan[11], inson soʻlagidan[12], [13] gubkalar bilan bogʻliq holatlardan[14], suvaraklardan[15], oltin konlaridan[16], asetat bilan oʻzgartirilgan suvli qatlam choʻkindilaridan[17] va boshqa muhitlardan topilgan (bar termofil). Yaqinda TM7 rDNK va butun hujayralar inson terisiga 99,7% TM7 va 98,6% inson ogʻziga TM7a bilan oʻxshashlik bilan tuproqlarda aniqlandi[18], atrof-muhit joylarida metabolik faol TM7 izolatlari model organizmlar boʻlib xizmat qilishi mumkin. TM7 turlarining inson salomatligidagi rolini oʻrganilmoqda.

Xususiyatlari

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TM7 oʻziga xos FISH problari bioreaktor loyidan aniqlangan turlarini gram-musbat hujayra konvertlari va bir nechta morfotiplar mavjudligini aniqladi: qobiqli filament (koʻp), qisqa zanjirlarda uchraydigan tayoqchalari, qalin filament va kokklari; birinchisi Eikelboom 0041 turining sababi boʻlishi mumkin (faollashtirilgan shtammlarining koʻpayishi bilan bogʻliq muammolar)[19]. Bakteriyalar oilasining aksariyati gram-manfiy didermalar koʻrinishida boʻlib, faqat Bacillota, Actinomycetota va Chloroflexota monodermlari koʻp uchraydi[20]. Saccharibacteria guruhiga oid 50 dan ortiq turli xil filotiplar aniqlangan boʻlib[21] u nisbatan oddiy intradivizion 16S rDNK ketma-ketligi 17% ni tashkil qiladi, bu koʻrsatgich 13 dan 33% gacha[22] jsPhyloSVG[23][24] qurilgan TM7 ning interaktiv filogenetik daraxti GenBank ketma-ketliklariga va daraxt shoxlari orasidagi masofa matritsasi hisoblariga tez kirish imkoniyatini berishi oʻziga xos xususiyatidir.

Barqaror izotoplarni tekshirish tadqiqotlari ushbu turlarning baʼzi aʼzolari toluolni parchalashi mumkinligini aniqlaganlar[25][26].

Taksonomiyasi

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Hozirgi vaqtda qabul qilingan taksonomiya Nomenklaturasida (LPSN)[27] va Milliy Biotexnologiya Axborot Markazi (NCBI)[28] bilan prokariotik nomlar roʻyxatiga asoslanadi.

  • " Saxarimonadiya „ sinfi . McLean va boshqalar. 2020 [“Nanoperiodontomorbia" korrig. McLean va boshqalar. 2020 ; „Nanosinkoksiya“ korrigiyasi. McLean va boshqalar. 2020 ]
    • Ordeni " Saccharimonadales „ McLean va boshqalar. 2020 [“Nanogingivalales" korrig. McLean va boshqalar. 2020 ; „Nanoperiodontomorbales“ korrigiyasi. McLean va boshqalar. 2020 ; „Nanosinbakterallar“ McLean va boshqalar. 2020 ; „Nanosyncoccales“ McLean va boshqalar. 2020 ]
      • "Ka. Chaera " korrig . Lemos va boshqalar. 2019
        • "C. C. Renei " korrig. Lemos va boshqalar. 2019
      • " Ca. Minimicrobia " Ibrohim va boshqalar. 2021 yil
        • „ Ca. M. naudis“ Ibrohim va boshqalar. 2021 yil
        • „ Ca. M. vallesae“ Ibrohim va boshqalar. 2021 yil
      • " Ca. Mycosynbacter " Batinovic va boshqalar. 2021 (JR1)
        • „ Ca. M. amalyticus“ Batinovich va boshqalar. 2021 yil
      • "Ka. Nanosynsaccharibacterium " korrig . McLean va boshqalar. 2020
      • Oila " Nanogingivalaceae " McLean va boshqalar. 2020
        • " Ca. Nanogingivalis " McLean va boshqalar. 2020 (CMJM_G6_1_HOT_870; UMGS1907)
          • „ C. N. gingivitcus“ McLean va boshqalar. 2020
      • Oila " Nanoperiodontomorbaceae " korrig. McLean va boshqalar. 2020
        • "Ka. Nanoperiodontomorbus " korrig . McLean va boshqalar. 2020 (EAM_G5_1_HOT_356; UBA1103)
          • „ Ca. N. periodonticus“ korrigiyasi. McLean va boshqalar. 2020
      • Oila " Nanosinbakteraceae " McLean va boshqalar. 2020
        • „ Ka. Nanosinbakter “ McLean va boshqalar. 2020 (TM7x)
          • „ Ca. N. lyticus“ McLean va boshqalar. 2020
      • Oila " Nanosinkoccaceae " McLean va boshqalar. 2020
        • " Ca. Nanosyncoccus " McLean va boshqalar. 2020 (G3_2_Rum_HOT_351B; UBA2866)
          • „ Ka . N. alces“ McLean va boshqalar. 2020
          • „ Ca. N. nanoralicus“ McLean va boshqalar. 2020
      • Oila " Saccharimonadaceae " McLean va boshqalar. 2020
        • " Ca. Saccharimonas " Albertsen va boshqalar. 2013 yil
          • „ Ka . S.“ Albertsen va boshqalar. 2013 yil
      • Oila UBA1547
        • "Ka. Microsaccharimonas " korrig . Lemos va boshqalar. 2019 (AMD02; UBA6175)
          • „ Ca. M. sossegonensis“ korrigiyasi. Lemos va boshqalar. 2019

Filogeniyasi

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TM7 filumining va uning eng yaqin qarindoshlarining munosabati[29] Dinis va boshqalarga koʻra nomlangan kichik guruhlarning soddalashtirilgan filogenetik daraxti. 2011-yil.[24]
 
 

Chloroflexota (outgroup)

 
Patescibacteria
 
Parcubacteria group
 

ABY1
(OD1-ABY1)

 
 

Gracilibacteria
(BD1-5 group)

 
(OD1)
 
 

Microgenomates
(OP11 group)

 
 

Dojkabacteria
(WS6)

 
 
 
 
 

Saccharibacteria
(TM7)

 
 
 

SC3

 
 
 

WS5

 
 

Guaymas1
(Thermodesulfobacteriota-related)

 
 
 
 
(CPR)
 
Saccharibacteria
 

Saccharibacteria I

 
 
 

Saccharibacteria II

 
 
 

Saccharibacteria IV

 
 
 

TM7a group

 
 

Saccharibacteria III

 
 
 
 
 

Yana qarang

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Manbalar

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  1. ↑ name="Saccharibacteria">Sayers. „Saccharibacteria“. National Center for Biotechnology Information (NCBI) taxonomy database. Qaraldi: 2021-yil 20-mart.
  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. PMID 19946133. PMC 2786576. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2786576. 
  3. ↑ He, Xuesong; McLean, Jeffrey S.; Edlund, Anna; Yooseph, Shibu; Hall, Adam P.; Liu, Su-Yang; Dorrestein, Pieter C.; Esquenazi, Eduardo et al. (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. doi:10.1073/pnas.1419038112. ISSN 0027-8424. PMID 25535390. PMC 4291631. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4291631. 
  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. PMID 25107981. PMC 4178647. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4178647. 
  6. ↑ McLean, Jeffrey S.; Lombardo, Mary-Jane; Badger, Jonathan H.; Edlund, Anna; Novotny, Mark; Yee-Greenbaum, Joyclyn; Vyahhi, Nikolay; Hall, Adam P. et al. (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. doi:10.1073/pnas.1219809110. ISSN 0027-8424. PMID 23754396. PMC 3696752. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3696752. 
  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. 
  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. PMID 7544094. PMC 167453. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=167453. 
  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. PMID 9212428. PMC 168577. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=168577. 
  10. ↑ name="fish">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. PMID 11133473. PMC 92593. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=92593. 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. Bibcode:2001ApEnM..67..411H. 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. PMID 9212415. PMC 168563. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=168563. 
  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. PMID 20920195. PMC 2997015. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2997015. 
  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. PMID 20656903. PMC 2944498. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2944498. 
  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. https://archive.org/details/sim_microbial-ecology_2007-07_54_1/page/101. 
  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. 
  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. PMID 24149512. PMC 3812714. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3812714. 
  18. ↑ name="pmid21701585">Dinis, J. M.; Barton, D. E.; Ghadiri, J.; Surendar, D.; Reddy, K.; Velasquez, F.; Chaffee, C. L.; Lee, M. C. W. et al. (2011). Yang, Ching-Hong. ed. "In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment". PLOS ONE 6 (6): e21280. doi:10.1371/journal.pone.0021280. PMID 21701585. PMC 3118805. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3118805. 
  19. ↑ name="fish">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. PMID 11133473. PMC 92593. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=92593. 
  20. ↑ name="giovannoni">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. https://archive.org/details/sim_annual-review-of-microbiology_2003_57/page/369. 
  21. ↑ 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. https://archive.org/details/sim_annual-review-of-microbiology_2003_57/page/369. 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.
  22. ↑ 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. PMID 11133473. PMC 92593. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=92593. 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. Bibcode:2001ApEnM..67..411H. doi:10.1128/AEM.67.1.411-419.2001. PMC 92593. PMID 11133473.
  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. doi:10.1371/journal.pone.0012267. PMID 20805892. PMC 2923619. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2923619. 
  24. ↑ 24,0 24,1 Dinis, J. M.; Barton, D. E.; Ghadiri, J.; Surendar, D.; Reddy, K.; Velasquez, F.; Chaffee, C. L.; Lee, M. C. W. et al. (2011). Yang, Ching-Hong. ed. "In Search of an Uncultured Human-Associated TM7 Bacterium in the Environment". PLOS ONE 6 (6): e21280. doi:10.1371/journal.pone.0021280. PMID 21701585. PMC 3118805. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3118805. 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.
  25. ↑ 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. 
  26. ↑ 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. PMID 19447956. PMC 2704817. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2704817. 
  27. ↑ J.P. Euzéby. „Saccharibacteria“. List of Prokaryotic names with Standing in Nomenclature (LPSN). Qaraldi: 2021-yil 27-iyun.
  28. ↑ Sayers. „Saccharibacteria“. National Center for Biotechnology Information (NCBI) taxonomy database. Qaraldi: 2021-yil 20-mart.Sayers; et al. „Saccharibacteria“. National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  29. ↑ name=giovannoni>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. https://archive.org/details/sim_annual-review-of-microbiology_2003_57/page/369. 

Havolalar

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