Hwa-Sook Kim

Draft Genome Sequence of Fusobacterium nucleatum subsp. fusiforme ATCC 51190T

Fusobacterium nucleatum, one of the major causative bacteria of periodontitis, is classified into five subspecies (nucleatum, polymorphum, vincentii, animalis, and fusiforme) on the basis of the several phenotypic characteristics and DNA homology. This is the first report of the draft genome sequence of F. nucleatum subsp. fusiforme ATCC 51190(T).

Draft Genome Sequence of Fusobacterium nucleatum subsp. animalis ChDC F324, Isolated from a Human Subgingival Plaque in the Republic of Korea

ABSTRACT Five subspecies of Fusobacterium nucleatum have been classified: animalis, nucleatum, polymorphum, vincentii, and fusiforme. F. nucleatum subsp. animalis ChDC F324 (KCOM 1325) was isolated from a human subgingival plaque in the Republic of Korea. Here, we report the draft genome sequence of the strain.

Draft Genome Sequence of Fusobacterium nucleatum ChDC F128, Isolated from a Periodontitis Lesion

Fusobacterium nucleatum is classified into five subspecies. F. nucleatum ChDC F128 was isolated from a periodontitis lesion and proposed as a new subspecies based on the comparison of the nucleotide sequences of the RNA polymerase beta subunit and zinc protease genes. Here, we report the draft genome sequence of the strain.

Draft Genome Sequence of Fusobacterium nucleatum subsp. nucleatum ChDC F316, Isolated from a Human Peri-implantitis Lesion in the Republic of Korea

ABSTRACT Fusobacterium nucleatum is a Gram-negative anaerobe and is one of the causative agents of periodontal diseases, including peri-implantitis. Fusobacterium nucleatum subsp. nucleatum ChDC F316 (KCOM 1322) was isolated from a human peri-implantitis lesion. Here, we report the draft genome sequence of this strain.

Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level

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.

Draft Genome Sequences of Fusobacterium nucleatum ChDC F145, ChDC F174, ChDC F206, and ChDC F300, Isolated from Human Subgingival Plaques in the Republic of Korea.

ABSTRACT Recently, five strains were isolated from human subgingival plaques and were proposed as a novel subspecies of Fusobacterium nucleatum. Here, we report the draft genome sequences of the strains, except one for which the draft sequence was already introduced.

Pi30 DNA Probe May Be Useful for the Identification of Prevotella intermedia at the Species or Strain Level

Recently, we introduced a new method for the rapid screening of bacterial species‐ or subspecies‐specific DNA probes, named the “inverted dot blot hybridization screening method.” This method has subsequently been then applied to develop species‐ or strain‐specific DNA probes for Prevotella intermedia and Prevotella nigrescens. In a previous study, the inverted dot blot hybridization data showed that a probe, Pi30, was specific for P. intermedia. In this study, the DNA probe Pi30 was evaluated by Southern blot analysis to determine if it could distinguish P. intermedia from P. nigrescens. The data showed that the probe Pi30 reacted with the genomic DNAs from the reference strains and clinical isolates of both P. intermedia and P. nigrescens, but the size of the signal bands was different. In addition, the probe Pi30 reacted with a 1.4 kbp fragment from the genomic DNAs digested with PstI of the P. intermedia strains but not with any fragments of P. nigrescens strains. The result indicates that the probe Pi30 could be useful for the identification of P. intermedia by restriction fragment length polymorphism (RFLP) at the species or strain level.

Preferential Expression of L-type Amino Acid Transporter 1 in Ameloblasts During Rat Tooth Development

Certain amino acid transport systems play an important role in supplying organic nutrients to each cell and for cell proliferation during tooth development. However, the mechanisms responsible for such actions are unclear. This study demonstrated for the first time that LAT1 and 4F2hc are expressed during tooth development in prenatal and postnatal rats, and that the transporters show cell‐specific expression in ameloblasts, which are the epithelium‐derived dental cells. LAT1 and 4F2hc expression was not observed in other dental cells of the developing teeth such as odontoblasts and cementoblasts. Overall, these results suggest that LAT1 and 4F2hc might play an important role in enamel formation.