Journal of Microbiology

Journal Articles

Effects of the loss of mismatch repair genes on single-strand annealing between divergent sequences in Saccharomyces cerevisiae: Ye-Seul Lim , Ju-Hee Choi , Kyu-Jin Ahn , Min-Ku Kim , Sung-Ho Bae; J. Microbiol. 2021;59(4):401-409. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1076-x

40 View
0 Download

Abstract: Eukaryotic genomes contain many duplicated genes closely located with each other, such as the hexose transporter (HXT) genes in Saccharomyces cerevisiae. They can potentially recombine via single-strand annealing (SSA) pathway. SSA between highly divergent sequences generates heteroduplex DNA intermediates with many mismatches, which can be corrected by mismatch repair (MMR), resulting in recombinant sequences with a single junction point. In this report, we demonstrate that SSA between HXT1 and HXT4 genes in MMR-deficient yeast cells produces recombinant genes with multiple-junctions resulting from alternating HXT1 and HXT4 tracts. The mutations in MMR genes had differential effects on SSA frequencies; msh6Δ mutation significantly stimulated SSA events, whereas msh2Δ and msh3Δ slightly suppressed it. We set up an assay that can identify a pair of recombinant genes derived from a single heteroduplex DNA. As a result, the recombinant genes with multiple-junctions were found to accompany genes with single-junctions. Based on the results presented here, a model was proposed to generate multiple-junctions in SSA pathway involving an alternative short-patch repair system.

Sutterella faecalis sp. nov., isolated from human faeces: Byeong Seob Oh , Ji-Sun Kim , Seung Yeob Yu , Seoung Woo Ryu , Seung-Hwan Park , Se Won Kang , Jam-Eon Park , Seung-Hyeon Choi , Kook-Il Han , Keun Chul Lee , Mi Kyung Eom , Min Kuk Suh , Han Sol Kim , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Je Hee Lee , Jung-Sook Lee , Ju Huck Lee; J. Microbiol. 2020;58(2):99-104. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9396-9

51 View
0 Download
7 Web of Science
7 Crossref

An obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming, and coccobacilli-shaped bacterial strain, designated KGMB03119T, was isolated from human faeces from a Korean. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the genus Sutterella and most closely related to Sutterlla wadsworthensis KCTC 15691T (96.8% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB03119T was 58.3 mol% as determined from its whole genome sequence. Strain KGMB03119T was asaccharolytic, catalase-positive, oxidase- and urease-negative. Furthermore, the isolate was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, arginine arylamidase, alanine arylamidase, and glycine arylamidase. The major cellular fatty acids (> 10%) of the isolate were C18:1ω9c and C16:0. Methylmenaquinone-5 (MMK-5, 100%) was the predominant isoprenoid quinone in the isolate. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain KGMB03119T represents a novel species, for which the name Sutterella faecalis sp. nov. is proposed. The type strain is KGMB03119T (= KCTC 15823T = NBRC 114254T).

Citations

Citations to this article as recorded by

In vitro gastrointestinal digestion and colonic fermentation of Mangiferin: Impacts on gut microbiota and metabolite profiles
Huilin Deng, Yaozhong Zheng, Qiongyao Wang, Jiaqi Peng, Weibin Bai, Lingmin Tian, Zouyan He, Rui Jiao
Journal of Functional Foods.2025; 124: 106667. CrossRef
An Analysis of the Digestive and Reproductive Tract Microbiota in Infertile Women with Obesity
Jose Bellver, Marta Gonzalez-Monfort, Sandra González, Bruno Toson, Elena Labarta, Gemma Castillón, Giulia Mariani, Carmina Vidal, Juan Giles, Fabio Cruz, Agustin Ballesteros, Marcos Ferrando, Juan Antonio García-Velasco, Diana Valbuena, Felipe Vilella, M
International Journal of Molecular Sciences.2024; 25(23): 12600. CrossRef
Update on novel validly published and included bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2023
Arianna Carella, Karen C. Carroll, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Short-chain fatty acids: Important components of the gut-brain axis against AD
Yan Huang, Yi Feng Wang, Jing Miao, Rui Fang Zheng, Jin Yao Li
Biomedicine & Pharmacotherapy.2024; 175: 116601. CrossRef
Bioinformatic Analysis of Sulfotransferases from an Unexplored Gut Microbe, Sutterella wadsworthensis 3_1_45B: Possible Roles towards Detoxification via Sulfonation by Members of the Human Gut Microbiome
Lauryn Langford, Dhara D. Shah
International Journal of Molecular Sciences.2024; 25(5): 2983. CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Longitudinal Study of the Effects of Flammulina velutipes Stipe Wastes on the Cecal Microbiota of Laying Hens
Jiali Wei, Huanwei Xiao, Yingbo Wei, Ivan Stève Nguepi Tsopmejio, Chang Sun, Haoyuan Wu, Zhouyu Jin, Hui Song, Suzanne Lynn Ishaq, Yunhe Xu
mSystems.2023;[Epub] CrossRef

Anaerotignum faecicola sp. nov., isolated from human faeces: Seung-Hyeon Choi , Ji-Sun Kim , Jam-Eon Park , Keun Chul Lee , Mi Kyung Eom , Byeong Seob Oh , Seung Yeob Yu , Se Won Kang , Kook-Il Han , Min Kuk Suh , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Je Hee Lee , Ju Huck Lee , Jung-Sook Lee , Seung-Hwan Park; J. Microbiol. 2019;57(12):1073-1078. Published online November 4, 2019; DOI: https://doi.org/10.1007/s12275-019-9268-3

135 View
0 Download
11 Web of Science
11 Crossref

Abstract

A strictly anaerobic bacterium, designated as strain KGMB- 03357T, was isolated from the faeces of a healthy Korean selected by Bundang Seoul National University based on health status. Cells of strain KGMB03357T are Gram-stain-positive, non-motile, non-spore-forming, and observed as straight or curved rods. The isolate grew at 10–45°C (optimum temperature of 40°C) and a pH range of 5.1–10.5 (optimum pH of 6.8). Analysis of phylogenetic trees based on the 16S rRNA gene sequences revealed that strain KGMB03357T forms a lineage within the genus Anaerotignum, and is most closely related to Anaerotignum lactatifermentans G17T (= KCTC 15066T, 96.1%), Anaerotignum propionicum DSM 1682T (= KCTC 5582T, 94.9%), Anaerotignum neopropionicum DSM 03847T (= KCTC 15564T, 94.9%), and Anaerotignum aminivorans SH021T (= KCTC 15705T, 94.8%). The ANI values between strain KGMB 03357T and members of the genus Anaerotignum were 73.3–71.0%, which are below the ANI criterion for interspecies identity. The DNA G + C content based on the whole-genome sequence is 47.3 mol%. The major cellular fatty acids of strain KGMB03357T are C16:0, C18:0, C18:1 cis 9, and anteiso-C15:0. Strain KGMB03357T contains meso-diaminopimelic acid as the diagnostic amino acid in the cell wall peptidoglycan. Based on the phenotypic, phylogenetic, and genomic properties, strain KGMB 03357T represents a novel species of the genus Anaerotignum, for which the name Anaerotignum faecicola sp. nov. is proposed. The type strain is KGMB03357T (= KCTC 15736T = DSM 107953T).

Citations

Citations to this article as recorded by

Dietary supplementation of solubles from shredded, steam-exploded pine particles modulates cecal microbiome composition in broiler chickens
Chris Major Ncho, Akshat Goel, Vaishali Gupta, Chae-Mi Jeong, Ji-Young Jung, Si-Young Ha, Jae-Kyung Yang, Yang-Ho Choi
Journal of Animal Science and Technology.2023; 65(5): 971. CrossRef
Cordyceps militaris polysaccharides modulate gut microbiota and improve metabolic disorders in mice with diet‐induced obesity
Shishi Huang, Yuan Zou, Hongbiao Tang, Jingyu Zhuang, Zhiwei Ye, Tao Wei, Junfang Lin, Qianwang Zheng
Journal of the Science of Food and Agriculture.2023; 103(4): 1885. CrossRef
Anaeropeptidivorans aminofermentans gen. nov., sp. nov., a mesophilic proteolytic salt-tolerant bacterium isolated from a laboratory-scale biogas fermenter, and emended description of Clostridium colinum
Nora Köller, Sarah Hahnke, Vladimir Zverlov, Daniel Wibberg, Andreas Klingl, Tobias Busche, Michael Klocke, Alfred Pühler, Andreas Schlüter, Wolfgang Liebl, Irena Maus
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Chakrabartyella piscis gen. nov., sp. nov., a member of the family Lachnospiraceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus
Bikiran Pardesi, Anthony M. Roberton, Emily M. Wollmuth, Esther R. Angert, Douglas I. Rosendale, William Lindsey White, Kendall D. Clements
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
New Insights into the Physiology of the Propionate Producers Anaerotignum propionicum and Anaerotignum neopropionicum (Formerly Clostridium propionicum and Clostridium neopropionicum)
Tina Baur, Peter Dürre
Microorganisms.2023; 11(3): 685. CrossRef
Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021
Erik Munson, Karen C. Carroll, Romney M. Humphries
Journal of Clinical Microbiology.2023;[Epub] CrossRef
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum
Sara Benito-Vaquerizo, Ivette Parera Olm, Thijs de Vroet, Peter J. Schaap, Diana Z. Sousa, Vitor A. P. Martins dos Santos, Maria Suarez-Diez
Microbial Cell Factories.2022;[Epub] CrossRef
Diarrhea with deficiency kidney-yang syndrome caused by adenine combined with Folium senna was associated with gut mucosal microbiota
Jiayuan Zhu, Xiaoya Li, Na Deng, Xinxin Peng, Zhoujin Tan
Frontiers in Microbiology.2022;[Epub] CrossRef
The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses
Irena Maus, Daniel Wibberg, Peter Belmann, Sarah Hahnke, Liren Huang, Cathrin Spröer, Boyke Bunk, Jochen Blom, Alexander Sczyrba, Alfred Pühler, Michael Klocke, Andreas Schlüter
Frontiers in Microbiology.2022;[Epub] CrossRef
The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity
Nicholas A. Lesniak, Alyxandria M. Schubert, Kaitlin J. Flynn, Jhansi L. Leslie, Hamide Sinani, Ingrid L. Bergin, Vincent B. Young, Patrick D. Schloss, Martin J. Blaser
mBio.2022;[Epub] CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 1443. CrossRef

Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces: Ji-Sun Kim , Keun Chul Lee , Min Kuk Suh , Kook-Il Han , Mi Kyung Eom , Ju Huck Lee , Seung-Hwan Park , Se Won Kang , Jam-Eon Park , Byeong Seob Oh , Seung Yeob Yu , Seung-Hyeon Choi , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Seung-Jo Yang , Jung-Sook Lee; J. Microbiol. 2019;57(1):38-44. Published online December 29, 2018; DOI: https://doi.org/10.1007/s12275-019-8550-8

78 View
0 Download
15 Web of Science
17 Crossref

Abstract

A Gram-stain-positive, obligately anaerobic, non-motile, nonspore- forming, and rod-shaped bacterial strain, designated KGMB01110T, was isolated from a faecal sample of a healthy male in South Korea. Phylogenetic analysis based on 16S rRNA gene showed that strain KGMB01110T belonged to Clostridium cluster XIVa and was most closely related to Mediterraneibacter glycyrrhizinilyticus KCTC 5760T (95.9% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB01110T based on its whole genome sequence was 44.1 mol%. The major cellular fatty acids (> 10%) of the isolate were C14:0 and C16:0. The strain KGMB01110T was positive for arginine dihydrolase, β-galactosidase-6-phosphatase, and alkaline phosphatase. The strain KGMB01110T also produced acid from D-glucose and D-rhamnose, and hydrolyzed gelatin and aesculin. Furthermore, HPLC analysis and UV-tests of culture supernatant revealed that the strain KGMB01110T produced butyrate as the major end product of glucose fermentation. Based on the phylogenetic and phenotypic characteristics, strain KGMB01110T represent a novel species of the genus Mediterraneibacter in the family Lachnospiraceae. The type strain is KGMB01110T (= KCTC 15684T = CCUG 72830T).

Citations

Citations to this article as recorded by

Desulfovibrio falkowii sp. nov., Porphyromonas miyakawae sp. nov., Mediterraneibacter flintii sp. nov. and Owariibacterium komagatae gen. nov., sp. nov., isolated from human faeces
Tomonari Hamaguchi, Misuzu Ohara, Atsushi Hisatomi, Kyohei Sekiguchi, Jun-ichi Takeda, Jun Ueyama, Mikako Ito, Hiroshi Nishiwaki, Tomoo Ogi, Masaaki Hirayama, Moriya Ohkuma, Mitsuo Sakamoto, Kinji Ohno
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study
Yanni Pu, Xiaofeng Zhou, Hao Cai, Tao Lou, Chenglin Liu, Mengmeng Kong, Zhonghan Sun, Yanren Wang, Ruyi Zhang, Yuxuan Zhu, Lin Ye, Yuanting Zheng, Baoli Zhu, Zhexue Quan, Guoping Zhao, Yan Zheng
Phenomics.2025;[Epub] CrossRef
Maternal nanoplastic ingestion induces an increase in offspring body weight through altered lipid species and microbiota
Bohyeon Jeong, Ji-Sun Kim, A Ra Kwon, Jangjae Lee, Subin Park, Jahong Koo, Wang Sik Lee, Jeong Yeob Baek, Won-Ho Shin, Jung-Sook Lee, Jinyoung Jeong, Won Kon Kim, Cho-Rok Jung, Nam-Soon Kim, Sung-Hee Cho, Da Yong Lee
Environment International.2024; 185: 108522. CrossRef
Dissemination of antibiotic resistance genes through fecal sewage treatment facilities to the ecosystem in rural area
Dachao Ma, Hongcheng Chen, Qingge Feng, Xuan Zhang, Deli Wu, Jinghang Feng, Shikun Cheng, Dongbo Wang, Zheng Liu, Qisong Zhong, Jinye Wei, Guozi Liu
Journal of Environmental Management.2023; 333: 117439. CrossRef
Metagenomic reconstructions of caecal microbiome in Landes, Roman and Zhedong White geese
J. Zhu, Y. Song, Y. Xiao, L. Ma, C. Hu, H. Yang, X. Wang, W. Lyu
British Poultry Science.2023; 64(5): 565. CrossRef
Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022
Erik Munson, Arianna Carella, Karen C. Carroll, Romney M. Humphries
Journal of Clinical Microbiology.2023;[Epub] CrossRef
Metatranscriptome analysis of blood in healthy individuals and irritable bowel syndrome patients
Lauma Jagare, Maija Rozenberga, Ivars Silamikelis, Laura Ansone, Ilze Elbere, Monta Briviba, Kaspars Megnis, Ilze Konrade, Ilze Birka, Zane Straume, Janis Klovins
Journal of Medical Microbiology .2023;[Epub] CrossRef
Comparative genomics reveals extensive intra-species genetic divergence of the prevalent gut commensal Ruminococcus gnavus
Rashidin Abdugheni, Chang Liu, Feng-Lan Liu, Nan Zhou, Cheng-Ying Jiang, Yonghong Liu, Li Li, Wen-Jun Li, Shuang-Jiang Liu
Microbial Genomics .2023;[Epub] CrossRef
Alterations of gut microbiota are associated with brain structural changes in the spectrum of Alzheimer's disease: the SILCODE study in Hainan cohort
Beiqi He, Can Sheng, Xianfeng Yu, Liang Zhang, Feng Chen, Ying Han
Frontiers in Aging Neuroscience.2023;[Epub] CrossRef
The evolution and competitive strategies of Akkermansia muciniphila in gut
Ji-Sun Kim, Se Won Kang, Ju Huck Lee, Seung-Hwan Park, Jung-Sook Lee
Gut Microbes.2022;[Epub] CrossRef
Fermentation outcomes of wheat cell wall related polysaccharides are driven by substrate effects as well as initial faecal inoculum
Shiyi Lu, Barbara A. Williams, Bernadine M. Flanagan, Hong Yao, Deirdre Mikkelsen, Michael J. Gidley
Food Hydrocolloids.2021; 120: 106978. CrossRef
Anaerococcus faecalis sp. nov., Isolated from Swine Faeces
Seung Yeob Yu, Byeong Seob Oh, Seoung Woo Ryu, Ji-Sun Kim, Jung-Sook Lee, Seung-Hwan Park, Se Won Kang, Jiyoung Lee, Mi-Kyung Lee, Hanna Choe, Won Yong Jung, Hyunjung Jung, Tai-Young Hur, Hyeun Bum Kim, Jae-Kyung Kim, Ju-Hoon Lee, Ju Huck Lee
Current Microbiology.2021; 78(7): 2589. CrossRef
In-Feed Supplementation of Resin Acid-Enriched Composition Modulates Gut Microbiota, Improves Growth Performance, and Reduces Post-Weaning Diarrhea and Gut Inflammation in Piglets
Md Karim Uddin, Shah Hasan, Md. Rayhan Mahmud, Olli Peltoniemi, Claudio Oliviero
Animals.2021; 11(9): 2511. CrossRef
Mechanism of gut butyric acid producing bacteria for prevention and treatment of inflammatory bowel disease
Ying-Yu Chen, Lian-Zhi Mao, Hua-Huan Liu, Su-Xia Sun
World Chinese Journal of Digestology.2019; 27(14): 907. CrossRef
Schaedlerella arabinosiphila gen. nov., sp. nov., a D-arabinose-utilizing bacterium isolated from faeces of C57BL/6J mice that is a close relative of Clostridium species ASF 502
Melissa Soh, Sou Miyake, Austin Lim, Yichen Ding, Henning Seedorf
International Journal of Systematic and Evolutionary Microbiology.2019; 69(11): 3616. CrossRef
Intestinibaculum porci gen. nov., sp. nov., a new member of the family Erysipelotrichaceae isolated from the small intestine of a swine
Ji-Sun Kim, Hanna Choe, Yu-Ri Lee, Kyung Mo Kim, Doo-Sang Park
Journal of Microbiology.2019; 57(5): 381. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef

First
Prev
Page of 1
Next
Last

Search