Article
Biodiversity Conservation
Nhan Le Thi Tuyet, Jaisoo Kim
Summary: A Gram-negative strain, RN2-1(T), was isolated from a Korean forest soil sample. It is characterized as aerobic, oxidase-positive, catalase-negative, non-motile, oval/rod-shaped, and can grow in a wide pH and temperature range. The strain belongs to a novel genus, Limobrevibacterium gyesilva gen. nov., sp. nov., and is closely related to Rhodovastum atsumiense G2-11(T). The whole genome analysis and phenotypic data of strain RN2-1(T) support its distinctive phylogenetic position.
Article
Microbiology
Ju Hye Baek, Dong Min Han, Jeong Min Kim, Baolei Jia, Ji Young Jung, Che Ok Jeon
Summary: Two Gram-stain-negative, facultative aerobic, catalase- and oxidase-positive, and non-motile rod bacteria, strains BLT and W38(T), were isolated from soil and freshwater, respectively. They belong to a novel genus Tahibacter and are named Tahibacter soli and Tahibacter amnicola.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Xue-Mei Chen, De-Feng An, Si-Rong He, Shao-Juan Yang, Zu-Zhen Yang, Lian-Shuang Xiong, Gui-Ding Li, Ming-Guo Jiang, Cheng-Lin Jiang, Yi Jiang
Summary: A Gram-negative coccobacillus strain, YIM 103518(T), was isolated from wild elephant feces in Xishuangbanna, Yunnan Province, West China. It was characterized as strictly aerobic, non-motile, catalase-positive and oxidase-negative. The strain belonged to the genus Acinetobacter and represented a novel species, Acinetobacter faecalis sp. nov., based on phenotypic, chemotaxonomic and phylogenetic analyses. The type strain is YIM 103518(T) (=CCTCC AB 2019201(T) = NBRC 114057(T)).
CURRENT MICROBIOLOGY
(2023)
Article
Microbiology
Hye Jeong Kang, Min-Kyeong Kim, Su Gwon Roh, Seung Bum Kim
Summary: The bacterium strain MMS17-SY002(T) was isolated from island soil, belonging to the genus Muriicola in the family Flavobacteriaceae, and identified as a novel species named Muriicola soli sp. nov. It exhibits specific growth conditions and biochemical activities that distinguish it from related species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Zeng-hong Gao, Qiu-mei Zhang, Ying-ying Lv, You-qi Wang, Bing-nan Zhao, Li-hong Qiu
Summary: Three novel bacterial strains were isolated from forest soil in Dinghushan Biosphere Reserve, Guangdong Province, China. Based on phenotypic, phylogenetic, genomic analyses and chemotaxonomic data, the strains represent two new species of the genus Paraburkholderia and one novel species in the genus Burkholderia.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Minji Bang, Myung Kyum Kim, Hee-Young Jung
Summary: Two novel bacterial strains, BT175(T) and BT728(T), belonging to the genus Hymenobacter, were isolated from soil in the Republic of Korea. They were found to possess distinct molecular and biological characteristics.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Ram Hari Dahal, Ji Yeon Han, Hyosun Lee, Dhiraj Kumar Chaudhary, Dong-Uk Kim
Summary: A novel bacterial strain, designated S2(T), belonging to the genus Aquabacterium, was isolated from soil in South Korea. The strain showed low sequence similarity and DNA-DNA hybridization values with phylogenetically related taxa. The genomic analysis revealed the presence of multiple putative biosynthetic gene clusters involved in secondary metabolite production.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Microbiology
Jia-Rui Lu, Guo-Hong Liu
Summary: A gram-staining-positive, rod-shaped bacterium, strain FJAT-51161(T), isolated from farmland soil in Fujian Province, China, is proposed as a novel species within the genus Lysinibacillus based on phylogenetic and genomic analysis.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Microbiology
Weilan Li, Leonid N. Ten, Myung Kyum Kim, Seung-Yeol Lee, In-Kyu Kang, Hee-Young Jung
Summary: A novel bacterial strain, Mucilaginibacter segetis sp. nov., was isolated from a soil sample collected on Dokdo Island, South Korea. The strain shows high sequence similarity with other Mucilaginibacter species and exhibits unique genotypic distinctiveness.
CURRENT MICROBIOLOGY
(2021)
Article
Microbiology
Yelim You, Chae Yung Woo, Jaisoo Kim
Summary: A new species of bacterium, designated CYS-01T, was isolated from soil in Suwon, Gyeonggi-do, Republic of Korea. The bacterium is white-pigmented, non-motile, Gram- stain-negative and rod-shaped. It belongs to the family Sphingobacteriaceae and the genus Pedobacter. The name Pedobacter montanisoli sp. nov. is proposed for this novel species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Janani Hariharan, Mallory J. Choudoir, Peter Diebold, Kevin Panke-Buisse, Daniel H. Buckley
Summary: A novel Streptomyces strain, named Streptomyces apricus sp. nov., was isolated from soils in Wisconsin, USA. Genome sequencing revealed that this strain had low similarity to type species of Streptomyces. The results of a polyphasic study confirmed the novelty of this isolate.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Chae Yung Woo, Jaisoo Kim
Summary: A novel bacterial strain, designated II4(T), belonging to the genus Lysobacter within the family Xanthomonadaceae, was isolated from soil in Seongnam, Gyeonggi-do, Republic of Korea. The strain was proposed to be named as Lyobacter terrestris sp. nov. based on genomic, chemotaxonomic, phenotypic, and phylogenetic data.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Nar Singh Chauhan, Neetha Joseph, Shraddha Shaligram, Nikita Chavan, Amaraja Joshi, Dhiraj Dhotre, Tushar Lodha, Yogesh Shouche
Summary: A novel rod-shaped bacterial strain SM69(T) was isolated from soil samples in Rohtak, Haryana, India. It belongs to the genus Paenibacillus and has been proposed as a new species named Paenibacillus oleatilyticus sp. nov.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Chung Mi Kim, Ji Won Jeong, Dong Hyeon Lee, Seung Bum Kim
Summary: Two novel species of Pseudomonas, named Pseudomonas guryensis and Pseudomonas ullengensis, were isolated from soil, showing distinct differences from other related species despite high similarities.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Ju Hye Baek, Woonhee Baek, Wenting Ruan, Hye Su Jung, Sung Chul Lee, Che Ok Jeon
Summary: A new species, Massilia soli sp. nov., strain R798(T), was isolated from soil in South Korea. It exhibits distinct morphological, physiological, and nutritional characteristics. The strain is most closely related to Massilia eurypsychrophila B528-3(T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Kwan Woo Kim, Sungmi Choi, Su-Kyoung Shin, Imchang Lee, Keun Bon Ku, Seong Jun Kim, Seil Kim, Hana Yi
Summary: The study successfully developed a time-efficient whole genome sequencing protocol to rapidly obtain complete genome sequences of MERS-CoV and related variants, which will contribute to rapid diagnosis of MERS in future coronavirus epidemics.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Dongwook Kim, Sein Park, Jongsik Chun
Summary: AAI is a crucial index in prokaryotic taxonomy, with EzAAI being a computational tool based on MMSeqs2 for rapid and accurate calculation, along with hierarchical clustering function for dendrogram creation.
JOURNAL OF MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Junwon Yang, Jongsik Chun
Summary: The gut microbiota plays a role in host health, with mouse models being extensively used in research. Advances in sequencing technology have led to an explosion of research on the mouse gut microbiota, accompanied by the development of public resources to explore this area further.
Article
Nutrition & Dietetics
Joo Hyun Oh, Je Hee Lee, Min Seok Cho, Hyeree Kim, Jongsik Chun, Joon Hyeok Lee, Yeup Yoon, Wonseok Kang
Summary: This study found that MAFLD patients had lower gut microbiome diversity and significant differences at phylum, class, family, and genus levels compared to healthy controls, such as increased abundance of Proteobacteria, Enterobactereriaceae, Citrobacter, and decreased abundance of Faecalibacterium. Additionally, butyrate-producing bacteria were decreased and ethanol-producing bacteria were increased in MAFLD patients. These findings suggest potential targets for therapeutic intervention in MAFLD.
Article
Microbiology
Jihyeon Kim, Seong-In Na, Dongwook Kim, Jongsik Chun
Summary: The study revised a new set of bacterial core genes, named UBCG2, which comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. This gene set was selected from a more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. The new gene set and complete pipeline are available online.
JOURNAL OF MICROBIOLOGY
(2021)
Article
Microbiology
Imchang Lee, Sung-Min Ha, Min-gyung Baek, Dong Wook Kim, Hana Yi, Jongsik Chun
Summary: This study developed a web-based prediction tool called VicPred to identify pathogenic traits of Vibrio cholerae using 796 whole-genome sequences. The tool classified O-antigen gene clusters, identified CTX prophages, and analyzed drug resistance elements, providing insights for analyzing newly sequenced strains. Further accumulation of genome data will facilitate the establishment of a more precise genome-based pathogenic traits analysis tool.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Imen Nouioui, Sung-Min Ha, Inwoo Baek, Jongsik Chun, Michael Goodfellow
Summary: This study identified a new species within the genus Nocardia, called Nocardia alni sp. nov, through a genome-based taxonomic analysis. The strain ncl2(T) showed unique characteristics and was closely related to Nocardia nova, Nocardia jiangxiensis, Nocardia miyuensis, and Nocardia vaccinii. The genomes of N. alni and N. vaccinii strains contained multiple biosynthetic gene clusters, suggesting the potential synthesis of novel specialized products, particularly antibiotics.
Article
Biochemistry & Molecular Biology
Junwon Yang, Jonghyun Park, Yeonjae Jung, Jongsik Chun
Summary: The Animal Microbiome Database (AMDB) is the first to provide taxonomic profiles of gut microbiota in various animal species, facilitating research on the relationship between gut microbiota and animal hosts.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Dongwook Kim, Cameron L. M. Gilchrist, Jongsik Chun, Martin Steinegger
Summary: Phylogenomics studies the evolutionary relationship of organisms using their genomic information. The UFCG database and pipeline provide a tool for genome-wide phylogenetic analysis of fungi.
NUCLEIC ACIDS RESEARCH
(2023)
Correction
Microbiology
Jihyeon Kim, Seong-In Na, Dongwook Kim, Jongsik Chun
JOURNAL OF MICROBIOLOGY
(2023)
Article
Microbiology
Seong-In Na, Michael James Bailey, Mauricio Chalita, Jae Hyoung Cho, Jongsik Chun
Summary: In the post-genomic era, phylogenomics is widely used to discover evolutionary relationships between microorganisms. This study established an up-to-date archaeal core gene set (UACG) for inferring archaeal phylogenomic trees. The UACG tool was found to be consistent with the orthoANIu dendrogram, in contrast to the 16S rRNA gene phylogeny which showed discrepancies. The UACG software tool is available at https://www.ezbiocloud.net/tools/uacg.
JOURNAL OF MICROBIOLOGY
(2023)
Correction
Microbiology
Dongwook Kim, Sein Park, Jongsik Chun
JOURNAL OF MICROBIOLOGY
(2023)
Article
Computer Science, Information Systems
Sunyoung Kwon, Gyuwan Kim, Byunghan Lee, Jongsik Chun, Sungroh Yoon, Young-Han Kim
Summary: Nucleic acid sequence classification is a fundamental task in bioinformatics, and NASUCP is a new method that captures the statistical structures of nucleotide sequences using compact context-tree models and universal probability from information theory. Experimental results show that NASUCP outperforms widely-used alternatives in efficiency, accuracy, and scalability, and can also be applied to other bioinformatics tasks.