Gracilicutes

Scanning electron micrograph of Treponema pallidum cells, copyright Centers for Disease Control and Prevention.

Belongs within: Life.
Contains: Spirochaetia, Planctobacteria, Bacteroidota, Deferribacteres, Aquificales, Campylobacteria, Acidobacteriota, Deltabacteria, Proteobacteria.

The Spirochaetes are a distinctive group of helically coiled, motile bacteria. Some species are notorious pathogens such as Treponema pallidum (causing syphilis) and Borrelia burgdorferi (causing Lyme disease). Pathogenic species of Borrelia are commonly transmitted by bites from ticks.

<==GracilicutesCD21
    |  i. s.: Marinisomatales [Marinisomatia, Marinisomatota]CD21
    |--Spirochaetota [Endoflagellata, Spirochaetae, Spirochaetes]CD21
    |    |  i. s.: Spirosymplokos deltaeiberiMS98
    |    |         Serpulina [Serpulinaceae]GH01a
    |    |--LeptospiraeCD21
    |    |    |--Turneriella [Turneriellaceae, Turneriellales]CD21
    |    |    |    `--T. parvaCD21
    |    |    `--Leptospiraceae [Leptospirales]GH01a
    |    |         |--Leptonema illiniGH01a, PHK96
    |    |         `--LeptospiraWK13
    |    |              |--L. biflexaWK13
    |    |              |--L. interrogansPHK96
    |    |              `--L. wolbachiiHP98
    |    `--+--Brevinematales [Brevinematia]CD21
    |       `--+--Brachyspira [Brachyspiraceae, Brachyspirae, Brachyspirales]CD21
    |          |    |--B. hyodysenteriaeCD21
    |          |    `--B. murdochiiWK13
    |          `--SpirochaetiaCD21
    `--+--+--ElusimicrobiotaCD21
       |  |    |--Elusimicrobium Geissinger et al. 2010VP IJSEM10 [ElusimicrobiaWK13, Elusimicrobiaceae, Elusimicrobiales]
       |  |    |    `--*E. minutum Geissinger et al. 2010VP IJSEM10
       |  |    `--EndomicrobiaCD21
       |  `--Candidatus Aerophobus [Aerophobetes]RS13
       |       `--A. profundusRS13
       `--+--+--+--Rhodopirellula balticaWK13
          |  |  |--PlanctobacteriaCD21
          |  |  `--Candidatus Omnitrophus [Omnitrophales, Omnitrophia, Omnitrophica, Omnitrophota]RS13
          |  |       `--O. fodinaeRS13
          |  `--+--Candidatus Hydrogenedens [Hydrogenedentes]RS13
          |     |    `--H. terephthalicusRS13
          |     `--+--+--Candidatus CloacamonasWK13 (see below for synonymy)
          |        |  |    `--C. acidaminovoransRS13
          |        |  `--GemmatimonadotaCD21
          |        |       |--GlassbacteriaCD21
          |        |       `--Gemmatimonas Zhang, Sekiguchi et al. 2003WK13, ZS03 (see below for synonymy)
          |        |            `--*G. aurantiaca Zhang, Sekiguchi et al. 2003ZS03
          |        `--+--FibrobacterotaCD21
          |           |    |--Chitinivibrio [Chitinivibrionaceae, Chitinivibrionales, Chitinivibrionia]CD21
          |           |    |    `--C. alkaliphilusCD21
          |           |    `--Fibrobacter [Fibrobacteraceae, Fibrobacterales, Fibrobacteres, Fibrobacteria]WK13
          |           |         |--F. intestinalisALS95
          |           |         `--F. succinogenesHP98 [=Bacteroides succinogenesCM92]
          |           `--+--Candidatus Latescibacter [Latescibacteria]RS13
          |              |    `--L. anaerobiusRS13
          |              `--+--BacteroidotaCD21
          |                 `--+--Caldithrix Miroshnichenko, Kostrikina et al. 2003RS13, MiKo03
          |                    |    `--*C. abyssi Miroshnichenko, Kostrikina et al. 2003MiKo03
          |                    `--Candidatus Marinimicrobium [Marinimicrobia]RS13
          |                         `--M. atlanticumRS13
          `--+--Babeliales [Babeliae, Dependentiae]CD21
             `--+--+--DeferribacteresCD21
                |  `--+--+--AquificalesCD21
                |     |  `--Candidatus Calescibacterium [Calescamantes]RS13
                |     |       `--C. nevadenseRS13
                |     `--CampylobacterotaCD21
                |          |--CampylobacteriaWK13
                |          `--Desulfurellales [Desulfurellia]CD21
                |               |--Desulfurella [Desulfurellaceae]MoKi03
                |               |    `--D. acetivoransMoKi03
                |               `--Hippea [Hippeaceae]CD21
                |                    `--H. jasoniaeCD21
                `--+--+--Candidatus Solibacter usitatusWK13
                   |  `--+--Candidatus Koribacter versatilisWK13
                   |     `--AcidobacteriotaCD21
                   `--+--+--DeltaproteobacteriaCD21
                      |  `--ProteobacteriaCD21
                      `--+--Candidatus Methylomirabilis oxyferaRS13
                         `--Nitrospirota [Nitrospirae]CD21
                              |--+--Candidatus Magnetobacterium Spring, Amann et al. 1993GH01b
                              |  |    `--Candidatus *M. bavaricum Spring, Amann et al. 1993GH01b
                              |  `--Thermodesulfovibrio Henry, Devereux et al. 1994VP WK13, GH01b (see below for synonymy)
                              |       `--*T. yellowstonii Henry, Devereux et al. 1994VP GH01b
                              `--+--Nitrospira Watson, Bock et al. 1986VP [Nitrospiraceae, Nitrospirales, Nitrospiria]GH01b
                                 |    `--*N. marina Watson, Bock et al. 1986VP GH01b
                                 `--Leptospirillum (ex Markosyan 1972) Hippe 2000VP GH01b
                                      |--*L. ferrooxidans (ex Markosyan 1972) Hippe 2000VP GH01b
                                      `--L. thermoferrooxidans Hippe 2000VP GH01b
Nomina invalida: Nitrospira moscoviensis Ehrich, Behrens et al. 1995GH01b
                 Thermodesulfovibrio islandicus Sonne-Hansen & Ahring 1999GH01b

Candidatus CloacamonasWK13 [=CloacimonasRS13; Cloacimonadaceae, Cloacimonadales, Cloacimonadia, Cloacimonadota, Cloacimonetes]

Gemmatimonas Zhang, Sekiguchi et al. 2003WK13, ZS03 [Gemmatimonadaceae, Gemmatimonadales, Gemmatimonadetes]

Thermodesulfovibrio Henry, Devereux et al. 1994VP WK13, GH01b [Thermodesulfovibrionales, Thermodesulfovibrionia]

*Type species of generic name indicated

References

[ALS95] Amann, R. I., W. Ludwig & K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59 (1): 143–169.

[CD21] Coleman, G. A., A. A. Davín, T. A. Mahendrarajah, L. L. Szánthó, A. Spang, P. Hugenholtz, G. J. Szöllősi & T. A. Williams. 2021. A rooted phylogeny resolves early bacterial evolution. Science 372: 588.

[CM92] Coughlan, M. P., & F. Mayer. 1992. The cellulose-decomposing bacteria and their enzyme systems. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 460–516. Springer-Verlag: New York.

[GH01a] Garrity, G. M., & J. G. Holt. 2001a. The road map to the Manual. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 119–166. Springer.

[GH01b] Garrity, G. M., & J. G. Holt. 2001b. Phylum BVIII. Nitrospirae phy. nov. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 451–464. Springer.

[HP98] Hugenholtz, P., C. Pitulle, K. L. Hershberger & N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology 180 (2): 366–376.

[IJSEM10] IJSEM. 2010. Validation list no. 132. List of new names and new combinations previously effectively, but not validly, published. International Journal of Systematic and Evolutionary Microbiology 60: 469–472.

[MS98] Margulis, L., & K. V. Schwartz. 1998. Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth 3rd ed. W. H. Freeman and Company: New York.

[MiKo03] Miroshnichenko, M. L., N. A. Kostrikina, N. A. Chernyh, N. V. Pimenov, T. P. Tourova, A. N. Antipov, S. Spring, E. Stackebrandt & E. A. Bonch-Osmolovskaya. 2003. Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage. International Journal of Systematic and Evolutionary Microbiology 53: 323–329.

[MoKi03] Mori, K., H. Kim, T. Kakegawa & S. Hanada. 2003. A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring. Extremophiles 7: 283–290.

[PHK96] Prescott, L. M., J. P. Harley & D. A. Klein. 1996. Microbiology 3rd ed. Wm. C. Brown Publishers: Dubuque (Iowa).

[RS13] Rinke, C., P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson, J.-F. Cheng, A. Darling, S. Malfatti, B. K. Swan, E. A. Gies, J. A. Dodsworth, B. P. Hedlund, G. Tsiamis, S. M. Sievert, W.-T. Liu, J. A. H. Eisen, S. J., N. Kyrpides, C., R. Stepanauskas, E. M. Rubin, P. Hugenholtz & T. Woyke. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431–437.

[WK13] Williams, K. P., & D. P. Kelly. 2013. Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. International Journal of Systematic and Evolutionary Microbiology 63 (8): 2901–2906.

[ZS03] Zhang, H., Y. Sekiguchi, S. Hanada, P. Hugenholtz, H. Kim, Y. Kamagata & K. Nakamura. 2003. Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. International Journal of Systematic and Evolutionary Microbiology 53: 1155–1163.

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