Article
Microbiology
Juan Zhou, Xiaoxia Wang, Mingchao Xu, Jing Yang, Xin-He Lai, Dong Jin, Shan Lu, Ji Pu, Caixin Yang, Sihui Zhang, Yuanmeihui Tao, Zehui Zhang, Liyun Liu, Jianguo Xu
Summary: In this study, six new actinobacteria strains were isolated from the Qinghai-Tibet Plateau of China and characterized using a taxonomic approach. The results revealed that these strains represent three new species within the genus Nocardioides.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Geeta Chhetri, Inhyup Kim, Minchung Kang, Jiyoun Kim, Yoonseop So, Taegun Seo
Summary: A novel actinomycete strain, Nocardioides baculatus sp. nov, was isolated from marigold roots in Goyang, Republic of Korea. The strain showed specific growth characteristics and biochemical features, belonging to the genus Nocardioides within the family Nocardiaceae.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Thitikorn Duangupama, Chakapong Intaraudom, Pattama Pittayakhajonwut, Chanwit Suriyachadkun, Sarin Tadtong, Pramote Sirirote, Somboon Tanasupawat, Chitti Thawai
Summary: The actinobacterium strain CH5-8(T) isolated from rhizosphere soil of Musa spp. exhibited unique characteristics within the Streptomyces genus. Chemical and genetic analysis confirmed it as a new species, named Streptomyces musisoli sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Ju Hee Kim, You Ju Ham, Seung Bum Kim
Summary: A novel actinobacterial strain, designated MMS20-HV4-12(T), with high hydrolytic potential, was isolated and characterized from a riverside soil sample. It showed optimal growth at 30 degrees C, without NaCl tolerance, and at pH 8. Based on the analysis of 16S rRNA gene sequence, it was identified as a new species of the genus Nocardioides, named Nocardioides okcheonensis sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Veeraya Weerawongwiwat, Seokmin Yoon, Jong-Hwa Kim, Jung-Hoon Yoon, Jung Sook Lee, Ampaitip Sukhoom, Wonyong Kim
Summary: A novel Photobacterium species named Photobacterium arenosum sp. nov. was isolated from marine sediment sand in Sido Island, Republic of Korea. This Gram-stain-negative bacterium is aerobic, motile, short rod-shaped, catalase-negative, and oxidase-positive. It shows high similarity to other members of the genus Photobacterium, with unique fatty acid profiles and polar lipid composition. Genomic analysis revealed a 4.8 Mb genome size with 50.1 mol% G+C content, supporting its classification as a distinct species within the Photobacterium genus.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Kaiwen Zhuang, Ya Liu, Yaling Dai, Jianrong Xu, Wenjun Li, Hong Ming, Sushmita Pradhan, Xin Ran, Chaoliang Zhang, Yu Feng, Yuping Ran
Summary: Strain WCH-YHL-001(T) is a novel actinomycete belonging to the genus Nocardia, with distinctive cellular fatty acids and polar lipid composition. It exhibits low average nucleotide identity and in silico DNA-DNA hybridization values compared to type strains of Nocardia species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Xing-Kui Zhou, Ying Huang, Ti-Kun Zhang, Jian-Jin Liu, Zi-Yi Liu, Ming-Liang Zhu, Li Ma, Tong Liu, Xue-Jian Wang, Ming-He Mo
Summary: Strain 1.0914(T) is a newly discovered actinobacterial species belonging to the genus Nocardioides, named Nocardioides stalactiti sp. nov., with a distinct phylogenetic position and unique chemical characteristics.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Rui Li, Gang-Qiang Jiang, Yun Wang, Yi-Guang Chen, En-Min Zhou, Shu-Kun Tang
Summary: Strain YIM 93776(T), a Gram-stain-positive actinobacterium isolated from a saline sediment sample in Xinjiang, China, was identified as a novel species within the genus Glycomyces through phylogenetic and chemotaxonomic analyses. The draft genome sequence revealed a size of 5.37 Mbp with 69.5% DNA G + C content, supporting its classification as Glycomyces salinus sp. nov.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Microbiology
Pawina Kanchanasin, Masahiro Yuki, Takuji Kudo, Moriya Ohkuma, Wongsakorn Phongsopitanun, Somboon Tanasupawat
Summary: A novel actinomycete strain ET3-3(T) isolated from soil in Thailand was taxonomically evaluated and identified as a new species of the genus Nocardia, with unique chemotaxonomic characteristics and high similarity in gene sequences. The draft genome of ET3-3(T) was 9.31 Mb with 8826 coding sequences.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Microbiology
Khanungkan Klanbut, Thitiya Rattanakavil, Thitikorn Duangupama, Chanwit Suriyachadkun, Paul Robert Herron, Chitti Thawai
Summary: A novel actinobacterium strain SS06011(T) was isolated from a solar saltern soil in Thailand and determined to be a new species of the genus Streptomyces, named Streptomyces salinarius sp. nov. The taxonomic position of the strain was confirmed using polyphasic taxonomic methods and 16S rRNA gene sequence analysis. The strain exhibited characteristic morphological and chemotaxonomic properties of the genus Streptomyces, such as grey aerial spore mass and major menaquinones MK-9(H6) and MK-9(H4). Additionally, physiological, biochemical, and genotypic data distinguished the strain from its closest relatives.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Lingxiao Liu, Ya Zhang, Qiuyu Chen, Qi Shen, Ludan Li, Chengliang Cao, Rongpeng Li, Jihong Jiang, Jinjuan Liu
Summary: A Gram-positive, aerobic actinomycete designated strain KLBMP 9356T was isolated from weathered potash tailings soil in Xuzhou, Jiangsu Province, PR China. The strain showed phylogenetic similarity to Nocardioides zhouii CGMCC 1.11084T (98.9%) and Nocardioides glacieisoli CGMCC 1.11097T (98.7%). It exhibited distinct characteristics such as cell wall peptidoglycan, menaquinone, fatty acids, and polar lipids. The strain represents a novel species named Nocardioides potassii sp. nov. with a G+C content of 71.6 mol%. Rating: 8/10.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Xue-Mei Zhang, Wan-Ting Mo, Yu-Qian Wei, Xin Li, Gui-Mei Ma, Yu-Sen Yang, Xue-Jian Wang, Jian-Jin Liu, Zi-Yi Liu, Xing-Kui Zhou, Ti-Kun Zhang
Summary: A new species of Nocardioides, named Nocardioides nematodiphilus sp. nov., was isolated from the rhizosphere soil of Arabidopsis thaliana in Yunnan Province, China. The genetic and phenotypic characteristics of this strain differentiate it from known Nocardioides species, indicating its novelty.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Jayoung Paek, Lu Bai, Yeseul Shin, Hongik Kim, Joong-Ki Kook, Young-Hyo Chang
Summary: Two bacterial strains isolated from soil samples were identified as a new species of Paenibacillus, with unique morphological characteristics and gene sequences. This discovery contributes to the study of microbial diversity and taxonomy.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Nisachon Tedsree, Somboon Tanasupawat, Boonchoo Sritularak, Nattakorn Kuncharoen, Kittisak Likhitwitayawuid
Summary: Three novel actinomycete strains were isolated from the roots of Dendrobium heterocarpum Lindl in Thailand and were characterized as a new species of the genus Amycolatopsis, named Amycolatopsis dendrobii sp. nov. The strains showed high similarity in genetic sequences and shared phenotypic and chemotaxonomic characteristics. The proposed type strain is DR6-1(T) with specific genomic features distinguishing it from closely related strains.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Yuna Park, Qingzhen Liu, Soohyun Maeng, Won Jung Choi, Yoonjee Chang, Wan-Taek Im
Summary: A novel bacterial strain, G188T, was isolated from ginseng field soil in Korea, and it was identified as a new species within the genus Nocardioides. The strain showed distinct characteristics in terms of phylogenetic analysis, genomic size, and fatty acid composition, supporting its classification as Nocardioides panacis G188T.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Gyeol Seong, Namil Kim, Je-Gun Joung, Eun Ran Kim, Dong Kyung Chang, Jongsik Chun, Sung Noh Hong, Young-Ho Kim
Article
Multidisciplinary Sciences
Ji In Park, Tae-Yoon Kim, Bumjo Oh, Hyunjeong Cho, Ji Eun Kim, Seong Ho Yoo, Jung Pyo Lee, Yon Su Kim, Jongsik Chun, Bong-Soo Kim, Hajeong Lee
SCIENTIFIC REPORTS
(2020)
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.
Article
Medicine, General & Internal
Kuenyoul Park, Jaewoong Lee, Kihyun Lee, Jiwon Jung, Sung Han Kim, Jina Lee, Mauricio Chalita, Seok Hwan Yoon, Jongsik Chun, Kyu Hwa Hur, Heungsup Sung, Mi Na Kim, Hae Kyung Lee
Summary: The study investigated epidemiological links between COVID-19 outbreaks at two university-affiliated hospitals in Seoul using whole genome sequencing (WGS). It revealed the role of patient transfer and caregivers as links of nosocomial outbreaks of COVID-19 in multiple hospitals, highlighting the usefulness of WGS in understanding the epidemiology of SARS-CoV-2.
JOURNAL OF KOREAN MEDICAL SCIENCE
(2021)
