Yeseul Shin

Peptoniphilus rhinitidis sp. nov., isolated from specimens of chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is an inflammatory disorder of the nasal cavity and paranasal sinus related to bacterial infection. A previous study suggested that a specific bacterial group may have an important role in the course of CRS. In this study, bacteria isolated from CRS patients were characterized. A total of 15 strains were identified as Gram-positive anaerobic cocci (GPAC), which were able to utilize peptone as a sole carbon source. Sequencing of the 16S ribosomal RNA gene revealed that the isolates were closely related to members of the genus Peptoniphilus (>97% similarity) within the Clostridiales Family XI. Incertae Sedis. Genotypic and phenotypic characterization suggests that these isolates represent a novel species of the genus Peptoniphilus associated with CRS. The type strain of Peptoniphilus rhinitidis is 1-13T (=KCTC 5985T=JCM 17448T).

Draft Genome Sequence of the Novel Peptoniphilus sp. Strain ChDC B134, Isolated from a Human Periapical Abscess Lesion

ABSTRACT The genus Peptoniphilus comprises butyrate-producing, nonsaccharolytic species that use peptone and amino acids as major energy sources. The novel Peptoniphilus sp. strain ChDC B134 (=KCOM 1628) was isolated from a human periapical abscess lesion. Here, we report the draft genome sequence of the 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.

Clostridium composti sp. nov., a new anaerobic bacteria isolated from compost

Strain YH-tan31T is a Gram-stain-positive, obligately anaerobic, spore-forming and mesophilic bacterium. The cells are rod-shaped and motile by means of peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Clostridium and is most closely related to Clostridium oryzae DSM 28571T (97 % sequence identity), followed by Clostridium cellulovorans DSM 3052T (92.4 %) and Clostridium butyricum KCTC 5387T (92.1 %). The G+C content of the isolate was 30.9 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant fatty acids were C14 : 0, C16 : 0, C16 : 0 DMA,and C19 : 0cis 11,12 DMA. The major end products of glucose fermentation were butyrate, acetate and lactate. This isolate represents a new species within the genus Clostridium, for which we propose the name Clostridiumcomposti sp. nov. (type strain, YH-tan31T; =KCTC 15630T=JCM 32793T).

Bacteroides koreensis sp. nov. and Bacteroides kribbi sp. nov., two new members of the genus Bacteroides

Three bacterial isolates from human faeces, YS-aM39T, R2F3-3-3T and R2F3-5-1, were characterized as Gram-negative, strictly anaerobic, non-spore-forming, non-motile, and rod-shaped. Isolate YS-aM39T formed a distinct line of descent, showing greatest 16S rRNA gene sequence relatedness with R2F3-3-3T (97.5 %), R2F3-5-1 (97.5 %), Bacteroides ovatus (98.8 %) and Bacteroides xylanisolvens (97.2 %). Isolates R2F3-3-3T and R2F3-5-1 also formed a distinct line of descent, sharing greatest 16S rRNA gene sequence relatedness with B. ovatus (98.2 %) and B. xylanisolvens (97.2 %). The DNA G+C content of YS-aM39T was 44.8 mol%, that of R2F3-3-3T was 42.4 mol% and that of R2F3-5-1 was 42.6 mol%. The respiratory quinone of all three isolates was menaquinone MK-10. Polar lipid analysis identified phosphatidylethanolamine as the major lipid. The predominant fatty acids in all three isolates were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 3-OH and iso-C17 : 0 3-OH. The major end products of glucose fermentation were acetic acid, lactic acid and formic acid. DNA-DNA hybridization data indicated that two isolates, YS-aM39T and R2F3-3-3T, represent a species distinct from B. ovatus and B. xylanisolvens. Finally, in this study, the two isolates represented two new species in the genus Bacteroides, for which we propose the names Bacteroides koreensis sp. nov. (type strain, YS-aM39T=KCTC 15520T=JCM 31393T) and Bacteroides kribbi sp. nov. (type strain, R2F3-3-3T=KCTC 15460T=JCM 31391T).