Streptococcus gwangjuense sp. nov., Isolated from Human Pericoronitis

Streptococcus taonis sp. nov., a novel bacterial species isolated from a blood culture of a patient

One Gram stain-positive, catalase-negative, α-hemolytic, chain-forming or paired cocci, designated ST22-14T, was isolated from a blood culture of a child with suspected infection. The results of 16S rRNA gene sequences analyses showed that the most closely related species to strain ST22-14T were "Streptococcus vulneris" DM3B3T (99.2%), Streptococcus mitis NCTC 12261T (99.0%), "Streptococcus gwangjuense" ChDC B345T, (99.0%), Streptococcus oralis subsp. dentisani 7747T (99.0%), Streptococcus downii CECT 9732T (99.0%), and Streptococcus infantis ATCC 700779T (98.9%). The genome of strain ST22-14T consists of 2,053,261 bp with a G + C content of 39.4%. Average nucleotide identity values between strain ST22-14T and Streptococcus mitis NCTC 12261T or other five species were from 82.2 to 88.0%. In silico DNA-DNA hybridization of ST22-14T showed an estimated DNA reassociation value of 34.6% with the closest species. The main cellular fatty acids of strain ST22-14T were 16:0, 18:0, 14:0, 18:1ω7c and 18:1ω6c. Based on these results, strain ST22-14T should be classified as a novel species of genus Streptococcus, for which the name Streptococcus taonis sp. nov. is proposed (type strain ST22-14T = NBRC 116002T = BCRC 81402T).

Performance assessment of the Bruker Biotyper MALDI-TOF MS for the identification of difficult-to-identify viridans group streptococci

Differentiating Streptococcus pneumoniae among nonpneumococcal viridans group streptococci (VGS) is challenging in conventional laboratories. Therefore, we aimed to evaluate the performance of the latest Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system in identifying VGS by comparing the results to those of the specific gene sequencing approach. Clinical isolates were initially identified using the BD Phoenix system to identify Streptococcus species. The optochin test was used to distinguish nonpneumococcal VGS from S. pneumoniae. The species of individual reference strains and clinical isolates were determined by comparing the sequences of the 16S rDNA, gyrB, sodA, groESL, or coaE genes with those in the GenBank sequence databases. We evaluated the performance of the Bruker Biotyper MALDI-TOF MS in VGS identification using two different machines with three databases. We collected a total of 103 nonpneumococcal VGS and 29 S. pneumoniae blood isolates at a medical center in northern Taiwan. Among these isolates, only seven could not be identified at the species level by the specific gene sequencing approach. We found that none of the nonpneumococcal VGS isolates were misidentified as pneumococci by the latest Biotyper system, and vice versa. However, certain strains, especially those in the mitis and bovis groups, could still not be correctly identified. The latest Bruker Biotyper 4.1 (DB_10833) showed significant improvement in identifying VGS strains. However, a specific gene sequencing test is still needed to precisely differentiate the species of strains in the mitis and bovis groups.

Characterisation of human milk bacterial DNA profiles in a small cohort of Australian women in relation to infant and maternal factors

Human milk is composed of complex microbial and non-microbial components that shape the infant gut microbiome. Although several maternal and infant factors have been associated with human milk microbiota, no study has investigated this in an Australian population. Therefore, we aimed to investigate associations between human milk bacterial composition of Australian women and maternal factors (body mass index (BMI), mode of delivery, breast pump use, allergy, parity) and infant factors (sex, mode of feeding, pacifier use, and introduction of solids). Full-length 16S rRNA gene sequencing was used to characterise milk bacterial DNA profiles. Milk from mothers with a normal BMI had a higher relative abundance of Streptococcus australis than that of underweight mothers, while milk from overweight mothers had a higher relative abundance of Streptococcus salivarius compared with underweight and obese mothers. Mothers who delivered vaginally had a higher relative abundance of Streptococcus mitis in their milk compared to those who delivered via emergency caesarean section. Milk of mothers who used a breast pump had a higher relative abundance of Staphylococcus epidermidis and Streptococcus parasanguinis. Milk of mothers whose infants used a pacifier had a higher relative abundance of S. australis and Streptococcus gwangjuense. Maternal BMI, mode of delivery, breast pump use, and infant pacifier use are associated with the bacterial composition of human milk in an Australian cohort. The data from this pilot study suggests that both mother and infant can contribute to the human milk microbiome.

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.

Streptococcus bouchesdurhonensis sp. nov. isolated from a bronchoalveolar lavage of a patient with pneumonia

Strain Marseille-Q6994 was isolated from a 72-year-old patient with pneumonia from Bouches-du-Rhône department, in France. Cells were Gram positive, non-motile, catalase and oxidase-negative cocci. The major fatty acids were hexadecanoic (47.4%) and tetradecanoic acids (28.3%). 16S rRNA gene sequence comparison suggested that strain Marseille-Q6994 was affiliated to the Streptococcus genus. GroEL phylogenetic analysis separated strain Marseille-Q6994 in a distinct branch from the closely related Streptococcus-type strains with standing in nomenclature. Whole genome sequencing-based methods (OrthoAverage Nucleotide Identity, digital DNA-DNA hybridization and pangenome analysis) supported the classification of the strain into a novel species. Therefore, based on the phenotypic, genomic, and phylogenetic analyses, we propose the name Streptococcus bouchesdurhonensis sp. nov for which strain Marseille-Q6994^T (CSUR Marseille-Q6994 = DSMZ 113892) is the type strain.

Streptococcus humanilactis sp.nov., isolated from healthy nursing mother's breast milk

Two bacterial strains were isolated from the breast milk of two healthy nursing mothers. The isolates were Gram-positive, catalase-negative, coccus-shaped, chain-forming organisms. Analysis of the 16S rRNA gene sequences of strain IMAU99125^T shared 99.7 and 99.6% similarity with Streptococcus mitis ATCC 49456 ^T and Streptococcus pseudopneumoniae ATCC BAA-960 ^T, respectively. The nearly complete 16S rRNA gene sequences of IMAU99125^T and IMAU99674 strains were very closely related (with only 0.06% difference between them). Sequence analysis of the gyrB and rpoB genes also indicated that IMAU99125^T was closely related to S. mitis ATCC 49456 ^T (94.7% and 97.1%, respectively) and S. pseudopneumoniae ATCC BAA-960 ^T (94.4% and 97.1%, respectively). Average nucleotide identity (ANI) values between strain IMAU99125^T and S. mitis ATCC 49456 ^T and S. pseudopneumoniae ATCC BAA-960 ^T, were 93.3% and 92.7%, respectively. Genome-to-genome distance (GGD) values between strain IMAU99125^T and S. mitis ATCC 99125 ^T and S. pseudopneumoniae ATCC BAA-960 ^T were 53.4% (50.7-56.0) and 50.4% (47.7-53.0), respectively. The major fatty acids of the strain were C_16:0 (51.4%). On the basis of the results of phenotypic and phylogenetic analyses, we propose that the two strains be classified as representing a novel species of the genus Streptococcus, namely Streptococcus humanilactis sp.nov. The type strain is IMAU99125^T (= GDMCC 1.1876 ^T = KCTC 21157 ^T). The genome of Streptococcus humanilactis sp. nov. is comprised of 2,027,143 bp. The DNA G + C content of the strain is 40.0 mol%.

Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci

Streptococci form a wide group of bacteria and are involved in both human and animal pathologies. Among pathogenic isolates, differences have been highlighted especially concerning their adaptation and virulence profiles. CRISPR-Cas systems have been identified in bacteria and many streptococci harbor one or more systems, particularly subtypes I-C, II-A, and III-A. Since the demonstration that CRISPR-Cas act as an adaptive immune system in Streptococcus thermophilus, a lactic bacteria, the diversity and role of CRISPR-Cas were extended to many germs and functions were enlarged. Among those, the genome editing tool based on the properties of Cas endonucleases is used worldwide, and the recent attribution of the Nobel Prize illustrates the importance of this tool in the scientific world. Another application is CRISPR loci analysis, which allows to easily characterize isolates in order to understand the interactions of bacteria with their environment and visualize species evolution. In this review, we focused on the distribution, diversity and roles of CRISPR-Cas systems in the main pathogenic streptococci.

Cytotoxic property of Streptococcus mitis strain producing two different types of cholesterol-dependent cytolysins

Streptococcus mitis strain Nm-65 secretes an atypical 5-domain-type cholesterol-dependent cytolysin (CDC) called S. mitis-derived human platelet aggregation factor (Sm-hPAF) originally described as a platelet aggregation factor. Sm-hPAF belongs to Group III CDC that recognize both membrane cholesterol and human CD59 as the receptors, and shows preferential activity towards human cells. Draft genome analyses have shown that the Nm-65 strain also harbors a gene encoding another CDC called mitilysin (MLY). This CDC belongs to Group I CDC that recognizes only membrane cholesterol as a receptor, and it is a homolog of the pneumococcal CDC, pneumolysin. The genes encoding each CDC are located about 20 kb apart on the Nm-65 genome. Analysis of the genomic locus of these CDC-encoding genes in silico showed that the gene encoding Sm-hPAF and the region including the gene encoding MLY were both inserted into a specific locus of the S. mitis genome. The results obtained using deletion mutants of the gene(s) encoding CDC in Nm-65 indicated that each CDC contributes to both hemolysis and cytotoxicity, and that MLY is the major hemolysin/cytolysin in Nm-65. The present study aimed to determine the potential pathogenicity of an S. mitis strain that produces two CDC with different receptor recognition properties and secretion modes.

Paenibacillus oralis sp. nov., Isolated from Human Subgingival Dental Plaque of Gingivitis Lesion

A Gram-stain-negative, facultative anaerobic, spore-forming, motile, and rod-shaped bacterium, strain ChDC PVNT-B20^T, was isolated from the human subgingival dental plaque of a gingivitis lesion. Phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) showed that the strain belonged to the genus Paenibacillus. BLAST analysis of 16S rDNA sequence of the strain displayed high identity to those of Paenibacillus faecis DSM 23593^T (97.7% similarity) and Paenibacillus macerans ATCC 8244^T (97.6% similarity). Draft genome of strain ChDC PVNT-B20^T was composed of 8,112,407 bp. The DNA G+C content of the strain was 51.3 mol%. Average nucleotide identity values between strain ChDC PVNT-B20^T and P. faecis DSM 23593^T or P. macerans ATCC 8244^T were 75.71% and 91.5%, respectively. Genome-to-genome distance values between strain ChDC PVNT-B20^T and P. faecis DSM 23593^T or P. macerans ATCC 8244^T were 21.6% (19.3-24.0%) and 44.9% (42.3-47.4%), respectively. Major cellular fatty acids of strain ChDC PVNT-B20^T were anteiso-C_15:0 (43.4%), C_16:0 (16.6%), iso-C_16:0 (14.4%), and anteiso-C_17:0 (12.4%). The sole respiratory quinone of the strain was menaqinone-7. Major polar lipids of the strain were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and one unidentified glycolipid (GL). Minor polar lipids were one unidentified aminolipid (AL), one unidentified phospholipid (PL), and three unidentified lipids (L1-L3). Based on these results, strain ChDC PVNT-B20^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus oralis sp. nov. is proposed. Type strain is ChDC PVNT-B20^T (= KCOM 3021^T = JCM 33462 ^T).

Streptococcus koreensis sp. nov., Isolated from Human Subgingival Dental Plaque of Periodontitis Lesion

A novel facultative anaerobic, Gram-stain-positive coccus, strain JS71^T, was isolated from the human subgingival dental plaque of a periodontitis lesion. Phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) revealed that the strain belonged to the genus Streptococcus. The 16S rDNA sequence had high similarity with Streptococcus rubneri DSM 26920^T (98.6%), Streptococcus parasanguinis ATCC 15912^T (98.5%), and Streptococcus australis CCUG 45919^T (98.3%). The genome of strain JS71^T was 2,009,592 bp in length. The DNA G+C content of the strain was 42.1 mol%. Average nucleotide identity values between strain JS71^T and S. rubneri DSM 26920^T, S. parasanguinis ATCC 15912^T, and S. australis CCUG 45919^T were 88.9%, 80.8%, and 92.4%, respectively. Genome-to-genome distance values between strain JS71^TS. rubneri DSM 26920^T, S. parasanguinis ATCC 15912^T, and S. australis CCUG 45919^T were 36.5% (34-39%), 26.3% (23.9-28.7%), and 48.0% (45.4-50.6%), respectively. The major fatty acids of the strain were C_16:0 (39.7%), C_{18:1 ω6c}/C_{18:1 ω7c} (15.5%), and C_18:0 (10.4%). Based on these results, strain JS71^T (= KCOM 2890^T = JCM 33454^T) should be a novel species of the genus Streptococcus, for which the name Streptococcus koreensis sp. nov. is proposed.

Streptococcus chosunense sp. nov., Isolated from Human Postoperative Maxillary Cyst

A novel facultative anaerobic, non-spore forming, non-motile, and Gram-stain-positive coccus, designated strain ChDC B353^T, was isolated from human postoperative maxillary cyst. The 16S ribosomal RNA gene (16S rDNA) sequence of the strain was most closely related to those of Streptococcus pseudopneumoniae ATCC BAA-960^T (99.4%), Streptococcus mitis NCTC 12261^T (99.3%), and Streptococcus pneumoniae NCTC 7465^T (99.2%). The major fatty acids of the strain were C_16:0 (43.2%) and C_{18:1 ω6c}/C_{18:1 ω7c} (20.2%). The genome of strain ChDC B353^T was composed of 1,902,053 bps. The DNA G+C content of the strain was 40.2 mol%. Average nucleotide identity (ANI) values between strain ChDC B353^T and S. pseudopneumoniae ATCC BAA-960^T, S. mitis NCTC 12261^T, and S. pneumoniae NCTC 7465^T were 91.9%, 93.5%, and 91.3%, respectively. Genome-to-genome distance (GGD) values between strain ChDC B353^T and S. pseudopneumoniae ATCC BAA-960^T, S. mitis NCTC 12261^T, or S. pneumoniae NCTC 7465^T were 46.6% (44.0-49.2%), 53.2% (50.5-55.9%), and 46.0% (43.5-48.7%), respectively. The threshold values of ANI and GGD for species discrimination are 95-96% and 70%, respectively. These results reveal that strain ChDC B353^T (= KCOM 1699^T = JCM 33453^T) is a novel species belonging to genus Streptococcus, for which a name of Streptococcus chosunense sp. nov. is proposed.