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Lookup NU author(s): Dr Halah Ahmed, Professor Nicholas JakubovicsORCiD
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© The Author(s) 2024.Background: Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences. Results: Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24. Conclusions: Based on these findings, strain NCTC 9931T (= ATCC 17982T = DSM 43331T = CIP 104728T = CCUG 18309T = NCTC 14978T = CGMCC 1.90328T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24T (= NCTC 14980T = CGMCC 1.90329T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health. Significance: This research reveals two Schaalia strains, NCTC 9931 T and C24T, as novel entities with distinct genomic features. Expanding the taxonomic framework of the genus Schaalia, this study offers a critical resource for probing the metabolic intricacies and resistance patterns of these bacteria. This work stands as a cornerstone for microbial taxonomy, paving the way for significant advances in clinical diagnostics.
Author(s): Tian X, Teo WFA, Yang Y, Dong L, Wong A, Chen L, Ahmed H, Choo SW, Jakubovics NS, Tan GYA
Publication type: Article
Publication status: Published
Journal: BMC Microbiology
Year: 2024
Volume: 24
Issue: 1
Online publication date: 28/05/2024
Acceptance date: 21/05/2024
Date deposited: 11/06/2024
ISSN (electronic): 1471-2180
Publisher: BioMed Central Ltd
URL: .10.1186/s12866-024-03346-w
DOI: 10.1186/s12866-024-03346-w
Data Access Statement: The genome sequence and 16S rRNA gene sequence of strain NCTC 9931 and C24 were deposited into the GenBank database. The accession number for 16S rRNA gene sequences for strains NCTC 9931 and C24 are OQ981483 and OQ981484, respectively. The accession number of whole genome sequences for strain NCTC 9931 and C24 were assigned as JASPFE000000000 and JASPEY000000000, respectively. These genome sequences can be accessed by searching PRJNA976213 in the NCBI database (https://www.ncbi.nlm.nih. gov/). The accession number of other genome sequences used in this study can be found in Supplementary Table S1-S2. The strains NCTC 9931 and C24 used in this study are available from the collections of the National Collection of Type Cultures (NCTC), United Kingdom, and China General Microbiological Culture Collection Center (CGMCC), China
PubMed id: 38802738
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