Veillonella orientalis sp. nov., an anaerobic Gram-stain-negaitve coccus isolated from saliva of a Thai child

Izumi Mashima-Usami; Citra F Theodorea; Kiyoshi Murata; Boonyanit Thaweboon; Sroisiri Thaweboon; Futoshi Nakazawa

doi:10.1016/j.anaerobe.2024.102921

Veillonella orientalis sp. nov., an anaerobic Gram-stain-negaitve coccus isolated from saliva of a Thai child

Anaerobe. 2024 Nov 22:102921. doi: 10.1016/j.anaerobe.2024.102921. Online ahead of print.

Authors

Izumi Mashima-Usami¹, Citra F Theodorea², Kiyoshi Murata³, Boonyanit Thaweboon⁴, Sroisiri Thaweboon⁵, Futoshi Nakazawa²

Affiliations

¹ Department of Oral Medical Science, School of Dentistry, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611 Japan. Electronic address: i-mashima@den.ohu-u.ac.jp.
² Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Salemba Raya No.4, Jakarta Pusat 10430 Indonesia.
³ Department of Pharmacognosy and Natural Resource Science, School of Pharmaceutical Science, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima 963-8611 Japan.
⁴ Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, 6 Yothi Street, Bangkok 10400 Thailand; Department of Oral Biosciences and Dental Public Health, International College of Dentistry, Walailak University, 87 Ranong 2 Rd Thanon Nakhon Chai Si, Bangkok 10300 Thailand.
⁵ Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, 6 Yothi Street, Bangkok 10400 Thailand.

PMID: 39581455
DOI: 10.1016/j.anaerobe.2024.102921

Abstract

Objective: The genus Veillonella is one of the major and important constitutions of the oral microbiome. A novel anaerobic, Gram-strain-negative coccus belonging to the genus Veillonella was isolated from the saliva of a Thai child coming from the east of Thailand. In the present study, the characterization of one strain, S12025-13^T is described with the comparison of established species of the genus Veillonella and proposed a novel oral species of the genus Veillonella.

Methods: Strain S12025-13^T was conclusively identified using phenotypic, phylogenetic, genomic and biochemical approach. In phylogenetic analysis, multi-locus species trees (MLST) analysis was also conducted in this study.

Results: The strain S12025-13^T showed typical phenotypic characteristics of members of the genus Veillonella. Under anaerobic conditions, the strain produced acetic acid and propionic acid as metabolic end products in a trypticase-yeast extract-heamin medium containing 1% (w/v) glucose, 1% (w/v) fructose and 1% (v/v) sodium lactate. Sequencing of their 16S rRNA genes confirmed that it belongs to the genus Veillonella. Comparative analysis of the 16S rRNA, dnaK and rpoB gene sequences indicated that phylogenetically the strain comprised a distinct novel branch within the genus Veillonella. The novel strain showed 99.77, 97.29, and 99.02% similarity to partial 16S rRNA, dnaK and rpoB gene sequencing, respectively, to the type strains of the most closely related species. In MLST (selected 79 genes) analysis, strain S12025-13^T formed a distinct taxon with robust bootstrap support (100%) within the genus Veillonella. Furthermore, strain S12025-13^T shared the highest average nucleotide identity (ANI) value (95.97%) with the type strain of the most closely related species, "Veillonella faecalis" which is not validly published under the International Code of Nomenclature of Prokaryotes (ICNP). Likewise, strain S12025-13^T showed the highest digital DNA-DNA hybridization (dDDH) value (65.00%) with the type strain of "V. faecalis". In addition, strain S12025-13^T formed a distinct branch in this clade with a bootstrap value of 72% with Veillonella nakazawae and 51% with "V. faecalis" related species of the genus Veillonella in the genome based phylogenetic tree.

Conclusion: The novel strain could be discriminated from previously reported species of the genus Veillonella based on partial dnaK gene sequencing, MLST analysis, ANI and dDDH values, and genome-based phylogeny. Based on these observations, this strain represents a novel species, for which the name Veillonella orientalis sp., nov. is proposed. The type strain is S12025-13^T (= JCM 33967^T = CCUG 74596^T).

Keywords: Oral anaerobic Gram-stain-negative coccus; Saliva; Veillonella orientalis sp. nov.; a Thai child.