Bulleidia extructa PP_925: Genome Reduction, Minimalist Metabolism, and Evolutionary Insights into Firmicutes Diversification

Evseev, Peter V.; Podoprigora, Irina V.; Chaplin, Andrei V.; Khabadze, Zurab S.; Malkov, Artem A.; Kafarskaia, Lyudmila I.; Shagin, Dmitriy A.; Urban, Yulia N.; Borisova, Olga Yu.; Efimov, Boris A.

doi:10.3390/ijms27010448

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Bulleidia extructa PP_925: Genome Reduction, Minimalist Metabolism, and Evolutionary Insights into Firmicutes Diversification

by

Peter V. Evseev

^1,*,

Irina V. Podoprigora

²,

Andrei V. Chaplin

¹

,

Zurab S. Khabadze

²

,

Artem A. Malkov

¹

,

Lyudmila I. Kafarskaia

¹,

Dmitriy A. Shagin

¹,

Yulia N. Urban

³,

Olga Yu. Borisova

³ and

Boris A. Efimov

^1,*

¹

Pirogov Russian National Research Medical University, Ostrovityanova Street 1, Moscow 117997, Russia

²

Institute of Medicine, Peoples’ Friendship University of Russia Named After Patrice Lumumba, Miklukho-Maklaya Street 6, Moscow 117998, Russia

³

G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Admirala Makarova Street 10, Moscow 125212, Russia

^*

Authors to whom correspondence should be addressed.

Int. J. Mol. Sci. 2026, 27(1), 448; https://doi.org/10.3390/ijms27010448

Submission received: 30 September 2025 / Revised: 10 December 2025 / Accepted: 28 December 2025 / Published: 31 December 2025

(This article belongs to the Section Molecular Genetics and Genomics)

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Abstract

Bulleidia extructa strain PP_925, isolated from the periodontal pocket of a patient with periodontitis, is a Gram-positive Bacillota with an unusually compact genome of 1.38 Mb. Phylogenomic analyses place PP_925 within Erysipelotrichales and show close relatedness of Bulleidia to Solobacterium and Lactimicrobium, as well as the existence of previously undescribed related clades. The metabolic repertoire of PP_925 is strongly reduced: it retains glycolysis, the phosphotransacetylase–acetate kinase pathway, and arginine catabolism but lacks the tricarboxylic acid cycle and most de novo biosynthetic pathways for amino acids, nucleotides, fatty acids, cofactors, and vitamins, implying reliance on salvage and cross-feeding. Phylogenetic inference indicates independent peptidoglycan losses in multiple mycoplasma-related Erysipelotrichia lineages, while PP_925 has retained an ancestral Gram-positive cell wall despite extensive genomic reduction. The genome preserves systems crucial for host interaction and adaptability, including a horizontally acquired tad locus encoding type IV pili, a comG competence system, and several adherence-associated virulence factors. Defense mechanisms are diverse and include a CRISPR-Cas II-A system, a type II restriction–modification module adjacent to Gao_Qat-like genes, and the Wadjet system in a genome without prophages; CRISPR spacers indicate repeated encounters with Bacillota phages. Comparative genomics of PP_925 and related strains reveals a small core genome with lineage-specific adhesion and defense modules, indicating recent shared ancestry combined with adaptive flexibility under substantial genome reduction.

Keywords: Bulleidia extructa PP_925; Bulleidia extructa; Bulleidia; Bacillota; Erysipelotrichaceae; Erysipelotrichales; Erysipelotrichia; Erysipelotrichia origin; Erysipelotrichia evolution; Erysipelotrichia taxonomy; Erysipelotrichia genomics; Erysipelotrichia pangenome; Erysipelotrichia metabolism; Erysipelotrichia phages; Mycoplasmatota evolution; genome reduction

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MDPI and ACS Style

Evseev, P.V.; Podoprigora, I.V.; Chaplin, A.V.; Khabadze, Z.S.; Malkov, A.A.; Kafarskaia, L.I.; Shagin, D.A.; Urban, Y.N.; Borisova, O.Y.; Efimov, B.A. Bulleidia extructa PP_925: Genome Reduction, Minimalist Metabolism, and Evolutionary Insights into Firmicutes Diversification. Int. J. Mol. Sci. 2026, 27, 448. https://doi.org/10.3390/ijms27010448

AMA Style

Evseev PV, Podoprigora IV, Chaplin AV, Khabadze ZS, Malkov AA, Kafarskaia LI, Shagin DA, Urban YN, Borisova OY, Efimov BA. Bulleidia extructa PP_925: Genome Reduction, Minimalist Metabolism, and Evolutionary Insights into Firmicutes Diversification. International Journal of Molecular Sciences. 2026; 27(1):448. https://doi.org/10.3390/ijms27010448

Chicago/Turabian Style

Evseev, Peter V., Irina V. Podoprigora, Andrei V. Chaplin, Zurab S. Khabadze, Artem A. Malkov, Lyudmila I. Kafarskaia, Dmitriy A. Shagin, Yulia N. Urban, Olga Yu. Borisova, and Boris A. Efimov. 2026. "Bulleidia extructa PP_925: Genome Reduction, Minimalist Metabolism, and Evolutionary Insights into Firmicutes Diversification" International Journal of Molecular Sciences 27, no. 1: 448. https://doi.org/10.3390/ijms27010448

APA Style

Evseev, P. V., Podoprigora, I. V., Chaplin, A. V., Khabadze, Z. S., Malkov, A. A., Kafarskaia, L. I., Shagin, D. A., Urban, Y. N., Borisova, O. Y., & Efimov, B. A. (2026). Bulleidia extructa PP_925: Genome Reduction, Minimalist Metabolism, and Evolutionary Insights into Firmicutes Diversification. International Journal of Molecular Sciences, 27(1), 448. https://doi.org/10.3390/ijms27010448

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Bulleidia extructa PP_925: Genome Reduction, Minimalist Metabolism, and Evolutionary Insights into Firmicutes Diversification

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