Complete Genome Sequence of Streptococcus ruminantium sp. nov. GUT-187T (=DSM 104980T =JCM 31869T), the Type Strain of S. ruminantium, and Comparison with Genome Sequences of Streptococcus suis Strains.

Streptococcus ruminantium sp. nov. of type strain GUT-187T, previously classified as Streptococcus suis serotype 33, is a recently described novel streptococcal species. This study was designed to determine the complete genome sequence of S. ruminantium GUT-187T using a combination of Oxford Nanopore and the Illumina platform, and to compare this sequence with the genomes of 27 S. suis representative strains. The genome of GUT-187T was 2,090,539 bp in size, with a GC content of 40.01%. This genome contained 1,961 predicted protein coding DNA sequences (CDSs); of these, 1,685 (85.9%) showed similarity with S. suis CDSs. Of the remaining 276 CDSs, 81 (29.3%) showed some degree of similarity with CDSs of other streptococcal species. The genome of GUT-187T contained no intact prophage. The numbers of prophages and CRISPR spacers, as well as the presence or absence of genes encoding CRISPR-associated proteins, differed in S. ruminantium and S. suis. A phylogenetic analysis indicates that GUT-187T may be outgroup to the S. suis strains in our sample, thereby justifying its classification as distinct species. Gene mapping indicated 10.2 times of massive genome rearrangements in average occurred between S. ruminantium and S. suis. There was no significant statistical difference in clusters of orthologous group distribution between S. ruminantium and S. suis.

Introduction

Streptococcus ruminantium is a recently described novel streptococcal species (Tohya et al., 2017). Although S. ruminantium was previously recognized to be Streptococcus suis serotype 33 (Tohya et al., 2017), several studies analyzing the taxonomic status of S. suis suggested that several serotype reference strains, including those for S. suis serotype 33, differed from the S. suis taxon, suggesting that these strains were not authentic S. suis (Tien le et al., 2013; Ishida et al., 2014; Arai et al., 2015). To further clarify that S. ruminantium and S. suis are distinct species, we sequenced the complete genome of the type strain S. ruminantium GUT-187T (=DSM 104980T=JCM 31869T) and compared its sequence with those of 27 S. suis representative strains.

Materials and Methods

Determination of the Whole Genome Sequence of S. ruminantium GUT-187T

The GUT-187T genome was prepared using enzymatic lysis methods as described previously (Nishijima et al., 2016) and subjected to MinION genome sequencing using a flow cell (R9.5) (Oxford NANOPORE). Libraries were prepared using Rapid sequencing kit R9 version (Oxford NANOPORE). Illumina sequencing was performed with Nextera XT to prepare a sequencing library, followed by MiSeq sequencing (Illumina), which yielded 301 bp pair end reads. Both procedures were performed according to the manufacturers’ instructions. Approximately 300 Mbp of Nanopore data and 598,228 pair end reads of Illumina were used for genome assembly.

Bioinformatics Analyses

Genome de novo assembly was performed using SPAdes (Esgleas et al., 2005) in hybrid and careful mode, resulting in two contigs. Gaps between contigs were filled by a standard PCR method using LATaq (Takara). Amplicons were sequenced by MiSeq, as described above. CDSs were identified and annotated by glimmer (Delcher et al., 2007), using commercial software (in silico Molecular Cloning; in silico biology, Japan). The genome sequence was registered at the DNA Data Bank of Japan (DDBJ) under accession number AP018400. Multi-locus sequence typing (MLST) was determined using S. suis MLST Databases (https://pubmlst.org/ssuis/; King et al., 2002). Prophages in the genomes were analyzed using PHAST (http://phast.wishartlab.com; Zhou et al., 2011). CRISPRs were detected using CRISPR finder (http://crispr.i2bc.paris-saclay.fr/Server; Grissa et al., 2007). Genome rearrangement maps were created using in silico Molecular Cloning software (in silico biology). The presence or absence of genes encoding CAS proteins in the genomes was analyzed using the TBlastX program and a custom streptococcal CAS protein database. Concatenated SNP sequences were aligned with MAFFT (Katoh et al. 2017). A Neighbor-Joining phylogenetic tree (Saitou and Nei 1987) was estimated using CLC genomics workbench (QIAGEN), a commercial software. The tree was midpoint rooted (Graur 2016). Gene mapping to analyze genome rearrangements and clusters of orthologous groups (COG) analysis was performed using in silico Molecular Cloning software (in silico biology). The proportions of COG categories were analyzed using CLC genomics workbench (QIAGEN).

Results

We utilized Oxford Nanopore and the Illumina platform to determine the complete genome sequence of GUT-187T. The hybrid assembly approach using data from both platforms was highly effective, as well as being less costly than other platforms.

The GUT-187T genome was 2,090,539 bp in size, with a GC content of 40.01%, comparable to those of the 27 S. suis representative strains in our study. The genome of GUT-187T contained 1,961 predicted protein coding DNA sequences (CDSs) (fig. 1, supplementary table S1, Supplementary Material online), comparable to the mean ± SD number of CDs in the 27 S. suis representative strains (1972.0 ± 88.4). Of the 1,961 CDSs in GUT-187T, 1,685 (85.9%) were homologous with CDSs of S. suis. Among the 276 remaining CDSs, 81 (29.3%) showed some degree of similarity with CDSs of other streptococcal species.

. 1.

—Circular representation of the genome of Streptococcus ruminantium sp. nov. GUT-187T. Circle 1 (outermost circle) indicates the distance from the putative origin of replication. Circle 2 shows annotated CDSs encoded on the forward (light blue) and reverse (yellow) chromosomal strands. The rRNA genes (green) are shown in circle 3. Circle 4 (innermost circle) shows the G + C content with greater and less than average (0.40) in blue and orange, respectively.

MLST of GUT-187T was unique when compared with those of the S. suis representative strains (supplementary table S1, Supplementary Material online). The GUT-187T genome contained no intact prophages and only one remnant of prophage, located in the 97,740–108,427 bp region. The numbers of prophages and CRISPR spacers, as well as the presence or absence of genes encoding CRISPR-associated proteins (CAS) proteins, differed between S. ruminantium and S. suis, with no associations between the presence or absence of CRISPR and CAS and the number of prophages although it is well known that CRISPR-CAS system counter-acts invasion of foreign genetic materials (supplementary table S1, Supplementary Material online; Marraffini and Sontheimer 2010).

The phylogenetic analysis in conjunction with midpoint rooting supports the hypothesis that GUT-187T belong to a spices other than S. suis (fig. 2). Notably, the S. suis strains harboring CAS clustered together in the phylogenetic tree and GUT-187T also harbored CAS.

. 2.

—Rooted phylogenetic tree of Streptococcus ruminantium and Streptococcus suis. The Neighbor-Joining phylogenetic tree was estimated using CLC genomics workbench (QIAGEN), a commercial software. Tip labels are aligned. The genetic distances between the major nodes and bootstrap values are shown. Strains harboring CRISPR-associated proteins (CAS) are indicated in boxes.

BLASTN analysis (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) using the complete genome sequence of GUT-187T as a query showed that the top 37 hits were S. suis, while the query coverage was around 50% (supplementary table S2, Supplementary Material online). When the genome sequence of S. suis 6407 (Accession # CP008921.1) was used as a query, the top 35 hits were S. suis strains and the query coverage ranged from 72% to 83% (data not shown), indicating a taxonomic difference between S. ruminantium and S. suis.

Mapping of genes in the GUT-187T genome against S. suis to analyze genome rearrangements showed that massive inversions had occurred at around 450 kbp and 1,550 kbp in all S. suis strains except strains NSUI060 and 90-1330 (supplementary table S3, Supplementary Material online). Detailed investigation of the inversion points indicated that number of inversions in the S. suis strains in comparison with GUT-187T are 10.2 ± 2.3 (mean ±SD, ranged from 6 to 15, supplementary table S3, Supplementary Material online). The inversion regions of S. ruminantium is different from the insertion point of prophage (97,740–108,427 bp region, locus_tag ranged SR187_0490 from to SR187_0525), and there are no obvious mobile genetic elements, such as insertion sequences or transposons in the inversion regions (data not shown). Thus, we are not able to show direct evidence how the rearrangement occurred.

The ratio of each category of COG was found to be relatively conserved in the S. ruminantium and S. suis strains (fig. 3). There were no significant differences in the proportions of COG categories between GUT-187 and S. suis strains or between CAS positive and negative strains (data not shown). COG categories J, L, G, and R and, to a lesser extent, COG categories M, E, and S, were relatively abundant among the strains.

. 3.

—Comparison of GUT-187T with the Streptococcus suis representative strains using clusters of orthologous groups (COG). Category abbreviations: J, translation, ribosomal structure, and biogenesis; K, transcription; L, replication, recombination, and repair; D, cell cycle control, cell division, and chromosomal partitioning; V, defense mechanisms; T, signal transduction mechanisms; M, cell wall/membrane/envelope biogenesis; N, cell motility; U, intracellular trafficking, secretion, and vesicular transport; O, posttranslational modification, protein turnover, and chaperones; C, energy production and conversion; G, carbohydrate transport and metabolism; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; P, inorganic ion transport and metabolism; Q, biosynthesis, transport, and catabolism of secondary metabolites; R, general function predicted only; S, function unknown. Streptococcus suis SS2-1 was omitted from this analysis because its genome information had not been annotated at the time of analysis.

In conclusion, the complete genome sequence of S. ruminantium further supports its classification as a distinct species. The sequence data may also enable the development of methods to analyze its epidemiology, as well as rapid diagnostic assays.

Supplementary Material

Supplementary data are available at Genome Biology and Evolution online.

Click here for additional data file.