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-positive, rod-shaped, endospore-forming bacterium, designated strain BLB-1T, was isolated from samples of tidal flat sediment from the Yellow Sea. 16S rRNA gene sequence analysis demonstrated that the isolate belonged to the Bacillus rRNA group 2 and was closely related to Bacillus massiliensis CIP 108446T (97.4 %), Bacillus odysseyi ATCC PTA-4993T (96.7 %), Lysinibacillus fusiformis DSM 2898T (96.2 %) and Lysinibacillus boronitolerans DSM 17140T (95.9 %). Sequence similarities with related species in other genera, including Caryophanon , Sporosarcina and Solibacillus , were <96.1 %. Chemotaxonomic data supported the affiliation of strain BLB-1T with the genus Lysinibacillus . The major menaquinone was MK-7, the cell-wall sugars were glucose and xylose, the cell-wall peptidoglycan type was A4α (l-Lys–d-Asp), the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown phospholipids, and the major fatty acids were anteiso-C15 : 0 (35.6 %), iso-C15 : 0 (25.6 %) and anteiso-C17 : 0 (16.5 %). The most closely related species, Bacillus massiliensis and Bacillus odysseyi , were also assigned to this genus based on phylogenetic analysis and phenotypic data. The results of DNA–DNA hybridizations and phenotypic tests supported the differentiation of all three taxa from species of the genus Lysinibacillus with validly published names. Thus, strain BLB-1T ( = KCTC 13296T  = JCM 15800T) represents a novel species, for which the name Lysinibacillus sinduriensis sp. nov. is proposed. It is also proposed that Bacillus massiliensis CIP 108446T ( = 4400831T = CCUG49529T  = KCTC 13178T) and Bacillus odysseyi NBRC 100172T ( = 34hs-1T  = ATCC PTA-4993T  = NRRL B-30641T  = DSM 18869T  = CIP 108263T  = KCTC 3961T) be transferred to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov., respectively.

A Gram-positive, rod-shaped, endospore-forming organism, strain BL3-6(T), was isolated from tidal flat sediments of the Yellow Sea in the region of Tae-An. A 16S rRNA gene sequence analysis demonstrated that this isolate belongs to the Bacillus cereus group, and is closely related to Bacillus mycoides (99.0% similarity), Bacillus thuringiensis (99.0%), Bacillus weihenstephanensis (99.0%), Bacillus cereus (98.9%), Bacillus anthracis (98.8%), and Bacillus pseudomycoides (98.1%). The phylogenetic distance from any validly described Bacillus species outside the Bacillus cereus group was less than 95.6%. The DNA G+C content of the strain was 39.4 mol% and the major respiratory quinone was menaquinone-7. The major cellular fatty acids were iso-C(14:0) (17.8%), iso-C(16:0) (15.8%), and iso-C(12:0) (11.3%). The diagnostic amino acid of the cell wall was meso-diaminopimelic acid and the major cell wall sugar was galactose. The results of DNA-DNA hybridization (<55.6%) and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain BL3-6(T) from the published Bacillus species. BL3-6(T) therefore represents a new species, for which the name Bacillus gaemokensis sp. nov. is proposed, with the type strain BL3-6(T) (=KCTC 13318(T) =JCM 15801(T)).

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.

No abstract