Spirochaetota

Spirochaetota (formerly Spirochaetes) is a monophyletic phylum of elongated, helically coiled or flat-wave diderm (Gram-negative-like) bacteria ranging from 3 to 500 μm in length but only 0.1 to 0.5 μm in diameter (frequently narrower than the diffraction resolution limit of standard bright-field microscopy, requiring dark-field or phase-contrast illumination). Spirochaetes are united by a unique ultrastructural synapomorphy found in no other bacterial phylum: periplasmic flagella (also termed endoflagella or axial filaments), which remain completely enclosed inside the periplasmic space between the inner peptidoglycan–cytoplasmic cylinder and a flexible outer membrane sheath.

By rotating these internal axial filaments inside a sealed envelope, spirochaetes convert rotary motor torque into whole-body helical waves or flat-wave undulations that allow them to corkscrew rapidly through high-viscosity viscoelastic media—such as hyaluronic-acid connective tissue matrices, mucus layers, endothelial tight junctions, and anoxic sediments—that completely immobilize externally flagellated bacteria like Escherichia coli or Salmonella.

The phylum encompasses free-living marine sediment anaerobes, mutualistic termite-hindgut symbionts (Treponema primitia), and the etiologic agents of three major human systemic infections:

1. Treponema pallidum subsp. pallidum — Causal agent of syphilis (as well as endemic treponematoses: yaws, bejel, and pinta).
2. Borrelia burgdorferi (Borreliella burgdorferi) and Borrelia recurrentis — Ixodid-tick-borne and louse-borne agents of Lyme borreliosis and relapsing fever.
3. Leptospira interrogans — Zoonotic waterborne agent of leptospirosis (Weil's disease).

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` Phylum Spirochaetota (Deep-branching diderm clade; 1 class Spirochaetia, 4 orders) ├── Order Spirochaetales │ ├── Spirochaetaceae (Free-living anaerobic Spirochaeta in sulfide muds; Cristispira in bivalve crystalline styles) │ └── Treponemataceae │ ├── Treponema pallidum (Syphilis; 1.14 Mb minimal genome, lacks LPS & TCA cycle) │ ├── Treponema denticola (Oral "red complex" periodontal pathogen alongside Porphyromonas gingivalis) │ └── Termite-Gut Treponema (T. primitia, T. azotonutricium: reductive acetogenesis & dinitrogen fixation) │ ├── Order Borreliales — Family Borreliaceae │ ├── Borreliella (Lyme Disease Group: Borrelia burgdorferi, B. afzelii, B. garinii; transmitted by Ixodes hard ticks) │ └── Borrelia sensu stricto (Relapsing Fever Group: B. hermsii, B. recurrentis; transmitted by Ornithodoros soft ticks & body lice) │ ├── Order Brachyspirales — Family Brachyspiraceae │ └── Brachyspira hyodysenteriae & B. pilosicoli (Anaerobic swine dysentery & human intestinal spirochetosis) │ └── Order Leptospirales — Family Leptospiraceae ├── Saprophytic Clade (Leptospira biflexa: free-living freshwater aerobes) └── Pathogenic Clade (Leptospira interrogans, L. borgpetersenii: obligate aerobes oxidizing long-chain fatty acids)

In externally flagellated bacteria (Pseudomonadota, Bacillota), the flagellar filament projects through the outer membrane into the surrounding liquid; when dynamic viscosity exceeds ~60–100 centipoise (cP), hydrodynamic drag stalls the external filament. Spirochaetes solve this problem by inverting the flagellar geometry:

1. Subpolar Insertion and Overlapping Ribbon: Between 1 (in Leptospira) and 100+ (in Cristispira) flagellar basal bodies are anchored into the cytoplasmic membrane near both cell poles. Rather than piercing the outer membrane, the flagellar hooks and filaments fold backward along the length of the protoplasmic cylinder inside the narrow periplasmic space, overlapping in the middle of the cell in Borrelia and Treponema.
2. Proteinaceous Collar and High-Torque Rotor: Cryo-electron tomography reveals that the spirochaete flagellar motor possesses an enlarged C-ring rotor (~55–62 nm diameter) surrounded by a ring of 16 torque-generating MotAB stator complexes stabilized by a phylum-specific periplasmic collar—generating up to ~4,000 pN·nm of torque (nearly double that of the E. coli motor).
3. Helical vs. Flat-Wave Elastohydrodynamics:
   • In Borrelia burgdorferi and Treponema pallidum, a stiff ribbon of 7 to 11 periplasmic flagella wraps around a flexible cylindrical cell body. Counter-rotation of the stiff flagellar ribbon against the peptidoglycan cylinder deforms the entire bacterium into a planar sinusoidal ("flat-wave") undulation propagating from anterior to posterior at 5–10 Hz, enabling the cell to weave between dermal collagen fibrils and traverse vascular endothelium during hematogenous dissemination.
   • In Leptospira interrogans, a single short periplasmic flagellum at each pole (coated in sheath proteins FlaA/FlaB) curves the cell ends into either a spiral-shaped anterior end (when rotating counterclockwise) or a hook-shaped posterior end (when rotating clockwise); asymmetric traction between the anterior spiral and the rotating right-handed helical body pulls the bacterium through gel-like media like a mechanical corkscrew.

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Discovered by Willy Burgdorfer in 1982 as the cause of Lyme disease (transmitted across North America and Eurasia by hard-bodied ticks of the genus Ixodes: I. scapularis, I. pacificus, I. ricinus, and I. persulcatus), Borrelia burgdorferi possesses three extraordinary molecular features:

1. The Most Segmented Genome in Bacteria (Linear Chromosome + 21 Plasmids)

The ~1.52-Mb genome of B. burgdorferi strain B31 is partitioned across a 910-kb linear chromosome plus 12 linear plasmids and 9 circular plasmids (the largest number of coexisting extrachromosomal replicons known in any bacterium). The linear chromosome and linear plasmids are terminated by covalently closed hairpin telomeres, which are replicated as inverted-repeat dimers and resolved into closed hairpins by the essential telomere resolvase ResT (homologous to the coliphage N15 protelomerase TelN).

2. Complete Elimination of Cellular Iron (Manganese-Dependent Life)

During mammalian infection, host macrophages and hepatocytes withhold free iron (Fe²⁺/Fe³⁺) via transferrin, lactoferrin, and hepcidin (nutritional immunity). Borrelia burgdorferi circumvented host nutritional immunity entirely by evolving a completely iron-free metabolism (Posey & Gherardini, 2000): its genome encodes zero iron-containing proteins (no cytochromes, no catalase, no TCA-cycle aconitase or succinate dehydrogenase, and no iron superoxide dismutase), relying exclusively on manganese (Mn²⁺) imported via the BmtA transporter to cofactor its superoxide dismutase (*SodA`) and metabolic enzymes.

3. Reciprocal Outer-Surface Protein (OspA/OspC) Switching and vlsE Recombination

• Tick-to-Mammal OspA → OspC Switch: Inside the unfed tick midgut, B. burgdorferi expresses OspA (which binds the tick midgut receptor TROSPA). When the tick takes a warm blood meal (37 °C, drop in pH, organic acids), the Rrp2–RpoN–RpoS sigma-factor cascade represses ospA and induces OspC, allowing the spirochaete to migrate to the tick salivary glands and establish early mammalian dermal infection (manifesting clinically as erythema migrans).
• Cassette-Driven vlsE Antigenic Variation: On linear plasmid lp28-1, the expressed lipoprotein gene vlsE sits adjacent to 15 silent, unexpressed cassette segments (vls2–vls16). Once inside a vertebrate host, segmental gene conversion continuously swaps fragments of the silent cassettes into the central variable region of vlsE (capable of generating $>10^{30}$ potential amino acid sequences), allowing Borrelia to evade host adaptive antibodies for months to years.

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• The "Stealth Pathogen" Treponema pallidum: With a streamlined 1.14-Mb circular chromosome lacking LPS, exotoxins, and biosynthetic pathways for nucleotides, fatty acids, and most amino acids, T. pallidum exposes 100-fold fewer integral outer-membrane proteins on its outer surface than E. coli (while anchoring its abundant immunogenic lipoproteins beneath the outer membrane in the periplasm). This lipid-smooth exterior evades innate pattern-recognition receptors, while subpopulations periodically vary the surface-exposed β-barrel protein TprK via gene conversion from 53 donor sites at the tprD locus—producing the relapsing clinical stages of primary (chancre), secondary (disseminated rash), latent, and tertiary (neurovascular/gummatous) syphilis.
• Mutualistic Termite-Gut Treponema: At the opposite ecological pole, non-pathogenic Treponema species (T. primitia, T. azotonutricium) make up up to 50% of all prokaryotes in the wood-eating termite hindgut (Blattodea), either swimming free in the anoxic lumen or attached as ectosymbionts propelling cellulolytic protists (Mixotricha paradoxa), where they perform H₂/CO₂ reductive acetogenesis via the Wood–Ljungdahl pathway and fix atmospheric dinitrogen (N₂) to feed the termite host.

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1. Charon, N. W., Cockburn, A., Li, C., Liu, J., Miller, K. A., Miller, M. R., ... & Wolgemuth, C. W. (2012). The unique paradigm of spirochete motility and chemotaxis. Annual Review of Microbiology, 66, 349–370. Google Scholar
2. Fraser, C. M., et al. (1997). Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature, 390(6660), 580–586. Google Scholar
3. Posey, J. E., & Gherardini, F. C. (2000). Lack of a role for iron in the Lyme disease pathogen. Science, 288(5471), 1651–1653. Google Scholar
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• Microbiome
• Pseudomonadota
• Blattodea
• Innate Immunity
• Antibiotic Resistance