Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child's oropharynx

Re-evaluation of boundaries of Streptococcus mitis and Streptococcus oralis and demonstration of multiple later synonyms of Streptococcus mitis, Streptococcus oralis and Streptococcus thalassemiae: description of Streptococcus mitis subsp. carlssonii subsp. nov. and emended description of Streptococcus mitis

The commensal species Streptococcus mitis and Streptococcus oralis are genetically diverse to a degree that challenges traditional definitions of species. This causes automatic identification based on DNA sequences or cellular extract profiles problematic. Based on an initial analysis of 266 genomes, we subjected a subset of 100 representative genomes to detailed phylogenetic, pairwise distance and gene pattern analyses. S. mitis and S. oralis constitute a continuum of clones that are genetically unique. To recognize most isolates as separate species is biologically and practically meaningless. We recommend bending the proposed similarity borders to accommodate the biological reality. Accordingly, we conclude that Streptococcus toyakuensis, Streptococcus chosunensis, Streptococcus gwangjuensis, Streptococcus humanilactis and Streptococcus hohhotensis are later heterotypic synonyms of S. mitis. Type strains of effectively but not validly published 'Streptococcus shenyangsis', 'Streptococcus symci' and 'Streptococcus vulneris' belong in S. mitis. Streptococcus parapneumoniae and Streptococcus nakanonensis are later synonyms of Streptococcus thalassemiae. Streptococcus downii is a later synonym of Streptococcus oralis subsp. dentisani, and the type of 'Streptococcus halitosis' belongs in Streptococcus oralis subsp. tigurinus. The genome sequence of the type of the recently proposed 'Streptococcus bouchesdurhonensis' is based on a mixed culture. Phylogenetic results and the pattern of presence/absence of accessory genes support the distinction of two subspecies of S. mitis, i.e. Sreptococcus mitis subsp. mitis subsp. nov. (type strain is NCTC 12261T) and Sreptococcus mitis subsp. carlssonii subsp. nov. (type strain is SK608=CCUG 55085T=LMG 33510T). The special population structure of the Streptococcus mitis-pneumoniae-pseudopneumoniae-thalassemiae complex renders automated classification of isolates based on average nucleotide identity or digital DNA-DNA hybridization values problematic. As an alternative, for initial taxonomic assignment, we present a whole-genome phylogeny-based method that enables phylogenetic comparison of new isolates in the context of a set of 117 well-characterized reference strains assigned to the Mitis/Sanguinis group.

A respiratory Streptococcus strain inhibits Acinetobacter baumannii from causing inflammatory damage through ferroptosis

BACKGROUND

Microecological equilibrium is essential for human health. Previous research has demonstrated that Streptococcus strain A, the main bacterial group in the respiratory tract, can suppress harmful microbes and protect the body. In this study, Streptococcus strain D19T was isolated from the oral and pharyngeal cavities of healthy children. Its antibacterial mechanism against Acinetobacter baumannii was examined, as well as its potential to prevent inflammatory damage to cells. We evaluated the effect of the fermentation conditions of D19T on inhibition of Acinetobacter baumannii growth; Isolation and purification of antibacterial active components of strain D19T and molecular mechanism of inhibition of Acinetobacter baumannii; Molecular mechanism of D19T antibacterial protein reversing cellular inflammatory injury induced by Acinetobacter baumannii.

RESULTS

The supernatant of fermentation broth of Streptococcus D19T was the active component against Acinetobacter baumannii, but the bacteria had no antibacterial activity. The supernatant of D19T fermentation broth was precipitated by (NH4)2SO4 solution, and the protein was the active antibacterial component. After gel filtration chromatography and anion gel filtration chromatography, the molecular weight of antibacterial protein was 53kD. D19T antibacterial protein can improve cell membrane permeability, limit extracellular soluble protein release, inhibit Acinetobacter baumannii biofilm formation, and prevent Acinetobacter baumannii adhesion. Acinetobacter baumannii induces inflammatory damage to respiratory cells via ferroptosis, and the D19T antibacterial protein can counteract this damage, protecting the respiratory tract.

CONCLUSION

Streptococcus strain D19T, as a potential probiotic, inhibits the growth of Acinetobacter baumannii and the inflammatory damage of respiratory cells, playing a protective role in human respiratory health.

Molecular characterization of a novel putative pathogen, Streptococcus nakanoensis sp. nov., isolated from sputum culture

Reports of novel species of α-hemolytic Streptococcus have increased recently. However, limited information exists regarding the pathogenicity of these species, with the exception of Streptococcus pneumoniae and Streptococcus pseudopneumoniae. In this study, a quinolone-resistant α-Streptococcus strain, MTG105, was isolated from the sputum of a patient with pneumonia. This strain was first identified as S. pneumoniae at the hospital laboratory; however, it exhibited unique genetic features upon further analysis. Digital DNA-DNA hybridization and average nucleotide identity based on BLAST values from whole-genome sequencing revealed MTG105 to be a novel species closely related to S. pseudopneumoniae. Although MTG105 carried two copies of the pneumolysin gene, similar to S. pseudopneumoniae, this isolate exhibited susceptibility to optochin under both aerobic and 5% CO2 conditions. Notably, no biochemical features could be used to definitively identify this species. In an infection assay using organotypic lung tissue models, MTG105 induced epithelial damage comparable to that of S. pneumoniae and S. pseudopneumoniae, possibly suggesting its potential as a pathogenic α-Streptococcus. The natural transformation abilities of Streptococcus species facilitate their exchange of genes within the same genus, resulting in the existence of species with increasingly more diverse genome structures. Therefore, the identification of this species highlights the importance of monitoring the emergence of novel species exhibiting virulence and/or multidrug resistance. This isolate was proposed as a novel species, designated Streptococcus nakanoensis sp. nov. The type strain was MTG 105T (= JCM 35953T = CCUG 76894T).

IMPORTANCE

The genus Streptococcus encompasses a wide range of bacteria with more than 60 species. Recently, there has been a notable increase in reports of novel species of α-Streptococcus based on genomic analysis data. However, limited information exists regarding the pathogenicity of these species. In this study, a quinolone-resistant α-hemolytic Streptococcus strain, MTG105, was isolated from a patient with pneumonia. Genetic analysis revealed that this species was a novel species closely related to S. pseudopneumoniae. In an infection assay using organotypic lung tissue models, MTG105 induced epithelial damage comparable to that caused by S. pneumoniae and S. pseudopneumoniae, strongly suggesting its potential as a pathogenic α-Streptococcus. The natural transformation abilities of Streptococcus species facilitate gene exchange within the same genus, leading to the emergence of species with increasingly diverse genome structures. Therefore, the identification of this species underscores the importance of monitoring the emergence of novel species exhibiting virulence and/or multidrug resistance.

Streptococcus taoyuanensis sp. nov., a Novel Species Isolated from a Patient with Bacteremia

Streptococcus spp. are important opportunistic pathogen of bacteremia in both immunocompetent and immunosuppressed patients. A streptococcal strain, designated ST2T, was isolated from the blood specimen of a bacteremic patient. Comparative analyses of 16S rRNA, rpoB and groEL gene sequences demonstrated that the novel strain ST2T is a member of the genus Streptococcus. Based on of 16S rRNA gene sequence similarities, the type strains of Streptococcus (S.) parasanguinis (99.2%), S. ilei (98.8%), S. oralis subsp. oralis (97.6%), S. australis (97.5%) and S. sanguinis (97.5%) were the closest neighbours to strain ST2T. The housekeeping gene sequences (rpoB and groEL) similarities of strain ST2T to these closely related type strains were 80.4-97.4%, respectively. The complete draft genome of strain ST2T consisted of 2,155,906 bp with a G + C content of 42.0%. Strain ST2T has an average nucleotide identity (ANI) value of 94.1 and 81.3% with S. parasanguinis ATCC 15912T and S. ilei I-G2T, respectively. The highest in silico DNA-DNA hybridization value with respect to the closest species S. parasanguinis was 55.6%, below the species cut-off of 70% hybridization. The primary cellular fatty acids of strain ST2T were C16:0, C18:1 ω9c, C18:0 and C14:0. Based on biochemical criteria and molecular genetic evidence, it is proposed that strain ST2T be assigned to a new species of the genus Streptococcus as Streptococcus taoyuanensis sp. nov. The type strain of Streptococcus taoyuanensis is ST2T (=NBRC 115928T = BCRC 81374T) as the type strain.

Identification and characterization of a novel α-haemolytic streptococci, Streptococcus parapneumoniae sp. nov., which caused bacteremia with pyelonephritis

OBJECTIVES

We report a case of bacteremia with pyelonephritis in an adult male with an underlying disease caused by α-hemolytic streptococci. α-Hemolytic streptococci were isolated from blood, but it was challenging to identify its species. This study aimed to characterize the causative bacterium SP4011 and to elucidate its species.

METHODS

The whole-genome sequence and biochemical characteristics of SP4011 were determined. Based on the genome sequence, phylogenetic analysis was performed with standard strains of each species of α-hemolytic streptococci. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were calculated.

RESULTS

SP4011 showed optochin susceptibility and bile solubility, but did not react with pneumococcal omni antiserum. Phylogenetic analysis of the whole-genome sequence showed that SP4011 clustered with S. pneumoniae and S. pseodopneumoniae and was most closely related to S. pseodopneumoniae. Genomic analysis revealed that ANI and dDDH values between SP4011 and S. pseodopneumoniae were 94.0 % and 56.0 %, respectively, and between SP4011 and S. pneumoniae were 93.3 % and 52.2 %, respectively. Biochemical characteristics also showed differences between SP4011 and S. pseodopneumoniae and between SP4011 and S. pneumoniae. These results indicate that SP4011 is a novel species.

CONCLUSION

Our findings indicate that SP4011 is a novel species of the genus Streptococcus. SP4011 has biochemical characteristics similar to S. pneumoniae, making it challenging to differentiate and requiring careful clinical diagnosis. This isolate was proposed to be a novel species, Streptococcus parapneumoniae sp. nov. The strain type is SP4011T (= JCM 36068T = KCTC 21228T).

Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups

IMPORTANCE

The role of the upper respiratory tract (URT) microbiome in predicting lung health has been documented in several studies. The dysbiosis in COVID patients has been associated with disease outcomes by modulating the host immune system. However, although it has been known that different SARS-CoV-2 variants manifest distinct transmissibility and mortality rates in human populations, their effect on the composition and diversity of the URT microbiome has not been studied to date. Unlike the older variant (Delta), the newer variant (Omicron) have become more transmissible with lesser mortality and the symptoms have also changed significantly. Hence, in the present study, we have investigated the change in the URT microbiome associated with Delta and Omicron variants and identified variant-specific signatures that will be useful in the assessment of lung health and can be utilized for nasal probiotic therapy in the future.

Streptococcus strain D19T as a probiotic candidate to modulate oral health

BACKGROUND

As probiotics protect host cells, they are used to treat bacterial infections. It has been indicated that probiotics may prevent or reduce the attachment of pathogens to host cells. In this study, Streptococcus strain D19T was isolated from the oropharynx of a healthy child, and its adhesion performance and Staphylococcus aureus adhesion inhibition effect were analysed using human bronchial epithelial (16-HBE) cells, as an in vitro cell model. We evaluated the probiotic properties of the D19T strain based on its acid-base, bile salt, and lysozyme tolerance; antibacterial activity; cytotoxicity; antibiotic sensitivity; in vitro adhesion to 16-HBE cells; and competitive, exclusion, and displacement effects against S. aureus.

RESULTS

Streptococcus strain D19T showed tolerance to a PH range of 2-5 and 0.5-1% bile. However, it was more tolerant to 0.5% bile than to 1% bile. The strain also demonstrated an ability to adapt to maladaptive oropharyngeal conditions (i.e., tolerating 200 µg/mL lysozyme). It was resistant to 0.8 mM H2O2. The results also demonstrated that D19T exhibited inhibitory activities against various common pathogenic bacteria. Furthermore, D19T was not toxic to 16-HBE cells at different multiplicities of infection and was sensitive to most antibiotics tested. The adhesion rate of D19T cells to 16-HBE cells was 47% ± 1.2%, which was significantly higher than that of S. aureus to 16-HBE cells. The competition, exclusion, and displacement assay results showed that D19T has good inhibitory effect against S. aureus adhesion.

CONCLUSIONS

The present study revealed that Streptococcus strain D19T has the potential to be developed as a respiratory microbiota preparations.

Dual functions of discoidinolysin, a cholesterol-dependent cytolysin with N-terminal discoidin domain produced from Streptococcus mitis strain Nm-76

Background

Some strains of Streptococcus mitis exhibit β-hemolysis due to the β-hemolytic activity of cholesterol-dependent cytolysin (CDC). Recently, a gene encoding an atypical lectinolysin-related CDC was found in S. mitis strain Nm-76. However, the product of this gene remains uncharacterized. We aimed to characterize this atypical CDC and its molecular functions and contribution to the pathogenicity of S. mitis strain Nm-76.

Methods

Phylogenetic analysis of the CDC gene was conducted based on the web-deposited information. The molecular characteristics of CDC were investigated using a gene-deletion mutant strain and recombinant proteins expressed in Escherichia coli.

Results

The gene encoding CDC found in Nm-76 and its homolog are distributed among many S. mitis strains. This CDC is phylogenetically different from other previously characterized CDCs, such as S. mitis-derived human platelet aggregation factor (Sm-hPAF)/lectinolysin and mitilysin. Because this CDC possesses an additional N-terminal domain, including a discoidin motif, it was termed discoidinolysin (DLY). In addition to the preferential lysis of human cells, DLY displayed N-terminal domain-dependent facilitation of human erythrocyte aggregation and intercellular associations between human cells.

Conclusion

DLY functions as a hemolysin/cytolysin and erythrocyte aggregation/intercellular association molecule. This dual-function DLY could be an additional virulence factor in S. mitis.

Standardized studies of the oral microbiome: From technology-driven to hypothesis-driven

The microbiome is in a symbiotic relationship with the host. Among the microbial consortia in the human body, that in the oral cavity is complex. Instead of repeatedly confirming biomarkers of oral and systemic diseases, recent studies have focused on a unified clinical diagnostic standard in microbiology that reduces the heterogeneity caused by individual discrepancies. Research has also been conducted on other topics of greater clinical importance, including bacterial pathogenesis, and the effects of drugs and treatments. In this review, we divide existing research into technology-driven and hypothesis-driven, according to whether there is a clear research hypothesis. This classification allows the demonstration of shifts in the direction of oral microbiology research. Based on the shifts, we suggested that establishing clear hypotheses may be the solution to major research challenges.

Streptococcus strain C17T as a potential probiotic candidate to modulate oral health

In the microbiome, probiotics modulate oral diseases. In this study, Streptococcus strain C17^T was isolated from the oropharynx of a five-year-old healthy child, and its potential probiotic properties were analysed using human bronchial epithelial cells (16-HBE) used as an in vitro oropharyngeal mucosal model. The results demonstrated that the C17^T strain showed tolerance to moderate pH ranges of 4-5 and 0.5-1% bile. However, it was more tolerant to 0.5% bile than 1% bile. It also demonstrated an ability to accommodate maladaptive oropharyngeal conditions (i.e., tolerating lysozyme at 200 μg mL-1) . It was also resistant to hydrogen peroxide at 0.8 mM . In addition, we found out that the strain possesses inhibitory activities against various common pathogenic bacteria. Furthermore, C17^T was not cytotoxic to 16-HBE cells at different multiplicities of infection. Scanning electron microscopy disclosed that C17^T adhesion to 16-HBE cells. Competition, exclusion, and displacement assays showed that it had good anti-adhesive effect against S. aureus. The present study revealed that Streptococcus strain C17^T is a potentially efficacious oropharyngeal probiotic.