Journal of Microbiology

Volume 59(5); May 2021

Review

[Minireview]Potential roles of condensin in genome organization and beyond in fission yeast: Kyoung-Dong Kim; J. Microbiol. 2021;59(5):449-459. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1039-2

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The genome is highly organized hierarchically by the function of structural maintenance of chromosomes (SMC) complex proteins such as condensin and cohesin from bacteria to humans. Although the roles of SMC complex proteins have been well characterized, their specialized roles in nuclear processes remain unclear. Condensin and cohesin have distinct binding sites and mediate long-range and short-range genomic associations, respectively, to form cell cycle-specific genome organization. Condensin can be recruited to highly expressed genes as well as dispersed repeat genetic elements, such as Pol III-transcribed genes, LTR retrotransposon, and rDNA repeat. In particular, mitotic transcription factors Ace2 and Ams2 recruit condensin to their target genes, forming centromeric clustering during mitosis. Condensin is potentially involved in various chromosomal processes such as the mobility of chromosomes, chromosome territories, DNA reannealing, and transcription factories. The current knowledge of condensin in fission yeast summarized in this review can help us understand how condensin mediates genome organization and participates in chromosomal processes in other organisms.

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Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA−Protein Complexes
Debayan Chakraborty, Balaka Mondal, D. Thirumalai
Journal of Chemical Theory and Computation.2024; 20(3): 1398. CrossRef
Contributions of transcriptional noise to leukaemia evolution: KAT2A as a case-study
Cristina Pina
Philosophical Transactions of the Royal Society B: Biological Sciences.2024;[Epub] CrossRef
Viral remodeling of the 4D nucleome
Kyoung-Dong Kim, Paul M. Lieberman
Experimental & Molecular Medicine.2024; 56(4): 799. CrossRef
BiFCo: visualizing cohesin assembly/disassembly cycle in living cells
Emilio González-Martín, Juan Jiménez, Víctor A Tallada
Life Science Alliance.2023; 6(7): e202301945. CrossRef

Journal Articles

Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi: Young Joon Oh , Joon Yong Kim , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi; J. Microbiol. 2021;59(5):460-466. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-0513-1

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Abstract

To date, all species in the genus Salicibibacter have been isolated in Korean commercial kimchi. We aimed to describe the taxonomic characteristics of two strains, NKC5-3T and NKC21-4T, isolated from commercial kimchi collected from various regions in the Republic of Korea. Cells of these strains were rod-shaped, Gram-positive, aerobic, oxidase- and catalase- positive, non-motile, halophilic, and alkalitolerant. Both strains, unlike other species of the genus Salicibibacter, could not grow without NaCl. Strains NKC5-3T and NKC21-4T could tolerate up to 25.0% (w/v) NaCl (optimum 10%) and grow at pH 7.0–10.0 (optimum 8.5) and 8.0–9.0 (optimum 8.5), respectively; they showed 97.1% 16S rRNA gene sequence similarity to each other and were most closely related to S. kimchii NKC1-1T (97.0% and 96.8% similarity, respectively). The genome of strain NKC5-3T was nearly 4.6 Mb in size, with 4,456 protein-coding sequences (CDSs), whereas NKC21-4T genome was nearly 3.9 Mb in size, with 3,717 CDSs. OrthoANI values between the novel strains and S. kimchii NKC1-1T were far lower than the species demarcation threshold. NKC5-3T and NKC21-4T clustered together to form branches that were distinct from the other Salicibibacter species. The major fatty acids in these strains were anteiso-C15:0 and anteiso-C17:0, and the predominant menaquinone was menaquinone-7. The polar lipids of NKC5-3T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and five unidentified phospholipids (PL), and those of NKC21-4T included DPG, PG, seven unidentified PLs, and an unidentified lipid. Both isolates had DPG, which is the first case in the genus Salicibibacter. The genomic G + C content of strains NKC5-3T and NKC21-4T was 44.7 and 44.9 mol%, respectively. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic analyses, strains NKC5-3T (= KACC 22040T = DSM 111417T) and NKC21-4T (= KACC 22041T = DSM 111418T) represent two novel species of the genus Salicibibacter, for which the names Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov. are proposed.

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Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef

Agromyces laixinhei sp. nov. isolated from bat feces in China: Yanpeng Cheng , Yibo Bai , Yuyuan Huang , Jing Yang , Shan Lu , Dong Jin , Ji Pu , Han Zheng , Junqin Li , Ying Huang , Suping Wang , Jianguo Xu; J. Microbiol. 2021;59(5):467-475. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0546-5

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Abstract

Three rod-shaped, Gram-stain-positive, and catalase-positive, phenotypically closely related isolates (HY052T, HY050, and HY045) were obtained from fecal samples collected from bats in Guangxi province and Chongqing city of China. Circular, smooth, light-yellow colonies appeared on brain heart infusion plate after 24–48 h incubation at 28°C. The optimal pH for growth was between 6.0 and 7.5. Based on 16S rRNA, the three isolates were phylogenetically related to Agromyces terreus DS-10T, Agromyces aureus AR33T, Agromyces salentinus 20-5T, Agromyces allii UMS-62T, Agromyces lapidis CD55T, and Agromyces italicus CD1T. Moreover, based on 296 core genes, the phylogenomic tree indicated that the three isolates clustered together, closest to Agromyces cerinus VKM Ac- 1340T and Agromyces fucosus VKM Ac-1345T but separated distantly from other Agromyces species. The average nucleotide identity values between strain HY052T and other Agromyces species ranged from 79.3% to 87.9%, lower than the 95–96% threshold. Furthermore, the genome of strain HY052T contains a circular chromosome of 3,437,203 bp with G + C content of 69.0 mol%. Main fatty acids were anteiso-C15:0 and anteiso-C17:0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Rhamnose, ribose, and glucose were the primary cell wall sugars. The major peptidoglycan amino acids included alanine, glutamic acid, glycine, and 2,4-diaminobutyric acid. An additional remarkable difference from other Agromyces species is that MK-12 was the sole menaquinone in strain HY052T. Based on results from the polyphasic characterizations performed in this study, our isolates are proposed to be members of a novel species in genus Agromyces, named Agromyces laixinhei. The type strain is HY052T (= CGMCC 1.17175T = JCM 33695T).

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Juan Guzman, Maite Ortúzar, Anja Poehlein, Rolf Daniel, Martha E. Trujillo, Andreas Vilcinskas
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
The Threat of Potentially Pathogenic Bacteria in the Feces of Bats
Yuyuan Huang, Yamin Sun, Qianni Huang, Xianglian Lv, Ji Pu, Wentao Zhu, Shan Lu, Dong Jin, Liyun Liu, Zhengli Shi, Jing Yang, Jianguo Xu, Biao He
Microbiology Spectrum.2022;[Epub] CrossRef
Morphological and genomic characteristics of two novel halotolerant actinomycetes, Tomitella gaofuii sp. nov. and Tomitella fengzijianii sp. nov. isolated from bat faeces
Yuyuan Huang, Jing Yang, Shan Lu, Xin-He Lai, Dong Jin, Juan Zhou, Sihui Zhang, Qianni Huang, Xianglian Lv, Wentao Zhu, Ji Pu, Ying Huang, Liyun Liu, Jianguo Xu
Systematic and Applied Microbiology.2022; 45(2): 126294. CrossRef
Phenotypic and genomic characteristics of Brevibacterium zhoupengii sp. nov., a novel halotolerant actinomycete isolated from bat feces
Yuyuan Huang, Lingzhi Dong, Jian Gong, Jing Yang, Shan Lu, Xin-He Lai, Dong Jin, Qianni Huang, Ji Pu, Liyun Liu, Jianguo Xu
Journal of Microbiology.2022; 60(10): 977. CrossRef

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity: Dongwook Kim , Sein Park , Jongsik Chun; J. Microbiol. 2021;59(5):476-480. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-1154-0

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Abstract

The average amino acid identity (AAI) is an index of pairwise genomic relatedness, and multiple studies have proposed its application in prokaryotic taxonomy and related disciplines. AAI demonstrates better resolution in elucidating taxonomic structure beyond the species rank when compared with average nucleotide identity (ANI), which is a standard criterion in species delineation. However, an efficient and easy-to-use computational tool for AAI calculation in large-scale taxonomic studies is not yet available. Here, we introduce a bioinformatic pipeline, named EzAAI, which allows for rapid and accurate AAI calculation in prokaryote sequences. The EzAAI tool is based on the MMSeqs2 program and computes AAI values almost identical to those generated by the standard BLAST algorithm with significant improvements in the speed of these evaluations. Our pipeline also provides a function for hierarchical clustering to create dendrograms, which is an essential part of any taxonomic study. EzAAI is available for download as a standalone JAVA program at http:// leb.snu.ac.kr/ezaai.

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Current Microbiology.2024;[Epub] CrossRef
Schauerella fraxinea gen. nov., sp. nov., a bacterial species that colonises ash trees tolerant to dieback caused by Hymenoscyphus fraxineus
Undine Behrendt, Valentin Burghard, Sonja Wende, Kristina Ulrich, Jacqueline Wolf, Meina Neumann-Schaal, Andreas Ulrich
Systematic and Applied Microbiology.2024; 47(4): 126516. CrossRef
Roseateles subflavus sp. nov. and Roseateles aquae sp. nov., isolated from artificial pond water and Roseateles violae sp. nov., isolated from a Viola mandshurica root
Haejin Woo, Geeta Chhetri, Inhyup Kim, Yoonseop So, Sunho Park, Yonghee Jung, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
New Drinking Water Genome Catalog Identifies a Globally Distributed Bacterial Genus Adapted to Disinfected Drinking Water Systems
Ashwin S Sudarshan, Zihan Dai, Marco Gabrielli, Solize Oosthuizen-Vosloo, Konstantinos T. Konstantinidis, Ameet J Pinto
Environmental Science & Technology.2024; 58(37): 16475. CrossRef
Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov.
Pravin Kumar, Ashish Verma, Pooja Yadav, Joyasree Das, Lalit Kumar, Srinivasan Krishnamurthi
Science of The Total Environment.2024; 933: 172995. CrossRef
Draft Genome Sequences of Three Janthinobacterium lividum Strains Producing Violacein
Yu Jeong Lee, Jae-Cheol Lee, Kira Moon, Aslan Hwanhwi Lee, Byung Hee Chun
Microbiology and Biotechnology Letters.2024; 52(2): 215. CrossRef
Eubacterium album sp. nov., a butyrate-producing bacterium isolated from faeces of a healthy human
Feng-Lan Liu, Rashidin Abdugheni, Cong-Guo Ran, Nan Zhou, Shuang-Jiang Liu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode
Daniel Tamarit, Stephan Köstlbacher, Kathryn E. Appler, Kassiani Panagiotou, Valerie De Anda, Christian Rinke, Brett J. Baker, Thijs J.G. Ettema
Systematic and Applied Microbiology.2024; 47(4): 126525. CrossRef
Alterisphingorhabdus coralli gen. nov. sp. nov., a novel aerobic anoxygenic phototrophic bacteria isolated from reef-building coral
Chang Yan, Kun Zhang, Songbiao Shi, Lili Jian, Beilin Chen, Syed Raziuddin Quadri, Xinpeng Tian
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Raúl Riesco, Martha E. Trujillo
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Polymorphospora lycopeni sp. nov., a lycopene-producing actinomycetes isolated from lakeside soil sample of Baiyangdian
Jiashan Liu, Shilong Li, Xiaomin Duan, Hongmei Li, Xiumin Zhang
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Reclassification of Butyrivibrio crossotus Moore et al. 1976 (Approved Lists 1980) into a novel genus as Eshraghiella crossota gen. nov., comb. nov.
Mehdi Fatahi-Bafghi
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system
Zhongshuai Tian, Tao Hu, Edward C Holmes, Jingkai Ji, Weifeng Shi
Virus Evolution.2024;[Epub] CrossRef
Fodinisporobacter ferrooxydans gen. nov., sp. nov.—A Spore-Forming Ferrous-Oxidizing Bacterium Isolated from a Polymetallic Mine
Zhen Jiang, Xiutong Li, Zonglin Liang, Zebao Tan, Nan Zhou, Ying Liu, Zhenghua Liu, Huaqun Yin, Kun Luo, Supawadee Ingsriswang, Shuangjiang Liu, Chengying Jiang
Microorganisms.2024; 12(5): 853. CrossRef
An abundant bacterial phylum with nitrite-oxidizing potential in oligotrophic marine sediments
Rui Zhao, Steffen L. Jørgensen, Andrew R. Babbin
Communications Biology.2024;[Epub] CrossRef
Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean
Xavier Rey-Velasco, Teresa Lucena, Ana Belda, Josep M. Gasol, Olga Sánchez, David R. Arahal, María J. Pujalte
Frontiers in Microbiology.2024;[Epub] CrossRef
Ignisphaera cupida sp. nov., a hyperthermophilic hydrolytic archaeon from a hot spring of Uzon (Kamchatka), and emended description of the genus Ignisphaera
Olga A. Podosokorskaya, Alexander G. Elcheninov, Alexandra A. Klyukina, Alexander Y. Merkel
Systematic and Applied Microbiology.2024; 47(5): 126541. CrossRef
Genomic diversity in Paenibacillus polymyxa: unveiling distinct species groups and functional variability
Adrian Wallner, Livio Antonielli, Ouiza Mesguida, Patrice Rey, Stéphane Compant
BMC Genomics.2024;[Epub] CrossRef
Taxonomic and genomic characterization of a siderophore-producing bacterium, Rhodoligotrophos ferricapiens sp. nov isolated from lettuce cultivation soil
Yu-Jin Kim, Yong-Seok Kim, Chang-Jun Cha
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Comparative genomic analyses of Cutibacterium granulosum provide insights into genomic diversity
Peishan Chen, Shaojing Wang, Hongyan Li, Xiaoye Qi, Yuanyuan Hou, Ting Ma
Frontiers in Microbiology.2024;[Epub] CrossRef
A new insight on the xyl upper operon revealed through genomic investigation strategy
Xuefeng Tian, Shaojing Wang, Peishan Chen, Mingbo Yang, Zhaoying Su, Yue Ming, Guoqiang Li, Ting Ma
International Biodeterioration & Biodegradation.2024; 189: 105748. CrossRef
Genome-based reclassification of Spiroplasma atrichopogonis Koerber et al. 2005 as a later heterotypic synonym of Spiroplasma mirum Tully et al. 1982
Vatsal Bhargava, Darshana Lahon, Sonal Gupta, Jasvinder Kaur, Pushp Lata
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Lysinibacillus piscis sp. nov. isolated from the gut of mottled spinefoot Siganus fuscescens
Hiyu Kanbe, Yuki Sano, Kazumori Mise, Shusei Kanie, Natsumi Ushijima, Keisuke Kawano, Minoru Kihara, Hideomi Itoh
Archives of Microbiology.2024;[Epub] CrossRef
Specific amino acid changes correlate with pathogenic flavobacteria
Vincent Gélinas, Valérie E. Paquet, Maude F. Paquet, Steve J. Charette, Antony T. Vincent
Genome.2024; 67(10): 368. CrossRef
Aurantiacibacter flavus sp. nov. and Aurantiacibacter gilvus sp. nov., isolated from the mudflat of Suaeda japonica colonies
Sunho Park, Inhyup Kim, Haejin Woo, Hyunji Lee, Subin Yook, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Splendidivirga corallicola gen. nov., sp. nov. and Agaribacillus aureus gen. nov., sp. nov., two bacteria isolated from coral Porites lutea, and proposal of Splendidivirgaceae fam. nov.
Jin Li, Jixin Luo, Mi Li, Chenyan Wang, Siyu Hu, Kun Lu, Guanghua Wang
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
The Genome of a New Halorubrum distributum Strain ICIS4 Isolated from the Culture of a Microalga Dunaliella salina
E. A. Selivanova, A. S. Balkin, Yu. A. Khlopko, V. Ya. Kataev, A. O. Plotnikov
Microbiology.2024; 93(4): 482. CrossRef
Peteryoungia algae sp. nov. isolated from seaweeds of Gouqi Island, China, and its unique genetic features among Peteryoungia strains
Jun Yin, Min He, Xiao-Xiao Liu, Chang-Bin Ren, Hou-Hong Liu, Hai Luo, Gen Chen, Ze-Fei Wang, Sanjit Chandra Debnath, Pin-Mei Wang, Hai-Xin Chen, Dao-Qiong Zheng
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Methylomonas rivi sp. nov., Methylomonas rosea sp. nov., Methylomonas aurea sp. nov. and Methylomonas subterranea sp. nov., type I methane-oxidizing bacteria isolated from a freshwater creek and the deep terrestrial subsurface
Christopher A. Abin, Christopher T. Garner, Krithivasan Sankaranarayanan, Reid A. Sindelar, Kyrah F. Kotary, Rosa M. Garner, Samantha C. Barclay, Haiyuan Cai, Paul A. Lawson, Lee R. Krumholz
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Phylogenomic discernments into Anaerolineaceae thermal adaptations and the proposal of a candidate genus Mesolinea
Katherine Bedoya-Urrego, Juan F. Alzate
Frontiers in Microbiology.2024;[Epub] CrossRef
Unraveling the genomic secrets of Tritonibacter mobilis AK171: a plant growth-promoting bacterium isolated from Avicennia marina
Amal Khalaf Alghamdi, Sabiha Parween, Heribert Hirt, Maged M. Saad
BMC Genomics.2024;[Epub] CrossRef
Ochrobactrum chromiisoli sp. nov., Isolated from Chromium-Contaminated Soil
Yi Yang, Zhe Xu, Li Yang, Meng-yao Hu, Guang-yang Jiang, Jia Chen, Yi-chen Yang, Yongqiang Tian
Current Microbiology.2024;[Epub] CrossRef
Spartinivicinus poritis sp. nov., a red pigment-producing bacterium isolated from a scleractinian coral Porites lutea
Sumbal Sajid, Guoqiang Zhang, Zongyao Zhang, Yishan Lu, Lianguo Chen, Lin Cai
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Tardiphaga alba sp. nov., a heavy-metal-tolerant bacterium isolated from garden soil
Zhihua Bao, Chaojun Wang, Jiahui Cao, Tingting Zhang, Yong Guo, Yoshinori Sato, Tomoyasu Nishizawa, Hiroyuki Ohta
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments
Yue Zheng, Baozhan Wang, Ping Gao, Yiyan Yang, Bu Xu, Xiaoquan Su, Daliang Ning, Qing Tao, Qian Li, Feng Zhao, Dazhi Wang, Yao Zhang, Meng Li, Mari-K H Winkler, Anitra E Ingalls, Jizhong Zhou, Chuanlun Zhang, David A Stahl, Jiandong Jiang, Willm Martens-H
The ISME Journal.2024;[Epub] CrossRef
Refining the taxonomy of the order Hyphomicrobiales (Rhizobiales) based on whole genome comparisons of over 130 type strains
George C. diCenzo, Yuqi Yang, J. Peter W. Young, Nemanja Kuzmanović
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Luteimonas flava sp. nov. and Aquilutibacter rugosus gen. nov., sp. nov., isolated from freshwater environments in China and re-examining the taxonomic status of genera Luteimonas and Lysobacter
Huibin Lu, Li Chen, Yujing Wang, Peng Xing, Qinglong Wu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken
Bibiana Rios-Galicia, Johan S. Sáenz, Timur Yergaliyev, Christoph Roth, Amélia Camarinha-Silva, Jana Seifert
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Parendozoicomonas callyspongiae sp. nov. Isolated from a Marine Sponge, Callyspongia elongate, and Reclassification of Sansalvadorimonas verongulae as Parendozoicomonas verongulae comb. nov.
Soo-Bin Kim, Kyung Hyun Kim, Jin-Sook Park
Current Microbiology.2024;[Epub] CrossRef
Novel phage infecting the Roseobacter CHUG lineage reveals a diverse and globally distributed phage family
Zuqing Wu, Luyuan Guo, Ying Wu, Mingyu Yang, Sen Du, Jiabing Shao, Zefeng Zhang, Yanlin Zhao, Michael J. Imperiale
mSphere.2024;[Epub] CrossRef
Biochip-Based Identification of Mycobacterial Species in Russia
Danila Zimenkov, Vyacheslav Zhuravlev, Anastasia Ushtanit, Marina Filippova, Uliana Semenova, Natalia Solovieva, Maria Sviridenko, Anastasia Khakhalina, Svetlana Safonova, Marina Makarova, Elizaveta Gordeeva, Elena Guselnikova, Yakov Schwartz, Natalia Sta
International Journal of Molecular Sciences.2024; 25(23): 13200. CrossRef
Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon
Gracee K. Tothero, Rene L. Hoover, Ibrahim F. Farag, Daniel I. Kaplan, Pamela Weisenhorn, David Emerson, Clara S. Chan, Arpita Bose
Applied and Environmental Microbiology.2024;[Epub] CrossRef
Svornostia abyssi gen. nov., sp. nov. isolated from the world’s deepest silver–uranium mine currently devoted to the extraction of radon-saturated water
Gabriela Kapinusova, Jachym Suman, Michal Strejcek, Petr Pajer, Tomas Cajthaml, Pavel Ulbrich, Meina Neumann-Schaal, Ondrej Uhlik
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Genomic analysis of the class Phycisphaerae reveals a versatile group of complex carbon-degrading bacteria
Wouter B. Lenferink, Theo A. van Alen, Mike S. M. Jetten, Huub J. M. Op den Camp, Maartje A. H. J. van Kessel, Sebastian Lücker
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Genome streamlining in Parcubacteria transitioning from soil to groundwater
Narendrakumar M. Chaudhari, Olga M. Pérez-Carrascal, Will A. Overholt, Kai U. Totsche, Kirsten Küsel
Environmental Microbiome.2024;[Epub] CrossRef
Sulfurospirillum diekertiae sp. nov., a tetrachloroethene-respiring bacterium isolated from contaminated soil
Huijuan Jin, Leitao Huo, Yi Yang, Yan Lv, Jingjing Wang, Julien Maillard, Christof Holliger, Frank E. Löffler, Jun Yan
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Description of Pseudocalidococcus azoricus gen. sp. nov. (Thermosynechococcaceae, Cyanobacteria), a Rare but Widely Distributed Coccoid Cyanobacteria
Rúben Luz, Rita Cordeiro, Jan Kaštovský, Amélia Fonseca, Ralph Urbatzka, Vitor Vasconcelos, Vítor Gonçalves
Diversity.2023; 15(12): 1157. CrossRef
The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea
Ramona Marasco, Grégoire Michoud, Fatmah O. Sefrji, Marco Fusi, Chakkiath P. Antony, Kholoud A. Seferji, Alan Barozzi, Giuseppe Merlino, Daniele Daffonchio
Frontiers in Microbiology.2023;[Epub] CrossRef
Danxiaibacter flavus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from forest soil on Danxia Mountain
Zhuo-Huan Zheng, Chun-Yan Lu, Wen-Hui Lian, Jia-Rui Han, Fang Chen, Ting Zhou, Shuai Li, Lei Dong, Wen-Jun Li
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure conditions
Jinbo Xu, Lu Wang, Weifeng Lv, Xinmin Song, Yong Nie, Xiao-Lei Wu
Frontiers in Microbiology.2023;[Epub] CrossRef
Comparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum
Ana Marina Pedrolo, Filipe Pereira Matteoli, Cláudio Roberto Fônseca Sousa Soares, Ana Carolina Maisonnave Arisi
Microbial Ecology.2023; 86(1): 563. 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
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
Phocaeicola oris sp. nov., an anaerobic bacterium isolated from the saliva of a patient with oral squamous cell carcinoma
Jiung-Wen Chen, Chao-Jen Shih, Li-Wha Wu, Yen-Chi Wu, Wei-Fan Chiang, Yuh-Ling Chen, Jer-Horng Wu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov.
Samuel Imisi Awala, Joo-Han Gwak, Yongman Kim, Chanmee Seo, Andrea Strazzulli, Song-Gun Kim, Sung-Keun Rhee
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov
Can Cui, Dong Han, Jing Hou, Heng-Lin Cui
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Complete genome sequence analysis of plant growth-promoting bacterium, Isoptericola sp. AK164 isolated from the rhizosphere of Avicennia marina growing at the Red Sea coast
Amal Khalaf Alghamdi, Sabiha Parween, Heribert Hirt, Maged M. Saad
Archives of Microbiology.2023;[Epub] CrossRef
Draft genome sequence of Hahella sp. CR1 and its ability in producing cellulases for saccharifying agricultural biomass
Melvin Chun Yun Tan, Muhammad Ramziuddin Zakaria, Kok Jun Liew, Chun Shiong Chong
Archives of Microbiology.2023;[Epub] CrossRef
Sedimenticola hydrogenitrophicus sp. nov. a chemolithoautotrophic bacterium isolated from a terrestrial mud volcano, and proposal of Sedimenticolaceae fam. nov. in the order Chromatiales
Galina Slobodkina, Alexander Merkel, Nataliya Ratnikova, Alexandra Kuchierskaya, Alexander Slobodkin
Systematic and Applied Microbiology.2023; 46(5): 126451. CrossRef
Comparative genomic assessment of members of genus Tenacibaculum: an exploratory study
Rohit Satyam, Shaban Ahmad, Khalid Raza
Molecular Genetics and Genomics.2023; 298(5): 979. CrossRef
Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species
Mina Bizic, Traian Brad, Danny Ionescu, Lucian Barbu-Tudoran, Luca Zoccarato, Joost W Aerts, Paul-Emile Contarini, Olivier Gros, Jean-Marie Volland, Radu Popa, Jessica Ody, Daniel Vellone, Jean-François Flot, Scott Tighe, Serban M Sarbu
The ISME Journal.2023; 17(3): 340. CrossRef
Solicola gregarius gen. nov., sp. nov., a soil actinobacterium isolated after enhanced cultivation with Micrococcus luteus culture supernatant
Marco A. Lopez Marin, Jachym Suman, Kunal Jani, Pavel Ulbrich, Tomas Cajthaml, Alena Filipova, Petr Pajer, Meina Neumann-Schaal, Michal Strejcek, Ondrej Uhlik
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation
Wen-Bo Nie, Guo-Jun Xie, Xin Tan, Jie Ding, Yang Lu, Yi Chen, Chun Yang, Qiang He, Bing-Feng Liu, Defeng Xing, Nanqi Ren
Environmental Science & Technology.2023; 57(17): 7029. CrossRef
Allocoprobacillus halotolerans gen. nov., sp. nov and Coprobacter tertius sp. nov., isolated from human gut microbiota
Nancy M. Y. Teng, Raymond Kiu, Rhiannon Evans, David J. Baker, Christian Zenner, Stephen D. Robinson, Lindsay J. Hall
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Aridibaculum aurantiacum gen. nov., sp. nov., isolated from the Kumtag Desert soil
Lei Dong, Shuai Li, Guo-Yuan Shi, Jia-Rui Han, Chun-Yan Lu, Wen-Hui Lian, Ling-Xiang Yue, Dalal Hussien M. Alkhalifah, Wael N. Hozzein, Wen-Jun Li
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Acidaminococcus homini s sp. nov., Amedibacillus hominis sp. nov., Lientehia hominis gen. nov. sp. nov., Merdimmobilis hominis gen. nov. sp. nov., and Paraeggerthella hominis sp. nov., isolated from human faeces
Rashidin Abdugheni, Dan-Hua Li, Yu-Jing Wang, Meng-Xuan Du, Nan Zhou, Chang Liu, Shuang-Jiang Liu
International Journal of Systematic and Evolutionary Microbiology.2023;[Epub] CrossRef
Vogesella aquatica sp. nov. and Vogesella margarita sp. nov., isolated from rivers in Southwest China
Huibin Lu, Li Chen, Lingyang Kong, Linpei Huang, Guangjie Chen
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Dermatobacter hominis gen. nov., sp. nov., a new member of the family Iamiaceae, revealed the potential utilisation of skin-derived metabolites
HyungWoo Jo, Chaeyun Baek, Young Mok Heo, Hye-Been Kim, Haeun Lee, Seunghyun Kang, Seyoung Mun, Yunseok Oh, Doyeong Ko, Kyudong Han, Raúl Riesco, Martha E. Trujillo, Dong-Geol Lee
Antonie van Leeuwenhoek.2023; 116(11): 1139. CrossRef
Dynamic Development of Viral and Bacterial Diversity during Grass Silage Preservation
Johan S. Sáenz, Bibiana Rios-Galicia, Bianca Rehkugler, Jana Seifert
Viruses.2023; 15(4): 951. CrossRef
Alteromonas gilva sp. nov. and Erythrobacter fulvus sp. nov., isolated from a tidal mudflat
Sunho Park, Inhyup Kim, Geeta Chhetri, Yoonseop So, Yonghee Jung, Haejin Woo, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Two novel alkalitolerant species Pseudalkalibacillus spartinae sp. nov. and Pseudalkalibacillus sedimenti sp. nov.
Guo-Hong Liu, Shuang Han, Bing Li, Rui-Li Li, Huai Shi, Qian-Qian Chen, Hend A. Alwathnani, Christopher Rensing, Shun-Gui Zhou
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Description of Brachybacterium sillae sp. nov., a thermophilic bacterium isolated from a hot spring
Dariimaa Ganbat, DoKyung Oh, Yong-Jik Lee, Dong-Woo Lee, Seong-Bo Kim, Won-Jae Chi, Ki-Eun Lee, Byoung-Hee Lee, You-Jung Jung, Jung-Sook Lee, Sang-Jae Lee
Antonie van Leeuwenhoek.2023; 116(8): 791. CrossRef
Bacillus mexicanus sp. nov., a biological control bacterium isolated from the common bean (Phaseolus vulgaris L.) crop in Sinaloa, Mexico
Sergio de los Santos Villalobos, Carmen María Félix Pablos, Valeria Valenzuela Ruiz, Fannie I. Parra Cota
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors
Patricia Bovio-Winkler, Leandro D. Guerrero, Leonardo Erijman, Pía Oyarzúa, María Eugenia Suárez-Ojeda, Angela Cabezas, Claudia Etchebehere
BMC Microbiology.2023;[Epub] CrossRef
Potential for homoacetogenesis via the Wood–Ljungdahl pathway in Korarchaeia lineages from marine hydrothermal vents
Francesca Vulcano, Petra Hribovšek, Emily Olesin Denny, Ida H. Steen, Runar Stokke
Environmental Microbiology Reports.2023; 15(6): 698. CrossRef
Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated
James G. Volmer, Rochelle M. Soo, Paul N. Evans, Emily C. Hoedt, Ana L. Astorga Alsina, Benjamin J. Woodcroft, Gene W. Tyson, Philip Hugenholtz, Mark Morrison
BMC Biology.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
Proposal to transfer Bacillus massiliigorillae to the genus Peribacillus as Peribacillus massiliigorillae comb. nov., and Bacillus sinesaloumensis to the genus Ferdinandcohnia as Ferdinandcohnia sinesaloumensis comb. nov
Awalagaway Dhulappa, Manik Prabhu Narsing Rao, Haijie Wang, Bhagwan Narayan Rekadwad, Ying-Qian Kang
Archives of Microbiology.2023;[Epub] CrossRef
Characterization and Antioxidant Activity of Exopolysaccharides Produced by Lysobacter soyae sp. nov Isolated from the Root of Glycine max L.
Inhyup Kim, Geeta Chhetri, Yoonseop So, Sunho Park, Yonghee Jung, Haejin Woo, Taegun Seo
Microorganisms.2023; 11(8): 1900. CrossRef
Leucobacter edaphi sp. nov., a highly chromate-tolerant bacterium isolated from chromium containing chemical plant soil
Bijun Zheng, Zhe Xu, Li Yang, Guangyang Jiang, Jia Chen, Yichen Yang, Yongqiang Tian
Antonie van Leeuwenhoek.2023; 116(12): 1433. CrossRef
Roseateles albus sp. nov., Roseateles koreensis sp. nov. and Janthinobacterium fluminis sp. nov., isolated from freshwater at Jucheon River, and emended description of Roseateles aquaticus comb. nov.
Sunho Park, Inhyup Kim, Geeta Chhetri, Yoonseop So, Yonghee Jung, Haejin Woo, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Isolation and Genomic Analysis of 3-Chlorobenzoate-Degrading Bacteria from Soil
Ifat Ara, Ryota Moriuchi, Hideo Dohra, Kazuhide Kimbara, Naoto Ogawa, Masaki Shintani
Microorganisms.2023; 11(7): 1684. CrossRef
Brytella acorum gen. nov., sp. nov., a novel acetic acid bacterium from sour beverages
Atena Sadat Sombolestani, Dries Bongaerts, Eliza Depoorter, Ilse Cleenwerck, Anneleen D. Wieme, Scott J. Britton, Stefan Weckx, Luc De Vuyst, Peter Vandamme
Systematic and Applied Microbiology.2023; 46(5): 126440. CrossRef
Complete genome sequence of Vibrio gazogenes PB1: an estuarine bacterium capable of producing prodigiosin from starch or cellulose
Bincy Baby, Dhanya Vijay, Pretty S. Philip, Afra A. Alnuaimi, Hessa M. Almansoori, Sarah O. Areidat, Gulfaraz Khan, Ranjit Vijayan, M. Kalim Akhtar
Frontiers in Marine Science.2023;[Epub] CrossRef
Tianweitania aestuarii sp. nov., isolated from a coastal dune, reclassification of Corticibacterium populi as Tianweitania populi comb. nov., and emended description of the genus Tianweitania
Ji Hyeon Song, Sooyeon Park, Jung-Sook Lee, Wonyong Kim, Jung-Hoon Yoon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Fluviispira vulneris sp. nov., isolated from human wound secretions
Peijuan Tang, Na Peng, Pengwen Ouyang, Sheng Long, Zhenhua Wei, Xingchun Chen, Pinghua Qu, Liangyi Xie
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Variations of microbial community in Aconitum carmichaeli Debx. rhizosphere soilin a short-term continuous cropping system: Xia Fei , Wang Lina , Chen Jiayang , Fu Meng , Wang Guodong , Yan Yaping , Cui Langjun; J. Microbiol. 2021;59(5):481-490. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0515-z

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Abstract

Aconitum carmichaeli Debx. (Ranunculaceae) is a potential source of an important herbal drug named “Fuzi”, which is derived from the lateral root of the plant. Increased therapeutic usage resulted in the great demand for artificial cultivation of A. carmichaeli, however, the obstacles caused by continuous cropping is a serious problem. Continuous cropping has shown to affect the soil biological and non-biological factors. The current study attempted to discover the variations of microbial communities and soil properties in shortterm continuous cropping of A. carmichaeli. An experimental procedure with A. carmichaeli planted two years continuously was established. The variation of the soil microbial community, disease incidence, soil properties, and the correlation between soil microbe and disease incidence were investigated. The disease incidence increased during the continuous cropping of A. carmichaeli. The PCoA and LefSe results indicated that fungal communities in rhizosphere soil were altered during the short-term continuous croppingand the bacterial community was disturbed by the cultivation of A. carmichaeli, however, in the following two years of continuous cropping period, the soil bacterial community has not changed obviously. Proportions of some fungal and bacterial genera were varied significantly (p < 0.05), and some genera of microflora showed a significant correlation with adisease incidence of A. carmichaeli. Microorganisms contributing to community composition discrepancy were also elucidated. Continuous cropping of A. carmichaeli disturbed the rhizosphere soil microbial community and altered the soil chemical parameters and soil pH. These variations in soil may be related to the occurrence of plant diseases. The current study will not only provide theoretical and experimental evidence for the A. carmichaeli continuous cropping obstacles but will also contribute to A. carmichaeli agricultural production and soil improvement.

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Li Ma, Wenquan Niu, Guochun Li, Erxin Zhang, Jun Sun, Qian Zhang, Kadambot H. M. Siddique
Land Degradation & Development.2023; 34(5): 1323. CrossRef
Strip intercropping with local crops increased Aconitum carmichaeli yield and soil quality
Chen Liu, Pengdong Yan, Zhenyu Liu, Jianglan Zhang, Guoyan Zhang, Langjun Cui
Frontiers in Plant Science.2023;[Epub] CrossRef
Variation of Soil Microbial Community and Sterilization to Fusarium oxysporum f. sp. niveum Play Roles in Slightly Acidic Electrolyzed Water-Alleviated Watermelon Continuous Cropping Obstacle
Xue Wu, Cuinan Wu, Daipeng Lu, Yiwen Wu, Zhangying Ye, Liru Xia, Yudong Sun, Encai Bao, Lin Ye, Yuxin Tang, Kai Cao
Frontiers in Microbiology.2022;[Epub] CrossRef
Microbial community diversity and function analysis of Aconitum carmichaelii Debeaux in rhizosphere soil of farmlands in Southwest China
Tingting Pu, Jie Liu, Jingjing Dong, Jun Qian, Zhongyu Zhou, Conglong Xia, Guangfei Wei, Baozhong Duan
Frontiers in Microbiology.2022;[Epub] CrossRef
Contributions of Beneficial Microorganisms in Soil Remediation and Quality Improvement of Medicinal Plants
Gang Wang, Ying Ren, Xuanjiao Bai, Yuying Su, Jianping Han
Plants.2022; 11(23): 3200. CrossRef
Crop rotation affects biological properties of rhizosphere soil and productivity of Kimchi cabbage (Brassica rapa ssp. pekinensis) compared to monoculture
Gye-ryeong Bak, Gye-jun Lee, Jung-tae Lee, Sam-nyu Jee
Horticulture, Environment, and Biotechnology.2022; 63(5): 613. CrossRef
Characteristics of Isolates of Pseudomonas aeruginosa and Serratia marcescens Associated With Post-harvest Fuzi (Aconitum carmichaelii) Rot and Their Novel Loop-Mediated Isothermal Amplification Detection Methods
Meng Fu, Xin Zhang, Bei Chen, Mingzhu Li, Guoyan Zhang, Langjun Cui
Frontiers in Microbiology.2021;[Epub] CrossRef

Raman spectroscopy reveals alteration of spore compositions under different nutritional conditions in Lysinibacillus boronitolerans YS11: Youngung Ryu , Minyoung Hong , Soo Bin Kim , Tae Kwon Lee , Woojun Park; J. Microbiol. 2021;59(5):491-499. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0679-6

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Abstract

Little is known about final spores components when bacteria undergo sporulation under different nutrient conditions. Different degrees of resistance and germination rates were observed in the three types of spores of Lysinibacillus boronitolerans YS11 (SD, Spores formed in Difco sporulation mediumTM; SC and SF, Spores formed in an agricultural byproduct medium with 10 mM CaCl2 and with 10 mM FeSO4, respectively). Stronger UV resistance was recorded for SF with 1.8–2.3-fold greater survival than SC and SD under UV treatment. The three spore types showed similar heat resistances at 80°C, but survival rates of SC and SD were much higher (~1,000 times) than those of SF at 90°C. However, germination capacity of SF was 20% higher than those of SD and SC on Luria-Bertani agar plates for 24 h. SF germinated more rapidly in a liquid medium with high NaCl concentrations than SC and SD, but became slower under alkaline conditions. Raman spectroscopy was used to analyze the heterogeneities in the three types of vegetative cells and their spores under different nutritional conditions. Exponentially grown-each vegetative cells had different overall Raman peak values. Raman peaks of SC, SD, and SF also showed differences in adenine and amide III compositions and nucleic acid contents. Our data along with Raman spectroscopy provided the evidence that spores formed under under different growth conditions possess very different cellular components, which affected their survival and germination rates.

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Characterization of the Bacillus cereus spore killed by plasma-activated water (PAW)
Xiao Hu, Pengfei Ge, Xiaomeng Wang, Xinyu Liao, Jinsong Feng, Ruiling Lv, Tian Ding
Food Research International.2024; 196: 115058. CrossRef
Alleviation of H2O2 toxicity by extracellular catalases in the phycosphere of Microcystis aeruginosa
Yerim Park, Wonjae Kim, Yeji Cha, Minkyung Kim, Woojun Park
Harmful Algae.2024; 137: 102680. CrossRef
Effects of sporulation conditions on the growth, germination, and resistance of Clostridium perfringens spores
Dong Liang, Xiaoshuang Cui, Miaoyun Li, Yaodi Zhu, Lijun Zhao, Shijie Liu, Gaiming Zhao, Na Wang, Yangyang Ma, Lina Xu
International Journal of Food Microbiology.2023; 396: 110200. CrossRef
Lysinibacilli: A Biological Factories Intended for Bio-Insecticidal, Bio-Control, and Bioremediation Activities
Qazi Mohammad Sajid Jamal, Varish Ahmad
Journal of Fungi.2022; 8(12): 1288. CrossRef
Discrimination of Stressed and Non-Stressed Food-Related Bacteria Using Raman-Microspectroscopy
Daniel Klein, René Breuch, Jessica Reinmüller, Carsten Engelhard, Peter Kaul
Foods.2022; 11(10): 1506. CrossRef
Detection of low numbers of bacterial cells in a pharmaceutical drug product using Raman spectroscopy and PLS-DA multivariate analysis
R. A. Grosso, A. R. Walther, E. Brunbech, A. Sørensen, B. Schebye, K. E. Olsen, H. Qu, M. A. B. Hedegaard, E. C. Arnspang
The Analyst.2022; 147(15): 3593. CrossRef
Linkage between bacterial community-mediated hydrogen peroxide detoxification and the growth of Microcystis aeruginosa
Minkyung Kim, Wonjae Kim, Yunho Lee, Woojun Park
Water Research.2021; 207: 117784. CrossRef

Role of melatonin in murine “restraint stress”-induced dysfunction of colonic microbiota: Rutao Lin , Zixu Wang , Jing Cao , Ting Gao , Yulan Dong , Yaoxing Chen; J. Microbiol. 2021;59(5):500-512. Published online February 25, 2021; DOI: https://doi.org/10.1007/s12275-021-0305-7

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Abstract

Intestinal diseases caused by physiological stress have become a severe public health threat worldwide. Disturbances in the gut microbiota-host relationship have been associated with irritable bowel disease (IBD), while melatonin (MT) has antiinflammatory and antioxidant effects. The objective of this study was to investigate the mechanisms by which MT-mediated protection mitigated stress-induced intestinal microbiota dysbiosis and inflammation. We successfully established a murine restraint stress model with and without MT supplementation. Mice subjected to restraint stress had significantly elevated corticosterone (CORT) levels, decreased MT levels in their plasma, elevated colonic ROS levels and increased bacterial abundance, including Bacteroides and Tyzzerella, in their colon tract, which led to elevated expression of Toll-like receptor (TLR) 2/4, p-P65 and p-IκB. In contrast, supplementation with 20 mg/kg MT reversed the elevation of the plasma CORT levels, downregulated the colon ROS levels and inhibited the changes in the intestinal microbiota induced by restraint stress. These effects, in turn, inhibited the activities of TLR2 and TLR4, p-P65 and p-IκB, and decreased the inflammatory reaction induced by restraint stress. Our results suggested that MT may mitigate “restraint stress”-induced colonic microbiota dysbiosis and intestinal inflammation by inhibiting the activation of the NF-κB pathway.

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Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders
Petra Zimmermann, Salome Kurth, Benoit Pugin, Nicholas A. Bokulich
npj Biofilms and Microbiomes.2024;[Epub] CrossRef
Toll-like receptor 4 plays a vital role in irritable bowel syndrome: a scoping review
Xuemeng Wan, Liyuan Wang, Zhiling Wang, Chaomin Wan
Frontiers in Immunology.2024;[Epub] CrossRef
Christensenella minuta mitigates behavioral and cardiometabolic hallmarks of social defeat stress
A. Agusti, GV. Molina-Mendoza, M. Tamayo, V. Rossini, MC. Cenit, C. Frances-Cuesta, V. Tolosa-Enguis, EM. Gómez Del Pulgar, A. Flor-Duro, Y. Sanz
Biomedicine & Pharmacotherapy.2024; 180: 117377. CrossRef
The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota–gut–brain axis perspective
Sarah‐Jane Leigh, Friederike Uhlig, Lars Wilmes, Paula Sanchez‐Diaz, Cassandra E. Gheorghe, Michael S. Goodson, Nancy Kelley‐Loughnane, Niall P. Hyland, John F. Cryan, Gerard Clarke
The Journal of Physiology.2023; 601(20): 4491. CrossRef
Melatonin as a Mediator of the Gut Microbiota–Host Interaction: Implications for Health and Disease
María-Ángeles Bonmatí-Carrión, Maria-Angeles Rol
Antioxidants.2023; 13(1): 34. CrossRef
INVESTIGATION OF THE ROLE OF STRESS IN MALE INFERTILITY AND THE EFFECT OF CURRENT MELATONIN HORMONE TREATMENTS
İshak GÖKÇEK, Leyla AYDIN
Veteriner Farmakoloji ve Toksikoloji Derneği Bülteni.2023; 14(1): 36. CrossRef
The double burden of malnutrition and environmental enteric dysfunction as potential factors affecting gut-derived melatonin in children under adverse environments
Alane N. Bezerra, Caroline L. Peixoto, Synara C. Lopes, Veralice M. S. Bruin, Pedro Felipe C. Bruin, Reinaldo B. Oriá
Frontiers in Nutrition.2023;[Epub] CrossRef
Melatonin: Both a Messenger of Darkness and a Participant in the Cellular Actions of Non-Visible Solar Radiation of Near Infrared Light
Dun-Xian Tan, Russel J. Reiter, Scott Zimmerman, Ruediger Hardeland
Biology.2023; 12(1): 89. CrossRef
Glucocorticoids coordinate the bladder peripheral clock and diurnal micturition pattern in mice
Ichiro Chihara, Hiromitsu Negoro, Jin Kono, Yoshiyuki Nagumo, Haruki Tsuchiya, Kosuke Kojo, Masanobu Shiga, Ken Tanaka, Shuya Kandori, Bryan J. Mathis, Hiroyuki Nishiyama
Communications Biology.2023;[Epub] CrossRef
The Microbiota-Dependent Worsening Effects of Melatonin on Gut Inflammation
Jefferson Luiz da Silva, Lia Vezenfard Barbosa, Camila Figueiredo Pinzan, Viviani Nardini, Irislene Simões Brigo, Cássia Aparecida Sebastião, Jefferson Elias-Oliveira, Vânia Brazão, José Clóvis do Prado Júnior, Daniela Carlos, Cristina Ribeiro de Barros C
Microorganisms.2023; 11(2): 460. CrossRef
The Effects of Stress and Diet on the “Brain–Gut” and “Gut–Brain” Pathways in Animal Models of Stress and Depression
Mauritz F. Herselman, Sheree Bailey, Larisa Bobrovskaya
International Journal of Molecular Sciences.2022; 23(4): 2013. CrossRef
Intestinal microbiota and melatonin in the treatment of secondary injury and complications after spinal cord injury
Yiwen Zhang, Rui Lang, Shunyu Guo, Xiaoqin Luo, Huiting Li, Cencen Liu, Wei Dong, Changshun Bao, Yang Yu
Frontiers in Neuroscience.2022;[Epub] CrossRef
Protective Effects and Mechanisms of Melatonin on Stress Myocardial Injury in Rats
Jia-yao Chen, Ting Li, Jiao-ling Wang, Zhan-le Wang, Yun Zhang, Lin-quan Zang
Journal of Cardiovascular Pharmacology.2022; 80(3): 417. CrossRef
Rescue of social deficits by early-life melatonin supplementation through modulation of gut microbiota in a murine model of autism
Xia Liu, Yi Cui, Yuhan Zhang, Guo Xiang, Meng Yu, Xianshu Wang, Bin Qiu, Xin-gang Li, Wei Liu, Di Zhang
Biomedicine & Pharmacotherapy.2022; 156: 113949. CrossRef
Roles of PRR-Mediated Signaling Pathways in the Regulation of Oxidative Stress and Inflammatory Diseases
Pengwei Li, Mingxian Chang
International Journal of Molecular Sciences.2021; 22(14): 7688. CrossRef

The effect of the HRB linker of Newcastle disease virus fusion protein on the fusogenic activity: Yaqing Liu , Ying Liu , Yanan Huang , Hongling Wen , Li Zhao , Yanyan Song , Zhiyu Wang; J. Microbiol. 2021;59(5):513-521. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0539-4

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Abstract

Newcastle disease, designated a class A disease of poultry by the Office international des epizooties (OIE), is an acute infection caused by Newcastle disease virus (NDV). The merging of the envelope of NDV with the membrane of a target host cell is the key step in the infection pathway, which is driven by the concerted action of two glycoproteins: haemagglutinin- neuraminidase (HN) and fusion (F) protein. When the HN protein binds to the host cell surface receptor, the F protein is activated to mediate fusion. The three-dimensional structure of the F protein has been reported to have low electron density between the DIII domain and the HRB domain, and this electron-poor region is defined as the HRB linker. To clarify the contributing role of the HRB linker in the NDV F protein-mediated fusion process, 6 single amino acid mutants were obtained by site-directed mutagenesis of the HRB linker. The expression of the mutants and their abilities to mediate fusion were analysed, and the key amino acids in the HRB linker were identified as L436, E439, I450, and S453, as they can modulate the fusion ability or expression of the active form to a certain extent. The data shed light on the crucial role of the F protein HRB linker in the acquisition of a normal fusogenic phenotype.

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Evaluation of Newcastle disease virus LaSota strain attenuated by codon pair deoptimization of the HN and F genes for in ovo vaccination
Fatma Eldemery, Changbo Ou, Taejoong Kim, Stephen Spatz, John Dunn, Robert Silva, Qingzhong Yu
Veterinary Microbiology.2023; 277: 109625. CrossRef
Prevalence and Molecular Characterization of Bovine Parainfluenza Virus Type 3 in Cattle Herds in China
Yunxin Ren, Cheng Tang, Hua Yue
Animals.2023; 13(5): 793. CrossRef
Direct interaction of the molecular chaperone GRP78/BiP with the Newcastle disease virus hemagglutinin-neuraminidase protein plays a vital role in viral attachment to and infection of culture cells
Chenxin Han, Ziwei Xie, Yadi Lv, Dingxiang Liu, Ruiai Chen
Frontiers in Immunology.2023;[Epub] CrossRef
Adaptor complex-mediated trafficking of Newcastle disease virus fusion protein is regulated by the YLMY motif of its cytoplasmic tail
Yawen Bu, Qingyuan Teng, Delan Feng, Rong Liang, Haoran Wang, Xuehui Zhang, Xiao Li, Wenfeng Jia, Jia Xue, Ye Zhao, Guozhong Zhang
Virulence.2022; 13(1): 1849. CrossRef
YLMY Tyrosine Residue within the Cytoplasmic Tail of Newcastle Disease Virus Fusion Protein Regulates Its Surface Expression to Modulate Viral Budding and Pathogenicity
Yawen Bu, Qingyuan Teng, Delan Feng, Lu Sun, Jia Xue, Guozhong Zhang, Peter Pelka
Microbiology Spectrum.2021;[Epub] CrossRef

Rab27b regulates extracellular vesicle production in cells infected with Kaposi’s sarcoma–associated herpesvirus to promote cell survival and persistent infection: Hyungtaek Jeon , Su-Kyung Kang , Myung-Ju Lee , Changhoon Park , Seung-Min Yoo , Yun Hee Kang , Myung-Shin Lee; J. Microbiol. 2021;59(5):522-529. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1108-6

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Abstract

Extracellular vesicles (EVs) play a crucial role in cell-to-cell communication. EVs and viruses share several properties related to their structure and the biogenesis machinery in cells. EVs from virus-infected cells play a key role in virus spread and suppression using various loading molecules, such as viral proteins, host proteins, and microRNAs. However, it remains unclear how and why viruses regulate EV production inside host cells. The purpose of this study is to investigate the molecular mechanisms underlying EV production and their roles in Kaposi’s sarcoma-associated herpesvirus (KSHV)-infected cells. Here, we found that KSHV induced EV production in human endothelial cells via Rab- 27b upregulation. The suppression of Rab27b expression in KSHV-infected cells enhanced cell death by increasing autophagic flux and autolysosome formation. Our results indicate that Rab27b regulates EV biogenesis to promote cell survival and persistent viral infection during KSHV infection, thereby providing novel insights into the crucial role of Rab- 27b in the KSHV life cycle.

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Engineered small extracellular vesicles as a novel platform to suppress human oncovirus-associated cancers
Iman Owliaee, Mehran khaledian, Armin Khaghani Boroujeni, Ali Shojaeian
Infectious Agents and Cancer.2023;[Epub] CrossRef
HMGB1, a potential regulator of tumor microenvironment in KSHV-infected endothelial cells
Myung-Ju Lee, Joohee Park, Seokjoo Choi, Seung-Min Yoo, Changhoon Park, Hong Seok Kim, Myung-Shin Lee
Frontiers in Microbiology.2023;[Epub] CrossRef
Alpha-2-macroglobulin as a novel diagnostic biomarker for human bladder cancer in urinary extracellular vesicles
Jisu Lee, Hyun Sik Park, Seung Ro Han, Yun Hee Kang, Ji Young Mun, Dong Wook Shin, Hyun-Woo Oh, Yoon-Kyoung Cho, Myung-Shin Lee, Jinsung Park
Frontiers in Oncology.2022;[Epub] CrossRef
Long non-coding RNAs in Sus scrofa ileum under starvation stress
Shu Wang, Yi Jia Ma, Yong Shi Li, Xu Sheng Ge, Chang Lu, Chun Bo Cai, Yang Yang, Yan Zhao, Guo Ming Liang, Xiao Hong Guo, Guo Qing Cao, Bu Gao Li, Peng Fei Gao
Animal Bioscience.2022; 35(7): 975. CrossRef

Differences in seroprevalence between epicenter and non-epicenter areas of the COVID-19 outbreak in South Korea: Hye Won Jeong , Hyun-Ha Chang , Eun Ji Kim , Yu Kyung Kim , Se-Mi Kim , Eun-Ha Kim , Young-Il Kim , Mark Anthony B. Casel , Seong-Gyu Kim , Rare Rollon , Seung-Gyu Jang , Kwang-Min Yu , Hee-Sung Kim , Hee Sue Park , Su-Jin Park , Yong-Dae Kim , Eung-Gook Kim , Young Ki Choi; J. Microbiol. 2021;59(5):530-533. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-1095-7

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Abstract

To compare the standardized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence of high epicenter region with non-epicenter region, serological studies were performed with a total of 3,268 sera from Daegu City and 3,981 sera from Chungbuk Province. Indirect immunofluorescence assay (IFA) for SARS-CoV-2 IgG results showed a high seroprevalence rate in the Daegu City (epicenter) compared with a non-epicenter area (Chungbuk Province) (1.27% vs. 0.91%, P = 0.0358). It is noteworthy that the highest seroprevalence in Daegu City was found in elderly patients (70’s) whereas young adult patients (20’s) in Chungbuk Province showed the highest seroprevalence. Neutralizing antibody (NAb) titers were found in three samples from Daegu City (3/3, 268, 0.09%) while none of the samples from Chungbuk Province were NAb positive. These results demonstrated that even following the large outbreak, the seropositive rate of SARS-CoV-2 in the general population remained low in South Korea.

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Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
The Seroprevalence of SARS-CoV-2 in Children During Early COVID-19 Pandemic in Korea: A Nationwide, Population-Based Study
Jin Lee, Young June Choe, Dohsik Minn, Jong-Hyun Kim
Journal of Korean Medical Science.2022;[Epub] CrossRef

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