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A novel facultative anaerobic, Gram-stain-positive coccus, strain JS71

A novel Gram-stain-negative, motile, and facultative anaerobic coccus, strain ChDC F240T was isolated from human subgingival dental plaque of a gingivitis lesion. The phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) sequence showed that the strain belonged to the genus Lautropia. 16S rDNA of strain ChDC F240T had the highest similarity to that of Lautropia mirabilis ATCC 51599T (98.8%). Major cellular fatty acids of strain ChDC F240T were C16:0 (43.9%) and C16:1ω6C/C16:1ω7C (38.1%). Draft genome of the strain was 3,834,139 bp in length and the G+C content was 65.0 mol%. Average nucleotide identity and genome-to-genome distance values between strain ChDC F240T and L. mirabilis ATCC 51599 T were 81.99% and 28.50% (26.1–30.9%), respectively. These results reveal that strain ChDC F240T is a novel species within the genus Lautropia, for which the name Lautropia dentalis sp. nov. is proposed; type strain is ChDC F240T (= KCOM 2505T = JCM 33297T).

A novel Gram-stain-positive, obligately anaerobic, spore-forming rod, designated strain ChDC B114T, was isolated from a human dental plaque of a gingivitis lesion. The strain was characterized by polyphasic taxonomic analysis to identify it at the species level. The 16S ribosomal RNA gene (16S rDNA) sequence analysis revealed that the strain belongs to the genus Lachnoanaerobaculum. The percent similarity of the 16S rDNA of the strain was closest to the homologous gene sequence of Lachnoanaerobaculum orale N1T (98.5%) and Lachnoanaerobaculum saburreum CCUG 28089T (97.6%). The major fatty acids of strain ChDC B114T were C16:0 (30.7%), C14:0 (17.7%), iso-C19:0 (14.9%), and C17:0 2OH (12.0%). The draft genome of strain ChDC B114T was 3,097,953 bp in length. The G+C content of the strain was 35.9 mol %. Average nucleotide identity values between strain ChDC B114T and L. orale N1T and L. saburreum CCUG 28089T were 83.2% and 82.0%, respectively. Genome-to-genome distance values between strain ChDC B114T and L. orale N1T and L. saburreum CCUG 28089T were 26.8% (24.5–29.3%) and 26.30% (24.0–28.8%), respectively. Based on these results, strain ChDC B114T (= KCOM 2030T = JCM 33452T) should be classified as a novel species of genus Lachnoanaerobaculum, for which the name Lachnoanaerobaculum gingivalis sp. nov. is proposed.

A novel facultative anaerobic, Gram-stain-negative coccus, designated strain ChDC B345T, was isolated from human pericoronitis lesion and was characterized by polyphasic taxonomic analysis. The 16S ribosomal RNA gene (16S rDNA) sequence revealed that the strain belonged to the genus Streptococcus. The 16S rDNA sequence of strain ChDC B345T was most closely related to those of Streptococcus mitis NCTC 12261T (99.5%) and Streptococcus pseudopneumoniae ATCC BAA-960T (99.5%). Complete genome of strain ChDC B345T was 1,972,471 bp in length and the G + C content was 40.2 mol%. Average nucleotide identity values between strain ChDC B345T and S. pseudopneumoniae ATCC BAA-960T or S. mitis NCTC 12261T were 92.17% and 93.63%, respectively. Genome-to-genome distance values between strain ChDC B345T and S. pseudopneumoniae ATCC BAA-960T or S. mitis NCTC 12261T were 47.8% (45.2–50.4%) and 53.0% (51.0–56.4%), respectively. Based on these results, strain ChDC B345T (= KCOM 1679T = JCM 33299T) should be classified as a novel species of genus Streptococcus, for which we propose the name Streptococcus gwangjuense sp. nov.

A novel Gram-negative, capnophilic, fusiform bacterium, designated strain ChDC OS43T, was isolated from a human refractory periapical abscess in the left mandibular second molar and was characterized by polyphasic taxonomic analysis. The 16S rRNA gene sequence revealed that the strain belongs to the genus Capnocytophaga, as it showed sequence similarities to Capnocytophaga ochracea ATCC 27872T (96.30%) and C. sputigena ATCC 33612T (96.16%). The prevalent fatty acids of strain ChDC OS43T were isoC15:0 (57.54%), C16:0 (5.93%), C16:0 3OH (5.72%), and C18:1 cis 9 (4.41%). The complete genome of strain ChDC OS43T was 3,412,686 bp, and the G+C content was 38.2 mol%. The average nucleotide identity (ANI) value between strain ChDC OS43T and C. ochracea ATCC 27872T or C. sputigena ATCC 33612T was >92.01%. The genome-to-genome distance (GGD) value between strain ChDC OS43T and C. ochracea ATCC 27872T or C. sputigena ATCC 33612T was 32.0 and 45.7%, respectively. Based on the results of phenotypic, chemotaxonomic, and phylogenetic analysis, strain ChDC OS43T (= KCOM 1579T = KCTC 5562T = KCCM 42841T = JCM 32133T) should be classified as the type strain of a novel species of genus Capnocytophaga, for which the name Capnocytophaga endodontalis sp. nov. is proposed.

Fusobacterium nucleatum is classified as four subspecies, subsp. nucleatum, polymorphum, vincentii, and animalis, based on DNA–DNA hybridization (DDH) patterns, phenotypic characteristics, and/or multilocus sequence analysis (MLSA). The gold standards for classification of bacterial species are DDH and 16S ribosomal RNA gene (16S rDNA) sequence homology. The thresholds of DDH and 16S rDNA similarity for delineation of bacterial species have been suggested to be >70 and 98.65%, respectively. Average nucleotide identity (ANI) and genome-to-genome distance (GGD) analysis based on genome sequences were recently introduced as a replacement for DDH to delineate bacterial species with ANI (95–96%) and GGD (70%) threshold values. In a previous study, F. hwasookii was classified as a new species based on MLSA and DDH results. 16S rDNA similarity between F. hwasookii type strain and F. nucleatum subspecies type strains was higher than that between F. nucleatum subspecies type strains. Therefore, it is possible that the four F. nucleatum subspecies can be classified as Fusobacterium species. In this study, we performed ANI and GGD analyses using the genome sequences of 36 F. nucleatum, five F. hwasookii, and one Fusobacterium periodonticum strain to determine whether the four F. nucleatum subspecies could be classified as species using OrthoANI and ANI web-based softwares provided by ChunLab and Kostas lab, respectively, and GGD calculator offered by German Collection of Microorganisms and Cell Cultures. ANI values calculated from OrthoANI and ANI calculators between the type strains of F. nucleatum subspecies ranged from 89.80 to 92.97 and from 90.40 to 91.90%, respectively. GGD values between the type strains of F. nucleatum subspecies ranged from 42.3 to 46.0%. ANI and GGD values among strains belonging to the same F. nucleatum subspecies, subsp. nucleatum, subsp. polymorphum, subsp. vincentii, and subsp. animalis were >96 and >68.2%, respectively. These results strongly suggest that F. nucleatum subsp. nucleatum, subsp. polymorphum, subsp. vincentii, and subsp. animalis should be classified as F. nucleatum, F. polymorphum, F. vincentii, and F. animalis, respectively.

A Gram-stain-negative, facultative anaerobic, spore-forming, motile, and rod-shaped bacterium, strain ChDC PVNT-B20T, 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 23593T (97.7% similarity) and Paenibacillus macerans ATCC 8244T (97.6% similarity). Draft genome of strain ChDC PVNT-B20T 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-B20T and P. faecis DSM 23593T or P. macerans ATCC 8244T were 75.71% and 91.5%, respectively. Genome-to-genome distance values between strain ChDC PVNT-B20T and P. faecis DSM 23593T or P. macerans ATCC 8244T were 21.6% (19.3–24.0%) and 44.9% (42.3–47.4%), respectively. Major cellular fatty acids of strain ChDC PVNT-B20T were anteiso-C15:0 (43.4%), C16:0 (16.6%), iso-C16:0 (14.4%), and anteiso-C17:0 (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-B20T 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-B20T (= KCOM 3021T = JCM 33462 T).

A novel facultative anaerobic, non-spore forming, non-motile, and Gram-stain-positive coccus, designated strain ChDC B353T, 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-960T (99.4%), Streptococcus mitis NCTC 12261T (99.3%), and Streptococcus pneumoniae NCTC 7465T (99.2%). The major fatty acids of the strain were C16:0 (43.2%) and C18:1 ω6c/C18:1 ω7c (20.2%). The genome of strain ChDC B353T 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 B353T and S. pseudopneumoniae ATCC BAA-960T, S. mitis NCTC 12261T, and S. pneumoniae NCTC 7465T were 91.9%, 93.5%, and 91.3%, respectively. Genome-to-genome distance (GGD) values between strain ChDC B353T and S. pseudopneumoniae ATCC BAA-960T, S. mitis NCTC 12261T, or S. pneumoniae NCTC 7465T 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 B353T (= KCOM 1699T = JCM 33453T) is a novel species belonging to genus Streptococcus, for which a name of Streptococcus chosunense sp. nov. is proposed.

A novel Gram-negative, obligately anaerobic, non-motile, non-spore forming, and rod-shaped bacterium, designated strain JS262T, was isolated from human subgingival plaque of periodontitis lesion and was characterized by polyphasic taxonomic analysis. Comparison of 16S ribosomal RNA gene (16S rDNA) sequence revealed that the strain belonged to the genus Prevotella. The percent similarity of 16S rDNA of strain JS262T was closest to those of Prevotella buccae ATCC 33574T (89.1%) and Prevotella shahii JCM 12083T (88.9%). The major fatty acids of strain JS262T were C16:0 (29.2%), iso-C15:0 (19.2%), and anteiso-C15:0 (16.9%). Complete genome of strain JS262T was 2,691,540 bp in length and the G+C content was 43.9 mol%. Average nucleotide identity and genome-to-genome distance values between strain JS262T and P. buccae ATCC 33574T or P. loescheii DSM 19665T were > 70.4% and > 30.1%, respectively. On the basis of these data, a novel Prevotella species is proposed: Prevotella koreensis sp. nov. The type strain of P. koreensis is JS262T (= KCOM 3155T = JCM 33298T).

The original version of this article contained errors in the description of novel species. These errors are corrected with this corrigendum.

In the present study, three strains (ChDC F213T, ChDC F251, and ChDC F267) were classified as novel species of genus Fusobacterium based on average nucleotide identity (ANI) and genome-to-genome distance (GGD) analysis and chemotaxonomic characterization. 16S rDNA sequences of strains ChDC F213T, ChDC F251, and ChDC F267 were highly similar to that of F. periodonticum ATCC 33693T (99.6, 99.4, and 99.4%, respectively). ANI and GGD values of the three isolates with F. periodonticum ATCC 33693T ranged from 92.5 to 92.6% and 47.7 to 48.2%, respectively. Considering that threshold of ANI and GGD values for bacterial species discrimination are 95-96% and 70%, respectively, these results indicate that the three isolates represent a novel Fusobacterium species. DNA G + C contents of the three isolates were 28.0 mol% each. Cellular fatty acid analysis of these strains revealed that C14:0, C16:0, and C16:1 ω6c/C16:1 ω7c were major fatty acids. Therefore, these three strains are novel species belonging to genus Fusobacterium. Strain ChDC F213T (= KCOM 1259T = KCTC 5677T = JCM 33009T) is the type strain of a novel species of genus Fusobacterium, for which a name of Fusobacterium pseudoperiodonticum sp. nov. is proposed.

In this study, we classified the five strains (ChDC F128(T), ChDC F145, ChDC F174, ChDC F206, and ChDC F300) as a novel species of genus Fusobacterium by DNA-DNA hybridization and multi-locus phylogenetic analysis (MLPA), based on a single sequence (24,715 bp) of 22 concatenated housekeeping genes, with morphological and chemotaxonomic characteristics. DNA-DNA hybridization data showed that the values of genomic relatedness between ChDC F128(T) and each of the other novel strains were ranged from 79.0 to 82.6 %, while those of genomic relatedness between ChDC F128(T) and type strain of each of subspecies of F. nucleatum or Fusobacterium periodonticum were ranged from 40.9 to 54.4 %. MLPA revealed that the 5 strains were clustered as one group and clearly discriminated with F. nucleatum and F. periodonticum with 100 % bootstrap value. The DNA G+C content of the five novel strains were ranged from 26.9 to 27.0 mol%. The cellular fatty acid analysis of clinical isolates and type strains revealed C14:0, C16:0, and cis-9 C16:1 as the major fatty acids. The cell wall peptidoglycan of the 5 strains was comprised of meso-lanthionine. These results show that the 5 strains are novel species and belong to the genus Fusobacterium. Strain ChDC F128(T) (=KCOM 1249(T) = KCTC 5108(T) = JCM 30218(T)) is suggested to be the type strain of a novel species of genus Fusobacterium, for which the name Fusobacterium hwasookii sp. nov. is proposed.

On the basis of the DNA-DNA hybridization patterns and phenotypic characteristics, Fusobacterium nucleatum was classified into five subspecies. Previous studies have suggested that F. nucleatum subsp. vincentii is genetically similar to F. nucleatum subsp. fusiforme. The aim of this study was to investigate the possibility of classifying these two subspecies into a single subspecies by phylogenetic analysis using a single sequence (24,715 bp) concatenated 22 housekeeping genes of eight F. nucleatum strains including type strains of five F. nucleatum subspecies. The phylogenetic analysis indicated that F. nucleatum subsp. vincentii and F. nucleatum subsp. fusiforme were clustered in the same group and each strain of other F. nucleatum subspecies were also separated into the same cluster. These results suggested that F. nucleatum subsp. fusiforme and F. nucleatum subsp. vincentii can be classified into a single subspecies. F. nucleatum subsp. vincentii was early published name; therefore, F. nucleatum subsp. fusiforme Gharbia and Shah 1992 can be regarded as a later synonym of F. nucleatum subsp. vincentii Dzink et al. 1990.

A novel Gram-positive, anaerobic, and coccus-shaped bacterium, designated as strain ChDC B134(T), was isolated from a human postoperative infectious lesion in the right maxilla between the lateral incisor and canine and was characterized by polyphasic taxonomic analysis. 16S rRNA gene sequence analysis revealed that the strain ChDC B134(T) belonged to the genus Peptoniphilus, as it showed sequence similarities to Peptoniphilus indolicus KCTC 15023(T) (94.0 %) and Peptoniphilus asaccharolyticus KCTC 3321(T) (93.8 %). The prevalent fatty acids of of strain ChDC B134(T) were C16:0 (20.3 %), C18:1 cis 9 (34.3 %), and C18:0 (13.2 %). The DNA G+C content was 30.9 mol%. The cell wall diamino acid was D-ornithine, which is a property shared by other reference type strains of the genus Peptoniphilus. Based on the results of phenotypic, chemotaxonomic, and phylogenetic analysis, strain ChDC B134(T) (=KCOM 1628(T) = KCTC 15227(T) = JCM 30223(T)) should be classified as the type strain of a novel species of genus Peptoniphilus, for which the name Peptoniphilus mikwangii sp. nov. is proposed.