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UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis
Jihyeon Kim , Seong-In Na , Dongwook Kim , Jongsik Chun
J. Microbiol. 2021;59(6):609-615.   Published online May 29, 2021
DOI: https://doi.org/10.1007/s12275-021-1231-4
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AbstractAbstract
Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with a set of bacterial core genes selected from 1,429 species covering 28 phyla. In this study, we revised a new bacterial core gene set, named UBCG2, that was selected from the more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. The new gene set and complete pipeline are available at http://leb.snu.ac.kr/ubcg2.

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    Tomoaki Kouya, Yohei Ishiyama, Shota Ohashi, Ryota Kumakubo, Takeshi Yamazaki, Toshiki Otaki, Guadalupe Virginia Nevárez-Moorillón
    PLOS ONE.2023; 18(6): e0286677.     CrossRef
  • Comparative Genomic Analysis and BTEX Degradation Pathways of a Thermotolerant Cupriavidus cauae PHS1
    Chandran Sathesh-Prabu, Jihoon Woo, Yuchan Kim, Suk Min Kim, Sun Bok Lee, Che Ok Jeon, Donghyuk Kim, Sung Kuk Lee
    Journal of Microbiology and Biotechnology.2023; 33(7): 875.     CrossRef
  • Complete genome sequence of the emerging pathogen Cysteiniphilum spp. and comparative genomic analysis with genus Francisella : Insights into its genetic diversity and potential virulence traits
    Changrui Qian, Mengxin Xu, Zeyu Huang, Miran Tan, Cheng Fu, Tieli Zhou, Jianming Cao, Cui Zhou
    Virulence.2023;[Epub]     CrossRef
  • Psychroserpens ponticola sp. nov. and Marinomonas maritima sp. nov., isolated from seawater
    Sylvia Kristyanto, Jaejoon Jung, Jeong Min Kim, Byeong Jun Choi, Dong Min Han, Sung Chul Lee, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Atopomonas sediminilitoris sp. nov., isolated from beach sediment of Zhairuo Island, China
    Kejing Li, Zhenbo Ye, Gen Chen, Kaiwen Zheng, Jun Yin, Sanjit Chandra Debnath, Cen Yan, Yi Hong, Zhen Guo, Pinmei Wang, Fabai Wu, Daoqiong Zheng
    Antonie van Leeuwenhoek.2023; 116(2): 97.     CrossRef
  • Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. Isolated from the Aquatic Environment, South Korea
    Miryung Kim, Yong-Seok Kim, Chang-Jun Cha
    Journal of Microbiology.2023; 61(1): 37.     CrossRef
  • Paenibacillus soyae sp. nov., isolated from the rhizosphere of soya bean
    Hui Zhao, Yue Su, Qihui Gu, Jumei Zhang, Xinqiang Xie, Qingping Wu
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Geothrix oryzisoli sp. nov., a ferric iron-reducing bacterium isolated from paddy soil
    Shuang Han, Rong Tang, Shang Yang, Cheng-Jie Xie, Manik Prabhu Narsing Rao, Christopher Rensing, Guo-Hong Liu, Shun-Gui Zhou
    Antonie van Leeuwenhoek.2023; 116(5): 477.     CrossRef
  • Description of Luteibacter aegosomatis sp. nov., Luteibacter aegosomaticola sp. nov., and Luteibacter aegosomatissinici sp. nov. isolated from the Intestines of Aegosoma sinicum Larvae
    Hae-In Joe, Jee-Won Choi, June-Young Lee, Hojun Sung, Su-Won Jeong, Yun-Seok Jeong, Jae-Yun Lee, Jin-Woo Bae
    Journal of Microbiology.2023; 61(6): 603.     CrossRef
  • Hoeflea algicola sp. nov. and Hoeflea ulvae sp. nov., isolated from phycosphere of marine algae
    Ju Hye Baek, Sylvia Kristyanto, Jeong Min Kim, Dong Min Han, Zhe-Xue Quan, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Muricauda myxillae sp. nov., isolated from a marine sponge (Myxilla rosacea), and reclassification of Flagellimonas hymeniacidonis as Muricauda symbiotica nom. nov.
    Yea-Lin Moon, Kyung-Hyun Kim, Jin-Sook Park
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Description and Genomic Characteristics of Weissella fermenti sp. nov., Isolated from Kimchi
    Jae Kyeong Lee, Ju Hye Baek, Dong Min Han, Se Hee Lee, So Young Kim, Che Ok Jeon
    Journal of Microbiology and Biotechnology.2023; 33(11): 1448.     CrossRef
  • Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil
    Kyeong Ryeol Kim, Jeong Min Kim, Jae Kyeong Lee, Dong Min Han, Lujiang Hao, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi
    Dongwook Kim, Cameron L M Gilchrist, Jongsik Chun, Martin Steinegger
    Nucleic Acids Research.2023; 51(D1): D777.     CrossRef
  • Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria
    Carlos J Pardo-De la Hoz, Nicolas Magain, Bryan Piatkowski, Luc Cornet, Manuela Dal Forno, Ignazio Carbone, Jolanta Miadlikowska, François Lutzoni, Claudia Lemus-Solis
    Systematic Biology.2023; 72(3): 694.     CrossRef
  • Zwartia vadi sp. nov., a Novel Species of the GKS98 Cluster Isolated from a Stream, and the Reclassification of ‘Achromobacter Panacis’ as Zwartia panacis comb. nov
    Miri S. Park, Ilnam Kang, Jang-Cheon Cho
    Microorganisms.2023; 11(9): 2150.     CrossRef
  • Comparative genomics reveals environmental adaptability and antimicrobial activity of a novel Streptomyces isolated from soil under black Gobi rocks
    Ying Wen, Binglin Zhang, Gaosen Zhang, Minghui Wu, Ximing Chen, Tuo Chen, Guangxiu Liu, Wei Zhang
    Antonie van Leeuwenhoek.2023; 116(12): 1407.     CrossRef
  • Phylogenomic Insights on the Xanthomonas translucens Complex, and Development of a TaqMan Real-Time Assay for Specific Detection of pv. translucens on Barley
    James T. Tambong, Renlin Xu, Maria Constanza Fleitas, Lipu Wang, Keith Hubbard, Randy Kutcher
    Phytopathology®.2023; 113(11): 2091.     CrossRef
  • Microvirga terrae sp. nov., Isolated from Soil
    Kyung Hyun Kim, Ju Hye Baek, Sang Eun Jeong, Lujiang Hao, Che Ok Jeon
    Current Microbiology.2023;[Epub]     CrossRef
  • Incidence, genetic diversity, and antimicrobial resistance profiles of Vibrio parahaemolyticus in seafood in Bangkok and eastern Thailand
    Chartchai Changsen, Somsak Likhitrattanapisal, Kamonwan Lunha, Wiyada Chumpol, Surasak Jiemsup, Anuphap Prachumwat, Darin Kongkasuriyachai, Supawadee Ingsriswang, Soraya Chaturongakul, Aekarin Lamalee, Suganya Yongkiettrakul, Sureemas Buates
    PeerJ.2023; 11: e15283.     CrossRef
  • Streptomonospora mangrovi sp. nov., isolated from mangrove soil showing similar metabolic capabilities, but distinct secondary metabolites profiles
    Cheng Zhen, Xin-Kai Chen, Xian-Feng Ge, Wen-Zheng Liu
    Archives of Microbiology.2023;[Epub]     CrossRef
  • Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emend
    Kyung Hyun Kim, Dong Min Han, Jae Kyeong Lee, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • UACG: Up-to-Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction
    Seong-In Na, Michael James Bailey, Mauricio Chalita, Jae Hyoung Cho, Jongsik Chun
    Journal of Microbiology.2023; 61(7): 683.     CrossRef
  • Alishewanella maricola sp. nov., isolated from seawater of the Yellow Sea
    Kyung Hyun Kim, Jeong Min Kim, Hyun Mi Jin, Lujiang Hao, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Cutibacterium equinum sp. nov., isolated from horse faeces
    Jeong Ui Yun, Hye Su Jung, Mi-Ja Jung, Hye Seon Song, Yeon Bee Kim, Yujin Kim, Joon-Gyu Kim, Seong Woon Roh, Se Hee Lee, Jun Sik Lee, Tae Woong Whon
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Sugar Concentration, Nitrogen Availability, and Phylogenetic Factors Determine the Ability of Acinetobacter spp. and Rosenbergiella spp. to Grow in Floral Nectar
    José R. Morales-Poole, Clara de Vega, Kaoru Tsuji, Hans Jacquemyn, Robert R. Junker, Carlos M. Herrera, Chris Michiels, Bart Lievens, Sergio Álvarez-Pérez
    Microbial Ecology.2023; 86(1): 377.     CrossRef
  • Silvimonas soli sp. nov., a new member of Chromobacteriaceae isolated from soil in Norrbyskär island, Sweden
    Martina Jerabkova, Tereza Smrhova, Eglantina Lopez-Echartea, Jiri Dresler, Jachym Suman, Gabriela Kapinusova, Tomas Cajthaml, Zdena Skrob, Robin Kyclt, Jonas Fagerman, Michal Strejcek, Ondrej Uhlik
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Actinophytocola gossypii sp. nov. and Streptomyces gossypii sp. nov., two novel actinomycetes isolated from rhizosphere soil of cotton
    Xianfeng Ge, Shenrong Yang, Cheng Zhen, Wenzheng Liu
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Phylogenomic analysis of the genus Rosenbergiella and description of Rosenbergiella gaditana sp. nov., Rosenbergiella metrosideri sp. nov., Rosenbergiella epipactidis subsp. epipactidis subsp. nov., Rosenbergiella epipactidis subsp. californiensis subsp.
    Sergio Álvarez-Pérez, Clara de Vega, Kristof Vanoirbeek, Kaoru Tsuji, Hans Jacquemyn, Tadashi Fukami, Chris Michiels, Bart Lievens
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Thermomonas mangrovi sp. nov., isolated from soil of a mangrove nature reserve
    Shanshan Xu, Junpeng Chen, Si Chen, Qiliang Lai, Zengzhi Liu, Ying Xu
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Tahibacter soli sp. nov., isolated from soil and Tahibacter amnicola sp. nov., isolated from freshwater
    Ju Hye Baek, Dong Min Han, Jeong Min Kim, Baolei Jia, Ji Young Jung, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov.
    Tengfei Ma, Han Xue, Chungen Piao, Ning Jiang, Yong Li
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Antarcticirhabdus aurantiaca gen. nov., sp. nov., isolated from Antarctic gravel soil
    Jie Du, Ying Zhang, Di Xin, Yuhua Xin, Jianli Zhang
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Caldimonas mangrovi sp. nov., Isolated from Mangrove Soil
    S. R. Yang, Y. Y. Liu, X. F. Ge, W. Z. Liu
    Microbiology.2023; 92(4): 500.     CrossRef
  • Chitinophaga horti sp. nov., Isolated from Garden Soil
    Dong Min Han, Ju Hye Baek, Dae Gyu Choi, Myeong Seo Jin, Che Ok Jeon
    Current Microbiology.2023;[Epub]     CrossRef
  • Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment
    Miku Takahashi, Shoya Shinohara, Moriyuki Hamada, Tomohiko Tamura, Hideo Dohra, Shinya Kodani, Youji Nakagawa, Susumu Kokubo, Masayuki Hayakawa, Hideki Yamamura
    The Journal of Antibiotics.2023; 76(2): 93.     CrossRef
  • MALDI-TOF MS analysis of Burkholderia pseudomallei and closely related species isolated from soils and water in Khon Kaen, Thailand
    Nut Nithimongkolchai, Yothin Hinwan, Benjawan Kaewseekhao, Pisit Chareonsudjai, Pipat Reungsang, Ratthaphol Kraiklang, Sorujsiri Chareonsudjai, Lumyai Wonglakorn, Ploenchan Chetchotisakd, Auttawit Sirichoat, Arnone Nithichanon, Kiatichai Faksri
    Infection, Genetics and Evolution.2023; 116: 105532.     CrossRef
  • Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil
    Yong-Seok Kim, Eun-Mi Hwang, Chang-Myeong Jeong, Chang-Jun Cha
    Journal of Microbiology.2023; 61(10): 891.     CrossRef
  • VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution
    Renmao Tian, Behzad Imanian
    Microbiome.2023;[Epub]     CrossRef
  • tilS and rpoB: New Molecular Markers for Phylogenetic and Biodiversity Studies of the Genus Thiothrix
    Nikolai V. Ravin, Dmitry D. Smolyakov, Nikita D. Markov, Alexey V. Beletsky, Andrey V. Mardanov, Tatyana S. Rudenko, Margarita Yu. Grabovich
    Microorganisms.2023; 11(10): 2521.     CrossRef
  • Thermomonas paludicola sp. nov., isolated from a lotus wetland
    Mirae Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Octadecabacter algicola sp. nov. and Octadecabacter dasysiphoniae sp. nov., isolated from a marine red alga and emended description of the genus Octadecabacter
    Myeong Seo Jin, Kyung Hyun Kim, Ju Hye Baek, Jeong Min Kim, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Flavihumibacter fluminis sp. nov. and Flavihumibacter rivuli sp. nov., isolated from a freshwater stream
    Miri S. Park, Hyeonuk Sa, Ilnam Kang, Jang-Cheon Cho
    Journal of Microbiology.2022; 60(8): 806.     CrossRef
  • Exploring the genome of Lactobacillaceae spp. Sy-1 isolated from Heterotrigona itama honey
    Syariffah Nuratiqah Syed Yaacob, Fahrul Huyop, Mailin Misson, Roswanira Abdul Wahab, Nurul Huda
    PeerJ.2022; 10: e13053.     CrossRef
  • Micrococcus porci sp. nov., Isolated from Feces of Black Pig (Sus scrofa)
    Ai-Yun Lee, Chia-Hsuan Chen, Jong-Shian Liou, Yu-Chun Lin, Moriyuki Hamada, Yu-Ting Wang, Lin-Liang Peng, Shen-Chang Chang, Chih-Chieh Chen, Chuen-Fu Lin, Lina Huang, Chien-Hsun Huang
    Life.2022; 12(11): 1749.     CrossRef
  • Pseudonocardia humida sp. nov., an Actinomycete Isolated from Mangrove Soil Showing Distinct Distribution Pattern of Biosynthetic Gene Clusters
    Zhen-Yu Zan, Xian-Feng Ge, Rui-Rui Huang, Wen-Zheng Liu
    Current Microbiology.2022;[Epub]     CrossRef
  • Occultella gossypii sp. nov., an alkali-resistant isolate from soil sampled in a cotton field
    Xianfeng Ge, Ruirui Huang, Wenzheng Liu
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Rhodococcus oxybenzonivorans sp. nov., a benzophenone-3-degrading bacterium, isolated from stream sediment
    Ju Hye Baek, Woonhee Baek, Sang Eun Jeong, Sung Chul Lee, Hyun Mi Jin, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology.2022;[Epub]     CrossRef
  • Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water
    Le Tran Tien Chau, Yong-Seok Kim, Chang-Jun Cha
    Antonie van Leeuwenhoek.2022; 115(3): 445.     CrossRef
  • Amsterdam urban canals contain novel niches for methane‐cycling microorganisms
    Koen A. J. Pelsma, Michiel H. in 't Zandt, Huub J. M. Op den Camp, Mike S. M. Jetten, Joshua F. Dean, Cornelia U. Welte
    Environmental Microbiology.2022; 24(1): 82.     CrossRef
  • Roseovarius carneus sp. nov., a novel bacterium isolated from a coastal phytoplankton bloom in Xiamen
    Xueqiong Sun, Dan Lin, Yu Han, Jia Sun, Jianing Ye, Beihan Chen, Kai Tang
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Tenacibaculum aquimarinum sp. nov., isolated from a marine alga and seawater
    Sylvia Kristyanto, Kyeong Ryeol Kim, Jaejoon Jung, Hyung Min Kim, Keunpil Kim, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Rheinheimera maricola sp. nov., isolated from seawater of the Yellow Sea
    Kyung Hyun Kim, Ju Hye Baek, Ruan Wenting, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Apilactobacillus apisilvae sp. nov., Nicolia spurrieriana gen. nov. sp. nov., Bombilactobacillus folatiphilus sp. nov. and Bombilactobacillus thymidiniphilus sp. nov., four new lactic acid bacterial isolates from stingless bees Tetragonula ca
    Scott A. Oliphant, Nathan S. Watson-Haigh, Krista M. Sumby, Jennifer Gardner, Scott Groom, Vladimir Jiranek
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
    Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
    Journal of Microbiology.2022; 60(6): 576.     CrossRef
  • Neokomagataea anthophila sp. nov., an osmotolerant acetic acid bacterium isolated in Thailand and emended description of the genus Neokomagataea
    Piyanat Charoenyingcharoen, Pattaraporn Yukphan, Sukunphat Malimas, Somsak Likhitrattanapisal, Somboon Tanasupawat, Yuzo Yamada
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Massilia soli sp. nov., isolated from soil
    Ju Hye Baek, Woonhee Baek, Wenting Ruan, Hye Su Jung, Sung Chul Lee, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma
    Ji-Ho Yoo, Jeong Eun Han, June-Young Lee, Su-Won Jeong, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Hojun Sung, Euon Jung Tak, Hyun Sik Kim, Pil Soo Kim, Jee-Won Choi, Do-Yeon Kim, In Chul Jeong, Do-Hun Gim, Seo Min Kang, Jin-Woo Bae
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Actinotalea soli sp. nov., isolated from Kubuqi Desert soil
    Jie Du, Weiwei Ping, Ya Chen, Huancheng Pang, Pengze Bai, Siqi Cui, Jianli Zhang
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Arsenicicoccus cauae sp. nov., isolated from the blood of a pediatric gastroenteritis patient
    Oh Joo Kweon, Kyung Hyun Kim, Hyung Min Kim, Shehzad Abid Khan, Ji Hun Jeong, Yong Kwan Lim, Hye Ryoun Kim, Che Ok Jeon, Mi-Kyung Lee
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Ramlibacter terrae sp. nov. and Ramlibacter montanisoli sp. nov., Isolated from Soil
    Shehzad Abid Khan, Hyung Min Kim, Ju Hye Baek, Hye Su Jung, Che Ok Jeon
    Journal of Microbiology and Biotechnology.2021; 31(9): 1210.     CrossRef
  • Ramlibacter algicola sp. nov., isolated from a freshwater alga Cryptomonas obovoidea
    Hyung Min Kim, Dong Min Han, Byung Hee Chun, Hye Su Jung, Kyung Hyun Kim, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef

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