Complete genome sequence of Streptococcus hominis isolated from subgingival biofilm

Abstract

Objective

Streptococcus hominis is a recently described species within the genus Streptococcus, yet its genomic characteristics remain poorly understood, particularly in the context of the oral microbiome. Previously, only two complete genomes from non-oral sources were available. To address this gap, we sequenced and analyzed S. hominis strain KHUD_010, isolated from the subgingival biofilm of a healthy Korean adult.

Data description

Genomic DNA from KHUD_010 was extracted and confirmed as S. hominis by 16 S rRNA gene sequencing. Whole-genome sequencing using the PacBio Sequel II platform generated 135,974 HiFi reads (N50: 10,345 bp). De novo assembly with SMRT Link v11.0 produced a single circular chromosome of 1,883,665 bp with 39.04% GC content. Annotation via the NCBI Prokaryotic Genome Annotation Pipeline predicted 1,793 protein-coding genes, four rRNA operons (5 S, 16 S, 23 S), and 120 tRNAs. BUSCO analysis showed 99.1% completeness. Comparative genomics with NSJ-17 and UMB6992B revealed 1,416 core, 223 dispensable, and 398 strain-specific gene clusters. KHUD_010 harbored 18 unique gene clusters comprising 20 genes, mostly assigned to COG category L (replication, recombination, repair). This high-quality genome expands the genomic landscape of S. hominis and provides a valuable reference for future studies on oral microbiome diversity and host adaptation.

Objective

The human oral cavity harbors a complex microbial ecosystem in which Streptococcus species play key roles in both maintaining oral health and contributing to disease [1]. These bacteria are among the earliest tooth colonizers and are involved in biofilm formation, nutrient metabolism, and immune modulation [1, 2]. While species such as S. mitis, S. oralis, S. sanguinis, and S. mutans have been well characterized [3], large-scale metagenomic studies employing NGS have revealed a broader diversity of oral streptococci, including previously uncultured and uncharacterized taxa [4–7]. Although Streptococcus remains one of the most dominant genera in the oral microbiota, many of its constituent species remain genomically undefined, limiting our understanding of their ecological functions and clinical relevance [8].

Streptococcus hominis is a recently described species with only two complete genomes currently available, both from extra-oral sources (fecal and urinary isolates). To date, no oral isolates have been sequenced. In this study we report the complete genome sequence of S. hominis strain KHUD_010, isolated from the subgingival biofilm of a healthy Korean adult. Comparative analysis with the two existing strains, NSJ-17 (feces, China) [9] and UMB6992B (urine, USA) [10], provides insight into species-level diversity and strain-specific genomic traits. This work expands the genomic repertoire of S. hominis and lays the groundwork for future studies of its role in the oral microbiome.

Data description

The S. hominis strain KHUD_010 was isolated from the subgingival biofilm of a healthy Korean female adult using Mitis Salivarius agar under anaerobic conditions at 37°C. Genomic DNA was extracted using the Wizard HMW DNA Extraction Kit (Promega, USA). Species identification was confirmed by sequencing the full-length 16S rRNA gene (~ 1.5 kb) amplified with universal bacterial primers (forward: 5’-AGAGTTTGATCCTGGCTCAG-3’; reverse: 5’-GGTTACCTTGTTACGACTT-3’) [11] and performing a BLAST search against the GenBank database.

Whole-genome sequencing was conducted using the PacBio Sequel II platform. A Single-Molecule Real-Time (SMRT) bell library was prepared according to the manufacturer’s protocol (Pacific Biosciences). One SMRT cell generated 135,974 HiFi reads, with an average read length of 9,396 bp and an N50 of 10,345 bp (Data file 1). De novo assembly was performed using the Microbial Genome Analysis pipeline in SMRT Link v11.0 (https://www.pacb.com/support/software-downloads/) with default parameters. Annotation was carried out using the NCBI Prokaryotic Genome Annotation Pipeline.

The complete genome of S. hominis KHUD_010 consists of a single circular chromosome of 1,883,665 bp with a G + C content of 39.04% (Data file 2 and 3). It encodes 1,793 protein-coding genes, four rRNA operons (5 S, 16 S, 23 S) and 120 tRNAs. Genome completeness was evaluated using Benchmarking Universal Single-Copy Orthologs (BUSCO) v5.8.2 [12] with the “bacteria_odb12” dataset (3,130 genomes, 116 BUSCOs), yielding a completeness score of 99.1% (Data file 4). Based on the NCBI taxonomy check, strain KHUD_010 showed 99.94% ANI and 99.86% coverage with S. hominis (GCA_014287335.1), supporting its species-level identification. Comparative genomic analysis was conducted using two publicly available S. hominis genomes: NSJ-17 (feces, China) and UMB6992B (urine, USA). Orthologous clustering identified 1,416 core gene clusters shared among the three strains, 223 dispensable clusters, and 398 strain-specific clusters (Data file 5). Strain KHUD_010 harbored 18 unique gene clusters containing 20 genes (Data file 6). Functional annotation of these genes revealed enrichment in COG category L (replication, recombination, and repair), with additional genes mapped to categories S (function unknown), V (defense mechanisms), and D (cell cycle control). These features suggest the presence of genomic adaptations relevant to survival in the subgingival environment.

The genome of KHUD_010 represents the first complete genome of an oral S. hominis isolate. It significantly expands the limited genomic repertoire of this species and provides a valuable resource for investigating strain-level diversity, host-specific adaptation, and the ecological roles of streptococci in the oral microbiome. As the third complete genome available for S. hominis, it enables broader comparative genomic analyses and functional studies of this understudied species. Table 1 summarizes Data files 1–6 and Datasets 1–2.

Table 1.

Overview of data files/data sets

Label	Name of data file/data set	File types (file extension)	Data repository and identifier (DOI or accession number)
Data file 1	HiFi read length distribution of Streptococcus hominis KHUD_010	Portable Data Format file (.pdf)	Figshare (10.6084/m9.figshare.29527361.v1) [13]
Data file 2	Genome features of Streptococcus hominis KHUD_010	Office Open XML Spreadsheet file (.xlsx)	Figshare (10.6084/m9.figshare.29527409.v2) [14]
Data file 3	Circular genome map of Streptococcus hominis KHUD_010 with annotated features	Portable Data Format file (.pdf)	Figshare (10.6084/m9.figshare.29527520.v1) [15]
Data file 4	Short BUSCO summary	Portable Data Format file (.pdf)	Figshare (10.6084/m9.figshare.29527457.v3) [16]
Data file 5	Upset plot of orthologous gene clusters among three Streptococcus hominis strains (KHUD_010, NSJ_17, and UMB6992B)	Portable Data Format file (.pdf)	Figshare (10.6084/m9.figshare.29527553.v1) [17]
Data file 6	KHUD_010 strain: 18 unique gene clusters containing 20 genes	Office Open XML Spreadsheet file (.xlsx)	Figshare (10.6084/m9.figshare.29527433.v5 [18]
Data set 1	Sequencing read dataset of Streptococcus hominis KHUD_010	Fastq file (.fastq.gz)	NCBI Sequence Read Archive (https://identifiers.org/ncbi/insdc.sra:SRX28051166)
Data set 2	Genome assembly of Streptococcus hominis KHUD_010	FASTA/GenBank/ASN.1	NCBI Genome assembly (https://identifiers.org/ncbi/insdc.gca:GCA_040207525.1) [20]

Limitation

None.

Abbreviations

NGS

Next Generation Sequencing

BLAST

Basic Local Alignment Search Tool

SMRT

Single-Molecule Real-Time

NCBI

National Center for Biotechnology Information

BUSCO

Benchmarking Universal Single-Copy Orthologs

COG

Clusters of Orthologous Groups of proteins

Authors’ contributions

JHM, KHK and HKK conceived and designed the experiments. SBY and SWK performed strain isolation, cultivation and DNA extraction. DK and JHL performed the genome analysis. The manuscript was written by SBY and DK and revised by KHK and HKK. The author(s) read and approved the final manuscript.

Funding

This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT, RS-2023-00280791, RS-2024-00358942), Korea Basic Science Institute (National research Facilities and Equipment Center) grant funded by the Korea government (MSIT, RS-2024-00404660).

Data availability

The raw sequencing reads have been deposited in the NCBI Sequence Read Archive (SRA) under accession number SRX28051166 (Data Set 1) [19]. The genome assembly of the S. hominis KHUD_010 was submitted to NCBI GenBank and are available under the accession number GCF_040207525.1 (Data set 2) [20].

Declarations

Ethics approval and consent to participate

This study was approved by the Ethical Committee of the Kyung Hee University Dental Hospital (KHD IRB 1606-5) and was conducted in accordance with the Helsinki Declaration of 1975, as revised in 2013. All subjects provided informed consent.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.