Journal of Microbiology

Journal Articles

Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter.: Hyeonsu Tak, Miri S Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho; J. Microbiol. 2024;62(9):739-748. Published online July 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00158-5

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Abstract: Two Gram-stain-negative, aerobic, motile by means of flagella, short rod-shaped bacterial strains, designated IMCC43200(T) and IMCC45268(T), were isolated from coastal seawater samples collected from the South Sea of Korea. Strains IMCC43200(T) and IMCC45268(T) shared 98.6% 16S rRNA gene sequence similarity and were closely related to Congregibacter litoralis KT71(T) (98.8% and 98.7%, respectively). Complete whole-genome sequences of IMCC43200(T) and IMCC45268(T) were 3.93 and 3.86 Mb in size with DNA G + C contents of 54.8% and 54.2%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 74.5% and 23.4%, respectively, revealing that they are independent species. The two strains showed ANI values of ≤ 75.8% and dDDH values of ≤ 23.0% to the type and only species of the genus Congregibacter (C. litoralis), indicating that each strain represents a novel species. Both strains contained summed feature 3 (comprising C(16:1) ω6c and/or C(16:1) ω7c) and summed feature 8 (comprising C(18:1) ω6c and/or C(18:1) ω7c) as major fatty acid constituents. The predominant isoprenoid quinone detected in both strains was ubiquinone-8 (Q-8). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and aminolipids. Based on the phylogenetic, genomic, and phenotypic characterization, strains IMCC43200(T) and IMCC45268(T) were considered to represent two novel species within the genus Congregibacter, for which the names Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. are proposed with IMCC43200(T) (= KCTC 8133(T) = NBRC 116295(T) = CCTCC AB 2023139(T)) and IMCC45268(T) (= KCTC 92921(T) = NBRC 116135(T)) as the type strains, respectively.

Pannonibacter tanglangensis sp. nov., a New Species Isolated from Pond Sediment.: Lei Wang, Yanpeng Cheng, Panpan Yang, Jinjin Zhang, Gui Zhang, Sihui Zhang, Jing Yang, Zhen Zhang, Lulu Hu, Ji Pu, Yanying Yang, Xin-He Lai, Jianguo Xu, Yinghui Li, Qinghua Hu; J. Microbiol. 2024;62(9):727-737. Published online July 5, 2024; DOI: https://doi.org/10.1007/s12275-024-00151-y

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Abstract: Two bacterial strains (XCT-34^T and XCT-53) isolated from sediment samples of an artificial freshwater reservoir were analyzed using a polyphasic approach. The two isolates are aerobic, Gram-stain-negative, oxidase-negative, catalase-positive, motile with polar flagella, rod-shaped, and approximately 1.4-3.4 × 0.4-0.9 μm in size. Phylogenetic analyses based on 16S rRNA gene and whole-genome sequences showed that the two strains formed a distinct branch within the evolutionary radiation of the genus Pannonibacter, closest to Pannonibacter carbonis Q4.6^T (KCTC 52466). Furthermore, lower than threshold average nucleotide identity values (ANI, 85.7-86.4%) and digital DNA-DNA hybridization values (dDDH, 22.3-30.5%) of the two strains compared to the nearest type strains also confirmed that they represented a novel species. Genomic analyses, including annotation of the KEGG pathways, prediction of the secondary metabolism biosynthetic gene clusters and PHI phenotypes, supported functional inference and differentiation of the strains from the closely related taxa. Results of chemotaxonomic and physiological studies revealed that their distinct phenotypic characteristics distinguished them from existing Pannonibacter species. Thus, the two strains are considered to represent a novel species of Pannonibacter, for which the name of Pannonibacter tanglangensis sp. nov. is proposed, with XCT-34^T (= KCTC 82332^T = GDMCC 1.1947^T) as the respective type strain.

Geographic diversity in Helicobacter pylori oipA genotype between Korean and United States isolates: Aeryun Kim , Jing Lai , D. Scott Merrell , Ji-Hye Kim , Hanfu Su , Jeong-Heon Cha; J. Microbiol. 2021;59(12):1125-1132. Published online October 31, 2021; DOI: https://doi.org/10.1007/s12275-021-1450-8

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Abstract: Helicobacter pylori outer membrane inflammatory protein A (OipA) was originally named for its role in inducing inflammation in the host, as evidenced by high mucosal IL-8 levels. Expression of OipA is regulated by phase variation of a CT dinucleotide-repeat located in the 5􍿁􀁇region of the gene. However, little is known about OipA geographic diversity across isolates. To address this gap, we conducted a large-scale molecular epidemiologic analysis using H. pylori clinical isolates obtained from two geographically distinct populations: Korea and the United States (US). Most Korean isolates (98.7%) possessed two copies of oipA located at two specific loci (A and B) while all US isolates contained only one copy of oipA at locus A. Furthermore, most Korean oipA (94.8%) possessed three or less CT repeats while most US oipA (96.6%) contained five or more CT repeats. Among the two copies, all Korean H. pylori possessed at least one oipA ‘on’ phase variant while the single copy of oipA in US isolates showed 56.2% ‘on’ and 43.8% ‘off.’ Thus, host differences seem to have driven geographic diversification of H. pylori across these populations such that OipA expression in US isolates is still regulated by phase variation with 5 or more CT repeats, while Korean isolates always express OipA; duplication of the oipA combined with a reduction of CT repeats to three or less ensures continued expression. En masse, these findings suggest that diversity in the oipA gene copy number, CT repeats, and phase variation among H. pylori from different populations may confer a benefit in adaptation to particular host populations.

Published Erratum

Erratum to: Protective and Pathogenic Role of Humoral Responses in COVID‑19: Uni Park , Nam-Hyuk Cho; J. Microbiol. 2023;61(7):713-713.; DOI: https://doi.org/10.1007/s12275-023-00058-0

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