Journal of Microbiology

Full article

Preliminary characterization of the skin microbiota in basal cell carcinoma: An exploratory pilot study in Korean patients: Hye Lim Keum, Woo Jun Sul, Suyeon Kim, In-Young Chung, Ara Koh, Hei Sung Kim; Received November 14, 2025 Accepted December 23, 2025 Published online February 13, 2026; DOI: https://doi.org/10.71150/jm.2511012 [Epub ahead of print]

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Abstract PDF: Basal cell carcinoma (BCC) is the most common form of skin cancer, with ultraviolet radiation recognized as the primary environmental driver; however, the potential contribution of alterations in the skin microbiota remains incompletely understood, particularly in Asian populations. This exploratory pilot study describes bacterial community patterns in BCC lesions compared with contralateral clinically normal skin in 20 Korean patients. Lesional and contralateral samples were obtained using paired skin swabs and punch biopsies and analyzed by full-length 16S rRNA gene sequencing, with targeted quantitative PCR (qPCR) of the roxP antioxidant gene of Cutibacterium acnes. Given the low-biomass nature of skin samples and the exploratory design, analyses focused on descriptive trends rather than confirmatory inference. Across available samples, C. acnes was the dominant taxon, with a trend toward lower relative abundance in BCC lesions, particularly in biopsy-derived datasets. Microbial evenness appeared higher in lesions than controls. Predictive functional profiling suggested reduced representation of vitamin B6 metabolism pathways in lesions, while qPCR analysis of swab samples showed a trend toward lower roxP/16S rRNA ratios in BCC-associated microbiota. These findings should be interpreted cautiously in light of methodological constraints, including sample heterogeneity, lidocaine exposure prior to biopsy, absence of sequencing-based negative controls, and reliance on predictive functional inference. Overall, this pilot study highlights potential differences in skin bacterial community structure between BCC lesions and contralateral skin in a Korean cohort. Larger, methodologically optimized studies incorporating metagenomic and functional validation will be required to determine whether these microbiota shifts contribute to, or result from, BCC-associated changes in the cutaneous environment.

Journal Article

Comprehensive Analysis of Gut Microbiota Alteration in the Patients and Animal Models with Polycystic Ovary Syndrome: Jing Zhou , Xuemei Qiu , Xuejing Chen , Sihan Ma , Zhaoyang Chen , Ruzhe Wang , Ying Tian , Yufan Jiang , Li Fan , Jingjie Wang; J. Microbiol. 2023;61(9):821-836. Published online October 12, 2023; DOI: https://doi.org/10.1007/s12275-023-00079-9

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Polycystic ovary syndrome (PCOS) is a common disease of endocrine–metabolic disorder, and its etiology remains largely unknown. The gut microbiota is possibly involved in PCOS, while the association remains unclear. The comprehensive analysis combining gut microbiota with PCOS typical symptoms was performed to analyze the role of gut microbiota in PCOS in this study. The clinical patients and letrozole-induced animal models were determined on PCOS indexes and gut microbiota, and fecal microbiota transplantation (FMT) was conducted. Results indicated that the animal models displayed typical PCOS symptoms, including disordered estrous cycles, elevated testosterone levels, and ovarian morphological change; meanwhile, the symptoms were improved after FMT. Furthermore, the microbial diversity exhibited disordered, and the abundance of the genus Ruminococcus and Lactobacillus showed a consistent trend in PCOS rats and patients. The microbiota diversity and several key genera were restored subjected to FMT, and correlation analysis also supported relevant conclusions. Moreover, LEfSe analysis showed that Gemmiger, Flexispira, and Eubacterium were overrepresented in PCOS groups. Overall, the results indicate the involvement of gut microbiota in PCOS and its possible alleviation of endocrinal and reproductive dysfunctions through several special bacteria taxa, which can function as the biomarker or potential target for diagnosis and treatment. These results can provide the new insights for treatment and prevention strategies of PCOS.

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Characteristics of Gut Microbiota in Patients with Polycystic Ovary Syndrome and Its Association with Metabolic Abnormalities: A Review
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Frontiers in Cellular and Infection Microbiology.2025;[Epub] CrossRef
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Navjot Kaur, Nisha Yadav, Sarika Sachan, Priya Sharma, Preeti Khetarpal
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Review

Envelope‑Stress Sensing Mechanism of Rcs and Cpx Signaling Pathways in Gram‑Negative Bacteria: Seung-Hyun Cho , Kilian Dekoninck , Jean-Francois Collet; J. Microbiol. 2023;61(3):317-329. Published online March 9, 2023; DOI: https://doi.org/10.1007/s12275-023-00030-y

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Abstract PDF

The global public health burden of bacterial antimicrobial resistance (AMR) is intensified by Gram-negative bacteria, which have an additional membrane, the outer membrane (OM), outside of the peptidoglycan (PG) cell wall. Bacterial twocomponent systems (TCSs) aid in maintaining envelope integrity through a phosphorylation cascade by controlling gene expression through sensor kinases and response regulators. In Escherichia coli, the major TCSs defending cells from envelope stress and adaptation are Rcs and Cpx, which are aided by OM lipoproteins RcsF and NlpE as sensors, respectively. In this review, we focus on these two OM sensors. β-Barrel assembly machinery (BAM) inserts transmembrane OM proteins (OMPs) into the OM. BAM co-assembles RcsF, the Rcs sensor, with OMPs, forming the RcsF-OMP complex. Researchers have presented two models for stress sensing in the Rcs pathway. The first model suggests that LPS perturbation stress disassembles the RcsF-OMP complex, freeing RcsF to activate Rcs. The second model proposes that BAM cannot assemble RcsF into OMPs when the OM or PG is under specific stresses, and thus, the unassembled RcsF activates Rcs. These two models may not be mutually exclusive. Here, we evaluate these two models critically in order to elucidate the stress sensing mechanism. NlpE, the Cpx sensor, has an N-terminal (NTD) and a C-terminal domain (CTD). A defect in lipoprotein trafficking
results
in NlpE retention in the inner membrane, provoking the Cpx response. Signaling requires the NlpE NTD, but not the NlpE CTD; however, OM-anchored NlpE senses adherence to a hydrophobic surface, with the NlpE CTD playing a key role in this function.

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Journal Articles

Fungal Catastrophe of a Specimen Room: Just One Week is Enough to Eradicate Traces of Thousands of Animals: Ji Seon Kim , Yoonhee Cho , Chang Wan Seo , Ki Hyung Park , Shin Nam Yoo , Jun Won Lee , Sung Hyun Kim , Wonjun Lee , Young Woon Lim; J. Microbiol. 2023;61(2):189-197. Published online February 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00017-9

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Abstract PDF

Indoor fungi obtain carbon sources from natural sources and even recalcitrant biodegradable materials, such as plastics and synthetic dye. Their vigorous activity may have negative consequences, such as structural damage to building materials or the destruction of precious cultural materials. The animal specimen room of the Seoul National University stocked 36,000 animal resources that had been well-maintained for over 80 years. Due to abandonment without the management of temperature and humidity during the rainy summer season, many stuffed animal specimens had been heavily colonized by fungi. To investigate the fungal species responsible for the destruction of the historical specimens, we isolated fungi from the stuffed animal specimens and identified them at the species level based on morphology and molecular analysis of the β-tubulin (BenA) gene. A total of 365 strains were isolated and identified as 26 species in Aspergillus (10 spp.), Penicillium (14 spp.), and Talaromyces (2 spp.). Penicillium brocae and Aspergillus sydowii were isolated from most sections of the animal specimens and have damaged the feathers and beaks of valuable specimens. Our findings indicate that within a week of mismanagement, it takes only a few fungal species to wipe out the decades of history of animal diversity. The important lesson here is to prevent this catastrophe from occurring again through a continued interest, not to put all previous efforts to waste.

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Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation
Geoffrey Michael Gadd, Marina Fomina, Flavia Pinzari, Mark D. Rose
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Development of a neutralization assay based on the pseudotyped chikungunya virus of a Korean isolate: Woo-Chang Chung , Kwang Yeon Hwang , Suk-Jo Kang , Jae-Ouk Kim , Moon Jung Song; J. Microbiol. 2020;58(1):46-53. Published online November 25, 2019; DOI: https://doi.org/10.1007/s12275-020-9384-0

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Abstract PDF

The Chikungunya virus (CHIKV) belongs to the Alphavirus genus of Togaviridae family and contains a positive-sense single stranded RNA genome. Infection by this virus mainly causes sudden high fever, rashes, headache, and severe joint pain that can last for several months or years. CHIKV, a mosquito- borne arbovirus, is considered a re-emerging pathogen that has become one of the most pressing global health concerns due to a rapid increase in epidemics. Because handling of CHIKV is restricted to Biosafety Level 3 (BSL-3) facilities, the evaluation of prophylactic vaccines or antivirals has been substantially hampered. In this study, we first identified the whole structural polyprotein sequence of a CHIKV strain isolated in South Korea (KNIH/2009/77). Phylogenetic analysis showed that this sequence clustered within the East/ Central/South African CHIKV genotype. Using this sequence information, we constructed a CHIKV-pseudotyped lentivirus expressing the structural polyprotein of the Korean CHIKV isolate (CHIKVpseudo) and dual reporter genes of green fluorescence protein and luciferase. We then developed a pseudovirus-based neutralization assay (PBNA) using CHIKVpseudo. Results from this assay compared to those from the conventional plaque reduction neutralization test showed that our PBNA was a reliable and rapid method to evaluate the efficacy of neutralizing antibodies. More importantly, the neutralizing activities of human sera from CHIKVinfected individuals were quantitated by PBNA using CHIKVpseudo. Taken together, these results suggest that our PBNA for CHIKV may serve as a useful and safe method for testing the neutralizing activity of antibodies against CHIKV in BSL-2 facilities.

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Facile quantitative diagnostic testing for neutralizing antibodies against Chikungunya virus
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Paenibacillus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter: Soo-Jin Kim , Hayoung Cho , Jae-Hyung Ahn , Hang-Yeon Weon , Jae-Ho Joa , Jeong-Seon Kim , Soon-Wo Kwon; J. Microbiol. 2019;57(10):836-841. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9118-3

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Abstract PDF

A Gram-stain-positive, rod-shaped, non-endospore-forming, motile by means of peritrichous flagella, facultatively anaerobic bacterium designated TI45-13arT was isolated from Nuruk, a Korean traditional Makgeolli fermentation starter. It grew at 4–35°C (optimum, 28–30°C), pH 5.0–9.0 (optimum, pH 7.0) and NaCl concentrations up to 5% (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain TI45-13arT belonged to the genus Paenibacillus and showed the highest sequence similarities with Paenibacillus kyungheensis DCY88T (98.5%), Paenibacillus hordei RH-N24T (98.4%) and Paenibacillus nicotianae YIM h-19T (98.1%). The major fatty acid was anteiso-C15:0. The DNA G+C content was 39.0 mol%, and MK-7 was the predominant isoprenoid quinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids, and one unidentified aminoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. On the basis of polyphasic taxonomy study, it was suggested that strain TI45-13arT represents a novel species within the genus Paenibacillus for which the name Paenibacillus nuruki sp. nov. is proposed. The type strain was TI45-13arT (= KACC 18728T = NBRC 112013T).

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Metagenomic and meta-metabolomic analysis of traditional Korean rice vinegar productions shows a large variability between producers
Louise Vermote, Byung Hee Chun, Shehzad Abid Khan, Luc De Vuyst, Che Ok Jeon, Stefan Weckx
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Review

[MINIREVIEW] Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea: Chi Nam Seong , Joo Won Kang , Ji Hee Lee , So Yeon Seo , Jung Jae Woo , Chul Park , Kyung Sook Bae , Mi Sun Kim; J. Microbiol. 2018;56(1):1-10. Published online January 4, 2018; DOI: https://doi.org/10.1007/s12275-018-7318-x

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Abstract PDF

This study assessed the taxonomic hierarchy of the phylum Firmicutes as well as elucidated the isolation and classification states of novel Firmicutes species isolated from Korean territory. The hierarchical classification system of the phylum Firmicutes has been developed since 1872 when the genus Bacillus was first reported and has been generally adopted since 2001. However, this taxonomic hierarchy is still being modified. Until Feb. 2017, the phylum Firmicutes consisted of seven classes (Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia), 13 orders, 45 families, and 421 genera. Firmicutes species isolated from various environments in Korea have been reported from 2000, and 187 species have been approved as of Feb. 2017. All Firmicutes species were affiliated with three classes (Bacilli, Clostridia, and Erysipelotrichia), four orders (Bacillales, Lactobacillales, Clostridiales, and Erysipelotrichales), 17 families, and 54 genera. A total of 173 species belong to the class Bacilli, of which 151 species were affiliated with the order Bacillales and the remaining 22 species with the order Lactobacillales. Twelve species belonging to the class Clostridia were affiliated within only one order, Clostridiales. The most abundant family was Bacillaceae (67 species), followed by the family Paenibacillaceae (56 species). Thirteen novel genera were created using isolates from the Korean environment. A number of Firmicutes species were isolated from natural environments in Korean territory. In addition, a considerable number of species were isolated from artificial resources such as fermented foods. Most Firmicutes species, belonging to the families Bacillaceae, Planococcaceae, and Staphylococcaceae, isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Firmicutes species were isolated from the whole territory of Korea, especially large numbers from Provinces Gyeonggi, Chungnam, and Daejeon.

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Characterization and phylogenetic analysis of Varicella-zoster virus strains isolated from Korean patients: Min Ho Kim , Jeong Seon Jeon , In Kyo Kim , Ji Seon Park , Hosun Park , Ok Sarah Shin , Chan Hee Lee; J. Microbiol. 2017;55(8):665-672. Published online July 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7171-3

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Varicella-zoster virus (VZV) is a causative agent of chickenpox in primary infection and shingles after its reactivation from latency. Complete or almost-complete genomic DNA sequences for various VZV strains have been reported. Recently, clinical VZV strains were isolated from Korean patients whose genome was sequenced using high-throughput sequencing technology. In this study, we analyzed single nucleotide polymorphism (SNP) of VZV strains to genetically characterize Korean clinical isolates. Phylogenetic analyses revealed that three Korean strains, YC01, YC02, and YC03, were linked to clade 2. Comprehensive SNP analysis identified 86 sites specific for the 5 VZV clades. VZV strains isolated from Korea did not form a phylogenetic cluster. Rather, YC02 and YC03 clustered strongly with Chinese strain 84-7 within clade 2, more specifically cluster 2a. Signature sequences for the cluster 2a were identified and found to play an important role in the separation of cluster 2a strains from other clade 2 strains, as shown in substitution studies. Further genetic analysis with additional strains isolated from Japan, China, and other Asian countries would provide a novel insight into the significance of two distinct subclades within clade 2.

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Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi§: Young Joon Oh , Hae-Won Lee , Seul Ki Lim , Min-Sung Kwon , Jieun Lee , Ja-Young Jang , Hae Woong Park , Young-Do Nam , Myung-Ji Seo , Hak-Jong Choi; J. Microbiol. 2016;54(9):588-593. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-6349-4

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A novel halophilic bacterium, strain K7T, was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0–25.0% (w/v) NaCl (optimum 10–15% NaCl), pH 5.5–8.5 (optimum pH 7.0–7.5), and 15–42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone- 7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio- C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7T and Gracilibacillus orientalis XH-63T (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7T is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7T (KACC 18669T; JCM 31344T).

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Research Support, Non-U.S. Gov'ts

Note] Oceanobacillus gochujangensis sp. nov., Isolated from gochujang a Traditional Korean Fermented Food: Seo-Jung Jang , Yu-Jin Kim , Sul-Hee Lee , Young-Seo Park , Jung-Min Park , Dong-Hoon Bai; J. Microbiol. 2014;52(12):1050-1055. Published online July 30, 2014; DOI: https://doi.org/10.1007/s12275-014-4220-z

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A Gram-stain-positive, polar flagella-containing, rod-shaped, obligate aerobic, endospore-forming bacterium, strain TK1655T, was isolated from the traditional Korean food gochujang. The 16S rRNA sequence of strain TK1655T was a member of the genus Oceanobacillus similar to that of the type strain of Oceanobacillus oncorhynchi subsp. incaldanensis DSM 16557T (97.2%), O. oncorhynchi subsp. oncorhynchi JCM 12661T (97.1%), O. locisalsi KCTC 13253T (97.0%), and O. sojae JCM 15792T (96.9%). Strain TK1655T was oxidase and catalase positive. Colonies were circular, smooth, low convex, cream in colour, and measured about 0.5–1.0 mm in diameter. The range for growth was 20–40°C (optimal, 30°C), pH 6.0– 10.0 (optimal, 7.0), and 2–16% (w/v) NaCl (optimal, 2%). Additionally, the cells contained meso-DAP, and the predominant isoprenoid quinone was MK-7. The complex polar lipids were consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylcholine (PC). The major cellular fatty acid components were iso-C15:0, anteiso-C15:0, iso-C16:0, and anteiso-C17:0, and the DNA G+C content was 40.5%. DNA-DNA relatedness of our novel strain and reference strain O. locisalsi KCTC 13253T, O. oncorhynchi subsp. incaldanensis DSM 16557T, O. oncorhynchi subsp. oncorhynchi JCM 12661T was 45.7, 43.8, and 41.9%. From the
results
of phenotypic, chemotaxonomic, and phylogenetic analyses of strain TK1655T, we propose the novel species Oceanobacillus gochujangensis sp. nov. The type strain is TK1655T (=KCCM 101304T =KCTC 33014T =CIP 110582T =NBRC 109637T).

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Characterization, Metabolites and Gas Formation of Fumarate Reducing Bacteria Isolated from Korean Native Goat (Capra hircus coreanae): Lovelia L. Mamuad , Seon Ho Kim , Sung Sil Lee , Kwang Keun Cho , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2012;50(6):925-931. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2497-3

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Fumarate reducing bacteria, able to convert fumarate to succinate, are possible to use for the methane reduction in rumen because they can compete for H2 with methanogens. In this, we isolated fumarate reducing bacteria from a rumen of Korean native goat and characterized their molecular properties [fumarate reductase A gene (frdA)], fumarate reductase activities, and productions of volatile fatty acids and gas. Eight fumarate reducing bacteria belonging to Firmicutes were isolated from rumen fluid samples of slaughtered Korean black goats and characterized their phylogenetic positions based on 16S rRNA gene sequences. PCR based analyses showed that only one strain, closely related to Mitsuokella jalaludinii, harbored frdA. The growths of M. jalaludinii and Veillonella parvula strains were tested for different media. Interestingly, M. jalaludinii grew very well in the presence of hydrogen alone, while V. parvula grew well in response of fumarate and fumarate plus hydrogen. M. jalaludinii produced higher levels of lactate (P≤0.05) than did V. parvula. Additionally, M. jalaludinii produced acetate, but not butyrate, whereas V. parvula produced butyrate, not acetate. The fumarate reductase activities of M. jalaludinii and V. parvula were 16.8 ± 0.34 and 16.9 ± 1.21 mmol NADH oxidized/min/mg of cellular N, respectively. In conclusion, this showed that M. jalaludinii can be used as an efficient methane reducing agent in rumen.

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Antimicrobial Effect of Korean Propolis Against the Mutans Streptococci Isolated from Korean: Min Jung Kim , Chun Sung Kim , Byung-Hoon Kim , Sang-Bok Ro , Yun Kyong Lim , Soon-Nang Park , Engene Cho , Jang-Hyuk Ko , Soon-Sung Kwon , Yeong-Mu Ko , Joong-Ki Kook; J. Microbiol. 2011;49(1):161-164. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-1002-8

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The aim of this study was to determine the optimal concentration of Korean propolis against clinical isolates of mutans streptococci (MS) from Koreans. The antimicrobial activity was evaluated using the minimum inhibitory concentration (MIC) and time-kill curves against mutans streptococci. The MIC90 values of propolis for MS were 35 μg/ml. Propolis had a bacteriostatic effect on Streptococcus mutans ATCC 25175T and bactericidal effects on Streptococcus sobrinus ATCC 33478T at > 2×MIC (70 μg/ml). These results suggest that the propolis can be used in the development of oral hygiene products for the prevention of dental caries.

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Timing and Evolution of the Most Recent Common Ancestor of the Korean Clade HIV Subtype B Based on Nef and Vif Sequences: Mi-Suk Kim , So-Young Jang , Chan-Seung Park , Keon-Myung Lee , Dong-Hun Lee , Chan-Hee Lee; J. Microbiol. 2009;47(1):85-90. Published online February 20, 2009; DOI: https://doi.org/10.1007/s12275-008-0240-x

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Molecular phylogenetic studies of the HIV-1 isolated from Koreans have suggested the presence of the so- called “Korean clade”, which can be defined as a cluster free of foreign isolates. The Korean clade accounts for more than 60% of Korean isolates and exerts characteristic amino acid sequences. Thus, it is merited to estimate when this Korean clade first emerged in order to understand the evolutionary pattern of the Korean clade. We analyzed and reconstructed the most recent common ancestor (MRCA) sequences from nef (n=229) and vif (n=179) Korean clade sequences. Linear regression analyses of sequence divergence estimates were plotted against sampling years to infer the year in which there was zero divergence from the MRCA sequences. MRCA sequences suggested the Korean clade was first emerged around 1984, before the first detection of HIV-1 in Korea in 1985. Further studies on synonymous and nonsynonymous substitution rates suggested positive selection event for the Korean clade, while other subtype B had undergone negative to neutral evolution.

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Generation of Infectious Transcripts from Korean Strain and Mild Mottle Strain of Potato Virus X: Sun Hee Choi , Ki Hyun Ryu; J. Microbiol. 2008;46(5):502-507. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0078-2

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Full-length cDNAs of two different strains of Potato virus X (PVX-Kr and PVX-Mo) have been directly amplified by long template reverse transcription polymerase chain reaction (RT-PCR) using the 5’-end primer containing a SP6 or T7 RNA promoter sequence and the virus-specific 3’-end primer, and then constructed in plasmid vectors. Capped in vitro transcripts from cloned full-length cDNAs as well as those RTPCR amplicons proved to be infectious systemically on tobacco plants. Symptom expression on tobacco plants from PVX-Mo transcripts was faster and severer than that from PVX-Kr. In replication stability test of transcripts derived from PVX clones, progeny viruses showed stable replication according to sequencing through passages. This highly infectious transcript system from the full-length cDNA clones for PVX can be useful for recombinant molecules for functional analysis of viral proteins in plant-virus interaction study as well as for expression of foreign protein in planta.

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Analysis of Substitution Events in HIV-1 vif Gene of the Korean Clade: Chan Seung Park , Mi Sook Kim , Hyun Ah Yi , Dong Hun Lee , Keon Myung Lee , Chan Hee Lee; J. Microbiol. 2007;45(1):75-78.; DOI: https://doi.org/2487 [pii]

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Abstract PDF: Nucleotide and amino acid substitution pattern in vif gene of the Korean clade of HIV-1 isolated from Koreans were analyzed using consensus sequences. At nucleotide level, transition/transversion substitution ratio was 1.88, and nonsynonymous/synonymous substitution ratio was 2.67, suggesting a divergent <br>evolution in the Korean clade. At amino acid level, there were 17 substitutions and G→E substitution at position 37 may be responsible for change in predicted secondary structure.

Molecular Phylogenetic Analysis of HIV-1 vif Gene from Korean Isolates: Chan Seung Park , Mi Sook Kim , Sung Duk Lee , Sung Soo Kim , Keon Myung Lee , Chan-Hee Lee; J. Microbiol. 2006;44(6):655-659.; DOI: https://doi.org/2461 [pii]

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Abstract PDF: Phylogenetic studies of nef, pol, and env gene sequences of HIV-1 isolated from Koreans suggested the presence of a Korean clade in which Korean sequences are clustered to the exclusion of foreign sequences. We attempted to identify and characterize the Korean clade using all vif gene sequences isolated from Koreans registered in the NCBI GenBank database (n = 233). Most (77%) of the Korean isolates belonged to the Korean clade as a large subcluster in subtype B, designated the Korean clade subtype B (KCB). KCB sequences were relatively homogenous compared to Korean subtype B sequences that did not belong to the KCB (non-Korean clade subtype B; NKCB). Comparison of amino acid frequencies of KCB and NKCB sequences revealed several positions where the amino acid frequencies were significantly different. These amino acid residues were critical in separating KCB from NKCB or from foreign sequences, since substitution of these amino acids in KCB with the NKCB amino acids relocated the KCB sequences to NKCB, and vice versa. Further analyses of KCB will help us to understand the origin and evolutionary history of KCB.

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