# Spirochaete

A spirochaete (/ˈspaɪroʊˌkiːt/) or spirochete is a member of the phylum Spirochaetota (also called Spirochaetes /ˌspaɪroʊˈkiːtiːz/), which contains distinctive diderm (double-membrane) Gram-negative bacteria, most of which have long, helically coiled (corkscrew-shaped or spiraled, hence the name) cells. Spirochaetes are chemoheterotrophic in nature, with lengths between 3 and 500 μm and diameters around 0.09 to at least 3 μm.
Spirochaetes are distinguished from other bacterial phyla by the location of their flagella, called endoflagella, or periplasmic flagella, which are sometimes called axial filaments. Endoflagella are anchored at each end (pole) of the bacterium within the periplasmic space (between the inner and outer membranes) where they project backwards to extend the length of the cell. These cause a twisting motion which allows the spirochaete to move. When reproducing, a spirochaete will undergo asexual transverse binary fission. Most spirochaetes are free-living and anaerobic, but there are numerous exceptions. Spirochaete bacteria are diverse in their pathogenic capacity and the ecological niches that they inhabit, as well as molecular characteristics including guanine-cytosine content and genome size.

## Pathogenicity

Many organisms within the Spirochaetota phylum cause prevalent diseases. Pathogenic members of this phylum include the following:
* Leptospira species, which causes leptospirosis
* Borrelia burgdorferi, B. mayonii, B. bissettiae, B. garinii, B. afzelii, B. spielmanii, B. lusitaniae, which cause Lyme disease.
* Borrelia recurrentis, which causes relapsing fever
* Treponema pallidum subspecies which cause treponematoses such as syphilis and yaws.
* Brachyspira pilosicoli and Brachyspira aalborgi, which cause intestinal spirochaetosis
Salvarsan, the first partially organic synthetic antimicrobial drug in medical history, was effective against spirochaetes and primarily used to cure syphilis. Additionally, oral spirochaetes are known to play a significant role in the pathogenesis of human periodontal disease.

## Taxonomy and molecular signatures

The class currently consists of 14 validly named genera across four orders and five families. The orders Brachyspirales, Brevinematales and Leptospirales each contain a single family, Brachyspiraceae, Brevinemataceae and Leptospiraceae, respectively. The Spirochaetales order harbours two families, Spirochaetaceae and Borreliaceae. Molecular markers in the form of conserved signature indels (CSIs) and CSPs have been found specific for each of the orders, with the exception of Brevinimetales, that provide a reliable means to demarcate these clades from one another within the diverse phylum. Additional CSIs have been found exclusively shared by each family within the Spirochaetales. These molecular markers are in agreement with the observed phylogenetic tree branching of two monophyletic clades within the Spirochaetales order. CSIs have also been found that further differentiate taxonomic groups within the Borreliaceae family that further delineate evolutionary relationships that are in accordance with physical characteristics such as pathogenicity (viz. Borrelia emend. Borreliella gen. nov.). However, this study has been criticized, and other studies using different approaches do not support the proposed split. The new naming system for the Lyme and relapsing fever Borrelia has not been adopted by the scientific literature.
A CSI has also been found exclusively shared by all Spirochaetota species. This CSI is a three-amino-acid insert in the flagellar basal body rod protein FlgC which is an important part of the unique endoflagellar structure shared by Spirochaetota species. Given that the CSI is exclusively shared by members within this phylum, it has been postulated that it may be related to the characteristic flagellar properties observed among Spirochaetota species.
Historically, all families belonging to the Spirochaetota phylum were assigned to a single order, the Spirochaetales. However, the current taxonomic view is more connotative of accurate evolutionary relationships. The distribution of a CSI is indicative of shared ancestry within the clade for which it is specific. It thus functions as a synapomorphic characteristic, so that the distributions of different CSIs provide the means to identify different orders and families within the phylum and so justify the phylogenetic divisions.

## Phylogeny

| 16S rRNA based LTP_10_2024 | 120 marker proteins based GTDB 09-RS220 |
| Brevinematia Brevinematales Brevinemataceae Brevinema Thermospiraceae Thermospira Spirochaetia Leptospirales Leptospiraceae Turneriella Leptonema Leptospira "Exilispirales" "Exilispiraceae" Exilispira Brachyspirales Brachyspiraceae Brachyspira Spirochaetales Sphaerochaetaceae Pleomorphochaeta Bullifex Sphaerochaeta Rectinemataceae Rectinema Breznakiellaceae Gracilinema Zuelzera Breznakiella Treponema primitia Helmutkoenigia Leadbettera Treponemataceae Brucepastera Teretinema Treponema Treponema species-group 2 Marispirochaetaceae Marispirochaeta Sediminispirochaetaceae Sediminispirochaeta Spirochaeta thermophila Salinispiraceae Spirochaeta lutea Salinispira Spirochaetaceae Spirochaeta Alkalispirochaetaceae Spirochaeta halophila Alkalispirochaeta Spirochaeta aurantia Spirochaetaceae 2 Spirochaeta cellobiosiphila Oceanispirochaeta Thiospirochaeta Spirochaeta species-group 2 "Entomospiraceae" Entomospira Borreliaceae Borrelia Borreliella | "Leptospirae" Leptospiria Turneriellales Turneriellaceae Turneriella Leptospirales Leptonemataceae Leptonema Leptospiraceae Leptospira "Euspirochaetae" Brevinematia Brevinematales Brevinemataceae Brevinema Thermospiraceae Thermospira Brachyspiria Brachyspirales Brachyspiraceae Brachyspira "Exilispiria" "Exilispirales" "Exilispiraceae" Exilispira Spirochaetia Borreliales Borreliaceae Borrelia Borreliella "Entomospirales" "Entomospiraceae" Entomospira DSM‑17781 DSM‑17781 Spirochaeta cellobiosiphila Spirochaetales_E "Thiospirochaetaceae" Thiospirochaeta DSM‑2461 Spirochaeta species-group 2 Spirochaetaceae_B Oceanispirochaeta Spirochaetales_A Spirochaetaceae_A Spirochaeta thermophila "Salinispirales" "Salinispiraceae" Spirochaeta lutea Salinispira DSM‑8902 Spirochaeta africana "Alkalispirochaetaceae" Alkalispirochaeta "Marispirochaetales" Marispirochaetaceae Marispirochaeta "Sediminispirochaetales" Sediminispirochaetaceae Sediminispirochaeta Sphaerochaetales Sphaerochaetaceae Parasphaerochaeta Sphaerochaeta Bullifex "Ca. Ornithospirochaeta" Treponematales Rectinemataceae Rectinema Breznakiellaceae Gracilinema Breznakiella Leadbettera Treponema primitia Treponemataceae "Ca. Gallitreponema" Treponema species-group 2 Brucepastera Teretinema "Ca. Avitreponema" Treponema |

## Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI).
* Phylum Spirochaetota Garrity and Holt 2021
** Genus ?"Spirosymplokos" Guerrero et al. 1993
** Class Leptospiria Chuvochina et al. 2024
*** Order Turneriellales Chuvochina et al. 2024
**** Family Turneriellaceae Chuvochina et al. 2024
***** Genus Turneriella Levett et al. 2005
*** Order Leptospirales Gupta et al. 2014
**** Family Leptonemataceae Chuvochina et al. 2024
***** Genus Leptonema Hovind-Hougen 1983
**** Family Leptospiraceae Hovind-Hougen 1979
***** Genus Leptospira Noguchi 1917
** Class Brachyspiria Chuvochina et al. 2024
*** Order Brachyspirales corrig. Gupta et al. 2014
**** Family Brachyspiraceae Paster 2012
***** Genus ?"Ca. Maribrachyspira" Matsuyama et al. 2017
***** Genus Brachyspira Hovind-Hougen et al. 1982 non Foliella non Pfeiffer 1855
** Class Brevinematia Chuvochina et al. 2024
*** Order Brevinematales Gupta et al. 2014
**** Family "Longinemataceae" Karnachuk et al. 2021
***** Genus ?"Longinema" corrig. Karnachuk et al. 2021
**** Family Brevinemataceae Paster 2012
***** Genus Brevinema Defosse et al. 1995
**** Family Thermospiraceae Ben Ali Gam et al. 2023
***** Genus Thermospira Ben Ali Gam et al. 2023
** Class Spirochaetia Paster 2020
*** Order Spirochaetales Buchanan 1917
**** Family "Pillotinaceae" Margulis & Hinkle 1992
***** Genus ?Pillotina Hollande and Gharagozlou 1967 ex Bermudes et al. 1988
**** Family Spirochaetaceae Swellengrebel 1907 ["Thiospirochaetaceae" Pallen, Rodriguez-R & Alikhan 2022]
***** Genus ?"Ca. Allospironema" Paster & Dewhirst 2000
***** Genus ?"Canaleparolina" Wier, Ashen & Margulis 2000
***** Genus ?Clevelandina Bermudes et al. 1988
***** Genus ?Diplocalyx Gharagozlou 1968 ex Bermudes et al. 1988 non Richard 1850 non Presl 1845
***** Genus ?"Candidatus Haliotispira" Sharma et al. 2024
***** Genus ?Hollandina To et al. 1978 ex Bermudes et al. 1988 non Haynes 1956
***** Genus ?"Mobilifilum" Margulis et al. 1990
***** Genus Oceanispirochaeta Subhash & Lee 2017b
***** Genus ?Spirochaeta Ehrenberg 1835 em. Pikuta et al. 2009 non Turczaninow 1851
***** Genus ?"Candidatus Thalassospirochaeta" Pragya et al. 2024
***** Genus Thiospirochaeta Dubinina et al. 2020
**** Family Alkalispirochaetceae Chuvochina et al. 2024
***** Genus Alkalispirochaeta Sravanthi et al. 2016
**** Family Salinispiraceae Chuvochina et al. 2024
***** Genus Salinispira Ben Hania et al. 2015
*** Order "Exilispirales" Pallen, Rodriguez-R & Alikhan 2022
**** Family "Exilispiraceae" Pallen, Rodriguez-R & Alikhan 2022
***** Genus Exilispira Imachi et al. 2008
*** Order Borreliales Chuvochina et al. 2024
**** Family Borreliaceae Gupta et al. 2014
***** Genus Borrelia Swellengrebel 1907 (relapsing fever Borrelia, reptile-associated Borrelia and Echidna-associated Borrelia)
***** Genus Borreliella Adeolu & Gupta 2015 (Lyme disease Borrelia)
***** Genus ?Cristispira Gross 1910
*** Order "Entomospirales" Pallen, Rodriguez-R & Alikhan 2022
**** Family "Entomospiraceae" Pallen, Rodriguez-R & Alikhan 2022
***** Genus Entomospira Grana-Miraglia et al. 2024 non Enderlein 1917
*** Order "Marispirochaetales" Pallen, Rodriguez-R & Alikhan 2022
**** Family Marispirochaetaceae Chuvochina et al. 2024
***** Genus Marispirochaeta Shivani et al. 2017
*** Order "Sediminispirochaetales" Pallen, Rodriguez-R & Alikhan 2022
**** Family Sediminispirochaetaceae Chuvochina et al. 2024
***** Genus Sediminispirochaeta Shivani et al. 2016
*** Order Sphaerochaetales Chuvochina et al. 2024
**** Family Sphaerochaetaceae Hördt et al. 2020
***** Genus Bullifex Wylensek et al. 2021 [incl. "Ca. Aphodenecus" Gilroy et al. 2021]
***** Genus "Ca. Ornithospirochaeta" Gilroy et al. 2021
***** Genus Parasphaerochaeta Bidzhieva et al. 2020
***** Genus "Ca. Physcosoma" Gilroy et al. 2022
***** Genus Pleomorphochaeta Arroua et al. 2016
***** Genus Sphaerochaeta Ritalahti et al. 2012
*** Order Treponematales Chuvochina et al. 2024
**** Family Rectinemataceae Brune et al. 2022
***** Genus Rectinema Koelschbach et al. 2017
**** Family Breznakiellaceae Brune et al. 2022
***** Genus Breznakiella Song et al. 2022
***** Genus Gracilinema Brune et al. 2022
***** Genus Helmutkoenigia Brune et al. 2022
***** Genus Leadbettera Brune et al. 2022
***** Genus Zuelzera Brune et al. 2022
**** Family Treponemataceae Robinson 1948
***** Genus "Ca. Avitreponema" Gilroy et al. 2021
***** Genus Brucepastera Song et al. 2023
***** Genus "Ca. Gallitreponema" Gilroy et al. 2021
***** Genus Teretinema Song et al. 2023
***** Genus Treponema Schaudinn 1905 em. Abt et al. 2013