Staff View: Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity

Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity

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...

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Main Authors:	Tian, Xuechen, Teo, Wee Fei Aaron, Yang, Yixin, Dong, Linyinxue, Wong, Aloysius, Chen, Li, Ahmed, Halah, Choo, Siew Woh, Jakubovics, Nicholas S., Tan, Geok Yuan Annie
Format:	Article
Published:	BioMed Central 2024
Subjects:	QH Natural history
Online Access:	http://eprints.um.edu.my/45214/ https://doi.org/10.1186/s12866-024-03346-w
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spelling	my.um.eprints.452142024-09-26T02:47:41Z http://eprints.um.edu.my/45214/ Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity Tian, Xuechen Teo, Wee Fei Aaron Yang, Yixin Dong, Linyinxue Wong, Aloysius Chen, Li Ahmed, Halah Choo, Siew Woh Jakubovics, Nicholas S. Tan, Geok Yuan Annie QH Natural history 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 9931(T) (= ATCC 17982(T) = DSM 43331(T) = CIP 104728(T) = CCUG 18309(T) = NCTC 14978(T) = CGMCC 1.90328(T)) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24(T) (= NCTC 14980(T) = CGMCC 1.90329(T)) 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 C24(T), 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. BioMed Central 2024-05 Article PeerReviewed Tian, Xuechen and Teo, Wee Fei Aaron and Yang, Yixin and Dong, Linyinxue and Wong, Aloysius and Chen, Li and Ahmed, Halah and Choo, Siew Woh and Jakubovics, Nicholas S. and Tan, Geok Yuan Annie (2024) Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity. BMC Microbiology, 24 (1). p. 185. ISSN 1471-2180, DOI https://doi.org/10.1186/s12866-024-03346-w <https://doi.org/10.1186/s12866-024-03346-w>. https://doi.org/10.1186/s12866-024-03346-w 10.1186/s12866-024-03346-w
institution	Universiti Malaya
building	UM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaya
content_source	UM Research Repository
url_provider	http://eprints.um.edu.my/
topic	QH Natural history
spellingShingle	QH Natural history Tian, Xuechen Teo, Wee Fei Aaron Yang, Yixin Dong, Linyinxue Wong, Aloysius Chen, Li Ahmed, Halah Choo, Siew Woh Jakubovics, Nicholas S. Tan, Geok Yuan Annie Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity
description	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 9931(T) (= ATCC 17982(T) = DSM 43331(T) = CIP 104728(T) = CCUG 18309(T) = NCTC 14978(T) = CGMCC 1.90328(T)) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24(T) (= NCTC 14980(T) = CGMCC 1.90329(T)) 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 C24(T), 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.
format	Article
author	Tian, Xuechen Teo, Wee Fei Aaron Yang, Yixin Dong, Linyinxue Wong, Aloysius Chen, Li Ahmed, Halah Choo, Siew Woh Jakubovics, Nicholas S. Tan, Geok Yuan Annie
author_facet	Tian, Xuechen Teo, Wee Fei Aaron Yang, Yixin Dong, Linyinxue Wong, Aloysius Chen, Li Ahmed, Halah Choo, Siew Woh Jakubovics, Nicholas S. Tan, Geok Yuan Annie
author_sort	Tian, Xuechen
title	Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity
title_short	Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity
title_full	Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity
title_fullStr	Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity
title_full_unstemmed	Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity
title_sort	genome characterisation and comparative analysis of schaalia dentiphila sp. nov. and its subspecies, s. dentiphila subsp. denticola subsp. nov., from the human oral cavity
publisher	BioMed Central
publishDate	2024
url	http://eprints.um.edu.my/45214/ https://doi.org/10.1186/s12866-024-03346-w
_version_	1811682103664836608
score	13.211869

Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity

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