Journal of Microbiology

Most-cited are based on citations from 2024 ~ 2025.

Reviews

Understanding the Diversity and Roles of the Ruminal Microbiome: Gi Beom Keum, Sriniwas Pandey, Eun Sol Kim, Hyunok Doo, Jinok Kwak, Sumin Ryu, Yejin Choi, Juyoun Kang, Sheena Kim, Hyeun Bum Kim; J. Microbiol. 2024;62(3):217-230. Published online April 25, 2024; DOI: https://doi.org/10.1007/s12275-024-00121-4

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The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fber that is difcult to digest, supplying about 70% of the energy needed by the host and 60–85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40–50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly infuenced by the host. It is known that the initial colonization of calves immediately after birth is mainly infuenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors afecting the rumen microbial community and their efects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efciency.

Citations

Citations to this article as recorded by

The microbiome’s influence on obesity: mechanisms and therapeutic potential
Dawit Adisu Tadese, James Mwangi, Lei Luo, Hao Zhang, Xiaoshan Huang, Brenda B. Michira, Shengwen Zhou, Peter Muiruri Kamau, Qiumin Lu, Ren Lai
Science China Life Sciences.2025; 68(3): 657. CrossRef
Mitigating enteric methane emissions: An overview of methanogenesis, inhibitors and future prospects
Xin Xie, Yurong Cao, Qiushuang Li, Qi Li, Xingze Yang, Rong Wang, Xiumin Zhang, Zhiliang Tan, Bo Lin, Min Wang
Animal Nutrition.2025; 21: 84. CrossRef
International Symposium on Ruminant Physiology: Stochastic and deterministic factors that shape the rumen microbiome
Samodha C. Fernando, Seidu Adams, Andrew Lakamp, Matthew L. Spangler
Journal of Dairy Science.2025; 108(7): 7576. CrossRef
Genome analysis of Lactococcus taiwanensis strain K_LL001 with potential cellulose degrading functions
Eun Sol Kim, Jin Ho Cho, Minho Song, Sheena Kim, Gi Beom Keum, Hyunok Doo, Jinok Kwak, Sriniwas Pandey, Sumin Ryu, Yejin Choi, Juyoun Kang, Hyeun Bum Kim, Ju-Hoon Lee
Journal of Animal Science and Technology.2025; 67(1): 273. CrossRef
Dynamic Changes in Rumen Microbial Diversity and Community Composition Within Rumen Fluid in Response to Various Storage Temperatures and Preservation Times
Chang Liu, Jin Cheng, Yunong Xie, Kehui Ouyang, Mingren Qu, Ke Pan, Qinghua Qiu
Veterinary Sciences.2025; 12(3): 234. CrossRef
Integrated multi-omics to elucidate the interplay between rumen microorganisms and host metabolism in Hu sheep supplemented with herbal preparations
Chunhui Wang, Qiao Li, Xingcai Qi, Huihui Wang, Yi Wu, Keyan Ma, Juanjuan Song, Zilong Liu, Youji Ma, Garret Suen
mSphere.2025;[Epub] CrossRef
Investigation on the action mechanisms of taurine on rumen microbial crude protein synthesis and nitrogen metabolism in beef steers using sodium sulfate as a contrast
Manman Fan, Jinming Hu, Cheng Liu, Shuo Zhang, Yufeng Liu, Guangyong Zhao
Animal Nutrition.2025; 22: 1. CrossRef
Sex-specific microbiota associations with backfat thickness, eye muscle area, and rumen fermentation in Qinchuan cattle
Yueting Pan, Gege Sun, Guo Li, Shuaicheng Chen, Haibing Liu, Huaxuan Li, Chugang Mei, Wucai Yang, Linsen Zan
BMC Microbiology.2025;[Epub] CrossRef
Growth performance, meat quality, rumen morphometrics and microbiota of finishing bulls fed diets supplemented with oregano essential oils
Stella Dokou, Ilias Giannenas, Ioanna Stylianaki, Eleftherios Bonos, Vangelis Economou, Georgios Arsenos
Animal Feed Science and Technology.2025; 327: 116405. CrossRef
Evaluation of kefir consumption on gut microbial diversity in a healthy young population using full-length 16S rRNA sequencing
Yejin Choi, Gi Beom Keum, Juyoun Kang, Hyunok Doo, Jinok Kwak, Haram Kim, Yeongjae Chae, Suyoung Lee, Hyunjin Yang, Sheena Kim, Xingmin Sun, Hyeun Bum Kim, Soo Jin Yoo
Frontiers in Microbiology.2025;[Epub] CrossRef
The interaction between rumen microbiota and neurotransmitters plays an important role in the adaptation of phenological changes in Tibetan sheep
Wei Huang, Yuzhu Sha, Qianling Chen, Xiaowei Chen, Min Gao, Xiu Liu, Yapeng He, Xu Gao, Jiang Hu, Jiqing Wang, Shaobin Li, Zhiyun Hao, Yanyu He
BMC Veterinary Research.2025;[Epub] CrossRef
Effects of Grazing in a Low Deciduous Forest on Rumen Microbiota and Volatile Fatty Acid Production in Lambs
Raúl Ávila-Cervantes, Pedro González-Pech, Carlos Sandoval-Castro, Felipe Torres-Acosta, José Ramos-Zapata, Mónica Galicia-Jiménez, Ramón Pacheco-Arjona
Animals.2025; 15(11): 1565. CrossRef
Metagenomic sequencing reveals the taxonomic and functional characteristics of rumen microorganisms in Dongliu buffalo
Wenwen Lu, Jinling Hua, Min Zhang, Longfei Yan, Huwei Zhao, Xiaokang Lv
Scientific Reports.2025;[Epub] CrossRef
The Effect of Sodium Humate on Sheep In Vitro Fermentation Characteristics and Rumen Bacterial Community
Na Yin, Yuchao Hu, Xiangting Cai, Long Gao, Wenwen Wang, Yuan Wang, Jingwei Qi
Microorganisms.2025; 13(6): 1266. CrossRef
A refined comparative mouse model of acute and chronic atopic dermatitis
Jinok Kwak, Hyunok Doo, Eun Sol Kim, Gi Beom Keum, Sumin Ryu, Yejin Choi, Juyoun Kang, Haram Kim, Yeongjae Chae, Sheena Kim, Ju-Hoon Lee, Hyeun Bum Kim
Journal of Animal Science and Technology.2025; 67(3): 636. CrossRef
Effect of Diet and Lifestyle Changes on Gut Microbial Diversity in Healthy Adolescents
Juyoun Kang, Yejin Choi, Gi Beom Keum, Hyunok Doo, Jinok Kwak, Haram Kim, Yeongjae Chae, Suyoung Lee, Hyunjin Yang, Sheena Kim, Xingmin Sun, Hyeun Bum Kim, Soo Jin Yoo
Journal of Microbiology and Biotechnology.2025;[Epub] CrossRef
Understanding the diversity and roles of the canine gut microbiome
Haram Kim, Yeongjae Chae, Jin Ho Cho, Minho Song, Jinok Kwak, Hyunok Doo, Yejin Choi, Juyoun Kang, Hyunjin Yang, Suyoung Lee, Gi Beom Keum, Suphot Wattanaphansak, Sheena Kim, Hyeun Bum Kim
Journal of Animal Science and Biotechnology.2025;[Epub] CrossRef
The ins and outs of integrative digestive biology
Carol Bucking, John S. Terblanche, Matthew D. Regan
Journal of Experimental Biology.2025;[Epub] CrossRef
Analysis of the Microbiota of Milk from Holstein–Friesian Dairy Cows Fed a Microbial Supplement
Bronwyn E. Campbell, Mohammad Mahmudul Hassan, Timothy Olchowy, Shahab Ranjbar, Martin Soust, Orlando Ramirez-Garzon, Rafat Al Jassim, Robert J. Moore, John I. Alawneh
Animals.2025; 15(14): 2124. CrossRef
Complete genome sequence of Lactiplantibacillus plantarum strain GA_C_14 with potential characteristics applicable in the swine industry
Sumin Ryu, Hyunok Doo, Eun Sol Kim, Gi Beom Keum, Jinok Kwak, Sriniwas Pandey, Yejin Choi, Juyoun Kang, Sheena Kim, Hyeun Bum Kim, Ju-Hoon Lee
Journal of Animal Science and Technology.2025; 67(4): 944. CrossRef
Heated drinking water in winter improves growth performance of male Hu sheep by modulating rumen quorum sensing and metabolites, and enhancing serum antioxidant capacity
Chang Liu, Lingyan Li, Jiaqi Dai, Mingren Qu, Kehui Ouyang, Qinghua Qiu
Animal Bioscience.2025; 38(10): 2280. CrossRef
Artificial Intelligence in Microbiome Research and Beyond: Connecting Human Health, Animal Husbandry, and Aquaculture
Silvio Rizzi, Giulio Saroglia, Violeta Kalemi, Simona Rimoldi, Genciana Terova
Applied Sciences.2025; 15(17): 9781. CrossRef
Effects of Oregano Essential Oil and/or Yeast Cultures on the Rumen Microbiota of Crossbred Simmental Calves
Ting Liu, Zhihao Luo, Tao Zhang, Huan Chen, Xuejiao Yi, Jiang Hu, Bingang Shi, Yuxi An, Changze Cui, Xiangyan Wang
Animals.2024; 14(24): 3710. CrossRef
Host-Associated Microbiome
Woo Jun Sul
Journal of Microbiology.2024; 62(3): 135. CrossRef
GnRH Immunocastration in Male Xizang Sheep: Impacts on Rumen Microbiome and Metabolite Profiles for Enhanced Health and Productivity
Xiaoming Zhang, Tianzeng Song, Guiqiong Liu, Jing Wu, Yangzong Zhaxi, Shehr Bano Mustafa, Khuram Shahzad, Xiaoying Chen, Wangsheng Zhao, Xunping Jiang
Animals.2024; 14(20): 2942. CrossRef
Gut Akkermansia muciniphila, Prevotellaceae, and Enterobacteriaceae spp. as Possible Markers in Women-Related Nutritional and Clinical Trials: Familial Mediterranean Fever Disease
Astghik Pepoyan
Women's Health Reports.2024; 5(1): 785. CrossRef
Exploring the Spatial Variation in the Microbiota and Bile Acid Metabolism of the Compound Stomach in Intensively Farmed Yaks
Shichun He, Zaimei Yuan, Sifan Dai, Zibei Wang, Shusheng Zhao, Bin Zhang, Huaming Mao, Dongwang Wu
Microorganisms.2024; 12(10): 1968. CrossRef
Investigation of the impact of multi-strain probiotics containing Saccharomyces cerevisiae on porcine production
Sheena Kim, Jinho Cho, Gi Beom Keum, Jinok Kwak, Hyunok Doo, Yejin Choi, Juyoun Kang, Haram Kim, Yeongjae Chae, Eun Sol Kim, Minho Song, Hyeun Bum Kim
Journal of Animal Science and Technology.2024; 66(5): 876. CrossRef
The Effects of Mixed Inoculum Storage Time on In Vitro Rumen Fermentation Characteristics, Microbial Diversity, and Community Composition
Chang Liu, Jing Ge, Jiaqi Dai, Mingren Qu, Kehui Ouyang, Qinghua Qiu
Animals.2024; 15(1): 5. CrossRef

Skin Deep: The Potential of Microbiome Cosmetics: Ju Hee Han, Hei Sung Kim; J. Microbiol. 2024;62(3):181-199. Published online April 16, 2024; DOI: https://doi.org/10.1007/s12275-024-00128-x

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Abstract PDF

The interplay between the skin microbiome and its host is a complex facet of dermatological health and has become a critical focus in the development of microbiome cosmetics. The skin microbiome, comprising various microorganisms, is essential from birth, develops over the lifespan, and performs vital roles in protecting our body against pathogens, training the immune system, and facilitating the breakdown of organic matter. Dysbiosis, an imbalance of these microorganisms, has been implicated in a number of skin conditions such as acne, atopic dermatitis, and skin cancer. Recent scientific findings have spurred cosmetic companies to develop products that preserve and enhance the skin's microbial diversity balance. These products may incorporate elements like prebiotics, probiotics, and postbiotics, which are beneficial for the skin microbiome. Beyond topical products, there's increasing interest in ingestible beauty supplements (i.e. oral probiotics), highlighting the connection between the gut and skin. This review examines the influence of the microbiome on skin health and the emerging trends of microbiome skincare products.

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Influence of Cosmetic Skincare Products with pH < 5 on the Skin Microbiome: A Randomized Clinical Evaluation
Ciska Janssens-Böcker, Claudia Doberenz, Marta Monteiro, Marta de Oliveira Ferreira
Dermatology and Therapy.2025; 15(1): 141. CrossRef
Current Approaches in Cosmeceuticals: Peptides, Biotics and Marine Biopolymers
Ulya Badilli, Ozge Inal
Polymers.2025; 17(6): 798. CrossRef
Cytoprotective effects of the fermented milk by Streptococcus thermophilus CGMCC 24468 against ROS damage in HaCaT cells
Tingting Zhang, Yan Li, Chunying Yuan, Xiaoce Zhu, Mingyu Wang, Suzhen Yang, Jian Kong
Journal of Functional Foods.2025; 128: 106829. CrossRef
Frontiers in Topical Photoprotection
Margaret Sullivan, Constancio Gonzalez Obezo, Zachary Lipsky, Abhishek Panchal, Jaide Jensen
Cosmetics.2025; 12(3): 96. CrossRef
Skin Lipids and Their Influence on Skin Microbiome and Skin Care
Raquel Allen Garcia Barbeto Siqueira, Iveta Hradkova, Vânia Rodrigues Leite-Silva, Newton Andréo-Filho, Patricia Santos Lopes
ACS Omega.2025; 10(27): 28534. CrossRef
Skin microbiota in atopic dermatitis: victim or executioner?
Chiara Maria Teresa Boggio, Federica Veronese, Marta Armari, Elisa Zavattaro, Elia Esposto, Paola Savoia, Barbara Azzimonti, Christopher Staley, Eman Adel Elmansoury, Yunhua Tu
Clinical Microbiology Reviews.2025;[Epub] CrossRef
Prebiotic Oligosaccharides in Skin Health: Benefits, Mechanisms, and Cosmetic Applications
Meijun Zeng, Yang Li, Jie Cheng, Jingyu Wang, Qiyu Liu
Antioxidants.2025; 14(6): 754. CrossRef
The Transformative Impact of Extracellular Vesicles on the Cosmetics Industry: A Comprehensive Review
Valéria Dal Col, Fábio Fernandes Ribas, Rodrigo Pinheiro Araldi
Cosmetics.2025; 12(5): 191. CrossRef
Hydroponic cultivation technique in Populus nigra (L.) for the sustainable production of root metabolites with antimicrobial and prebiotic potential for skin microbiota
Sonia Malik, Maria Michela Salvatore, Laura Bauchet, Margot Bruat, Benoît Roubinet, Sabine Carpin, Anna Andolfi, Alessio Cimmino, Ludovic Landemarre, Marco Masi, Frédéric Lamblin
Industrial Crops and Products.2025; 235: 121717. CrossRef
Host-Associated Microbiome
Woo Jun Sul
Journal of Microbiology.2024; 62(3): 135. CrossRef
Skin Microbiome and Acne: Microbial Imbalances and Impact – Interview with Three Key Opinion Leaders
Brigitte Scott
EMJ Dermatology.2024; : 83. CrossRef
Cosmeceuticals: A Review of Clinical Studies Claiming to Contain Specific, Well-Characterized Strains of Probiotics or Postbiotics
Ioannis M. Theodorou, Dorothea Kapoukranidou, Markos Theodorou, Joulia K. Tsetis, Alexandra Eleftheria Menni, Georgios Tzikos, Stella Bareka, Anne Shrewsbury, George Stavrou, Katerina Kotzampassi
Nutrients.2024; 16(15): 2526. CrossRef
Effect of Staphylococcus aureus colonization and immune defects on the pathogenesis of atopic dermatitis
Evrim Özdemіr, Lütfiye Öksüz
Archives of Microbiology.2024;[Epub] CrossRef
A New Generation of Postbiotics for Skin and Scalp: In Situ Production of Lipid Metabolites by Malassezia
Martin Patrick Pagac, Mathias Gempeler, Remo Campiche
Microorganisms.2024; 12(8): 1711. CrossRef
Antimelanogenic and Antioxidant Effects of Postbioics of Lactobacillus Strains in α-MSH-Induced B16F10 Melanoma Cells via CREB/MITF and MAPKs Signaling Pathway
Hye-Won Lee, Yu-Rim Lee, Kyung-Min Park, Na-Kyoung Lee, Hyun-Dong Paik
Journal of Microbiology and Biotechnology.2024; 34(11): 2279. CrossRef
Evaluation of the Effects of Age, Sex, and Dexpanthenol-Containing Skin Care on the Facial and Body Skin Microbiome
Zainab Qaizar, Raffaella de Salvo, Gregor Bieri, Katrin Unbereit, Shannon Montgomery, Erwan Peltier
Cosmetics.2024; 11(6): 213. CrossRef

Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms: Wonjae Kim, Yerim Park, Jaejoon Jung, Che Ok Jeon, Masanori Toyofuku, Jiyoung Lee, Woojun Park; J. Microbiol. 2024;62(3):249-260. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00115-2

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Abstract PDF

The proliferation of harmful cyanobacterial blooms dominated by Microcystis aeruginosa has become an increasingly serious problem in freshwater ecosystems due to climate change and eutrophication. Microcystis-blooms in freshwater generate compounds with unpleasant odors, reduce the levels of dissolved O₂, and excrete microcystins into aquatic ecosystems, potentially harming various organisms, including humans. Various chemical and biological approaches have thus been developed to mitigate the impact of the blooms, though issues such as secondary pollution and high economic costs have not been adequately addressed. Red clays and H₂O₂ are conventional treatment methods that have been employed worldwide for the mitigation of the blooms, while novel approaches, such as the use of plant or microbial metabolites and antagonistic bacteria, have also recently been proposed. Many of these methods rely on the generation of reactive oxygen species, the inhibition of photosynthesis, and/or the disruption of cellular membranes as their mechanisms of action, which may also negatively impact other freshwater microbiota. Nevertheless, the underlying molecular mechanisms of anticyanobacterial chemicals and antagonistic bacteria remain unclear. This review thus discusses both conventional and innovative approaches for the management of M. aeruginosa in freshwater bodies.

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Strong inhibitory effects of Desmodesmus sp. on Microcystis blooms: Potential as a biological control agent in aquaculture
Bo Yang, Yuhua Li, Zihan Wang, Zhiguang Yue, Junqi Wen, Xueqin Zhao, Hu Zhang, Xianfeng Wang, Xiufen Wang, Man Zhang
Aquaculture Reports.2025; 40: 102579. CrossRef
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Zhaozhe Chen, Jiyoung Lee, Molly Mills, Abigail Volk, Ozeas S. Costa
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HABS-BLOCKS© Inhibited Microcystis and Planktothrix and Reduced Microcystin Concentrations in a Lake Water Mesocosm Study
Cameron Gastaldo, Stephen Vesper
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Synergistic radical-mediated algal inactivation via FeMoS2/ZnO-persulfate visible-light photocatalysis
Yingjian Ma, Yuxuan Tian, Ning Ding, Hong Liu
Composites Part B: Engineering.2025; 305: 112740. CrossRef
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Xuhan Wang, Siqi Zhu, Shenchen Tao, Shaoyong Zhang, Ruijun Wang, Liqin Zhang
Toxins.2025; 17(7): 354. CrossRef
Public goods-mediated bacterial interplay in aquatic ecosystems
Yerim Park, Wonjae Kim, Jihye Bae, Woojun Park
Water Research.2025; 287: 124310. CrossRef
Molecular mechanisms underlying the bloom-forming cyanobacterium Microcystis defence against predation by flagellates
Yan Chen, Xiao Zhang, Xinyang Bai, Yonglan Xu, Hangzhou Xu, Li Li
Journal of Water Process Engineering.2025; 77: 108611. CrossRef
Utilizing allelopathy from the invasive plant Solidago canadensis to control Microcystis aeruginosa blooms: An integrated metabolomic and bioassay approach
Miao Wu, Huiyuan Liu, Jiaxin Shen, Zhaohui Xie, Siyuan Yang, Jiahui Guo, Yijiang Liu, Huiting Lian, Dingli Wang
Journal of Hazardous Materials.2025; 499: 140043. CrossRef
Artificial Intelligence-Based Microfluidic Platform for Detecting Contaminants in Water: A Review
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Harmful Algae.2024; 137: 102680. CrossRef
Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems
Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park
Journal of Microbiology.2024; 62(11): 933. CrossRef
Laboratory-Simulated Inhibitory Effects of the Floating-Bed Plants on Microcystis aeruginosa and Their Microbial Communities’ Responses to Microcystins
Shuwen Zhang, Yuanpu Sha, Yuanyuan Tang, Longjie Li, Feihu Wang, Jing Dong, Xuejun Li, Yunni Gao, Xiaofei Gao, Huatao Yuan, Jingxiao Zhang
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Journal of Microbiology.2024; 62(3): 135. CrossRef

MAPK Cascades in Plant Microbiota Structure and Functioning: Thijs Van Gerrewey, Hoo Sun Chung; J. Microbiol. 2024;62(3):231-248. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00114-3

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Abstract PDF

Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, infuencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent fndings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.

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Adenoviral Vector System: A Comprehensive Overview of Constructions, Therapeutic Applications and Host Responses: Anyeseu Park, Jeong Yoon Lee; J. Microbiol. 2024;62(7):491-509. Published online July 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00159-4

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Abstract PDF

Adenoviral vectors are crucial for gene therapy and vaccine development, offering a platform for gene delivery into host cells. Since the discovery of adenoviruses, first-generation vectors with limited capacity have evolved to third-generation vectors flacking viral coding sequences, balancing safety and gene-carrying capacity. The applications of adenoviral vectors for gene therapy and anti-viral treatments have expanded through the use of in vitro ligation and homologous recombination, along with gene editing advancements such as CRISPR-Cas9. Current research aims to maintain the efficacy and safety of adenoviral vectors by addressing challenges such as pre-existing immunity against adenoviral vectors and developing new adenoviral vectors from rare adenovirus types and non-human species. In summary, adenoviral vectors have great potential in gene therapy and vaccine development. Through continuous research and technological advancements, these vectors are expected to lead to the development of safer and more effective treatments.

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Andrey Vyacheslavovich Vasilyev, Irina Alekseevna Nedorubova, Viktoria Olegovna Chernomyrdina, Anastasiia Yurevna Meglei, Viktoriia Pavlovna Basina, Anton Vladimirovich Mironov, Valeriya Sergeevna Kuznetsova, Victoria Alexandrovna Sinelnikova, Olga Anatol
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Balancing Act of the Intestinal Antimicrobial Proteins on Gut Microbiota and Health: Ye Eun Ra, Ye‑Ji Bang; J. Microbiol. 2024;62(3):167-179. Published online April 17, 2024; DOI: https://doi.org/10.1007/s12275-024-00122-3

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Abstract PDF

The human gut houses a diverse and dynamic microbiome critical for digestion, metabolism, and immune development, exerting profound efects on human health. However, these microorganisms pose a potential threat by breaching the gut barrier, entering host tissues, and triggering infections, uncontrolled infammation, and even sepsis. The intestinal epithelial cells form the primary defense, acting as a frontline barrier against microbial invasion. Antimicrobial proteins (AMPs), produced by these cells, serve as innate immune efectors that regulate the gut microbiome by directly killing or inhibiting microbes. Abnormal AMP production, whether insufcient or excessive, can disturb the microbiome equilibrium, contributing to various intestinal diseases. This review delves into the complex interactions between AMPs and the gut microbiota and sheds light on the role of AMPs in governing host-microbiota interactions. We discuss the function and mechanisms of action of AMPs, their regulation by the gut microbiota, microbial evasion strategies, and the consequences of AMP dysregulation in disease. Understanding these complex interactions between AMPs and the gut microbiota is crucial for developing strategies to enhance immune responses and combat infections within the gut microbiota. Ongoing research continues to uncover novel aspects of this intricate relationship, deepening our understanding of the factors shaping gut health. This knowledge has the potential to revolutionize therapeutic interventions, ofering enhanced treatments for a wide range of gut-related diseases.

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Furan-based Chalcone Annihilates the Multi-Drug-Resistant Pseudomonas aeruginosa and Protects Zebra Fish Against its Infection: Santosh Pushpa Ramya Ranjan Nayak , Catharine Basty , Seenivasan Boopathi , Loganathan Sumathi Dhivya , Khaloud Mohammed Alarjani , Mohamed Ragab Abdel Gawwad , Raghda Hager , Muthu Kumaradoss Kathiravan , Jesu Arockiaraj; J. Microbiol. 2024;62(2):75-89. Published online February 21, 2024; DOI: https://doi.org/10.1007/s12275-024-00103-6

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The emergence of carbapenem-resistant Pseudomonas aeruginosa, a multi-drug-resistant bacteria, is becoming a serious public health concern. This bacterium infects immunocompromised patients and has a high fatality rate. Both naturally and synthetically produced chalcones are known to have a wide array of biological activities. The antibacterial properties of synthetically produced chalcone were studied against P. aeruginosa. In vitro, study of the compound (chalcone derivative named DKO1), also known as (2E)-1-(5-methylfuran-2-yl)-3-(4-nitrophenyl) prop-2-en-1-one, had substantial antibacterial and biofilm disruptive action. DKO1 effectively shielded against P. aeruginosa-induced inflammation, oxidative stress, lipid peroxidation, and apoptosis in zebrafish larvae. In adult zebrafish, the treatment enhanced the chances of survivability and reduced the sickness-like behaviors. Gene expression, biochemical analysis, and histopathology studies found that proinflammatory cytokines (TNF-α, IL-1β, IL-6, iNOS) were down regulated; antioxidant enzymes such as superoxide dismutase (SOD) and catalase (CAT) levels increased, and histoarchitecture was restored in zebrafish. The data indicate that DKO1 is an effective antibacterial agent against P. aeruginosa demonstrated both in vitro and in vivo.

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Chalcone derivative enhance poultry meat preservation through quorum sensing inhibition against Salmonella (Salmonella enterica serovar Typhi) contamination
S.P. Ramya Ranjan Nayak, Pratik Pohokar, Anamika Das, L.S. Dhivya, Mukesh Pasupuleti, Ilavenil Soundharrajan, Bader O. Almutairi, Kathiravan Muthu Kumaradoss, Jesu Arockiaraj
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Targeted inhibition of PqsR in Pseudomonas aeruginosa PAO1 quorum-sensing network by chalcones as promising antibacterial compounds
Negin Arami, Amineh Sadat Tajani, Maryam Hashemi, Tahoura Rezaei, Razieh Ghodsi, Vahid Soheili, Bibi Sedigheh Fazly Bazzaz
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Exposure to bisphenol A and sodium nitrate found in processed meat induces endocrine disruption and dyslipidemia through PI3K/AKT/SREBP pathway in zebrafish larvae
Santosh Pushpa Ramya Ranjan Nayak, Anamika Das, Karthikeyan Ramamurthy, Mukesh Pasupuleti, Rajakrishnan Rajagopal, Jesu Arockiaraj
The Journal of Nutritional Biochemistry.2025; 140: 109887. CrossRef
Starch films with triethanolamine and chalcone derivative for improved durability and antimicrobial properties in poultry packaging
S.P. Ramya Ranjan Nayak, Pratik Pohokar, L.S. Dhivya, Aveeda Herold, V. Chitra, Mansour K. Gatasheh, Selvaraj Arokiyaraj, Kathiravan Muthu Kumaradoss, Jesu Arockiaraj
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Testing of Anti-EMT, Anti-Inflammatory and Antibacterial Activities of 2′,4′-Dimethoxychalcone
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Furan-based chalcone protects β-cell damage and improves glucose uptake in alloxan-induced zebrafish diabetic model via influencing Peroxisome Proliferator-Activated Receptor agonists (PPAR-γ) signaling
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Review

Progress and challenges in CRISPR/Cas applications in microalgae: Quynh-Giao Tran, Trang Thi Le, Dong-Yun Choi, Dae-Hyun Cho, Jin-Ho Yun, Hong Il Choi, Hee-Sik Kim, Yong Jae Lee; J. Microbiol. 2025;63(3):e2501028. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501028

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Abstract PDF

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have emerged as powerful tools for precise genome editing, leading to a revolution in genetic research and biotechnology across diverse organisms including microalgae. Since the 1950s, microalgal production has evolved from initial cultivation under controlled conditions to advanced metabolic engineering to meet industrial demands. However, effective genetic modification in microalgae has faced significant challenges, including issues with transformation efficiency, limited target selection, and genetic differences between species, as interspecies genetic variation limits the use of genetic tools from one species to another. This review summarized recent advancements in CRISPR systems applied to microalgae, with a focus on improving gene editing precision and efficiency, while addressing organism-specific challenges. We also discuss notable successes in utilizing the class 2 CRISPR-associated (Cas) proteins, including Cas9 and Cas12a, as well as emerging CRISPR-based approaches tailored to overcome microalgal cellular barriers. Additionally, we propose future perspectives for utilizing CRISPR/Cas strategies in microalgal biotechnology.

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Ki Jun Jeong
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Progress and prospects in metabolic engineering approaches for isoprenoid biosynthesis in microalgae
Sonia Mohamadnia, Borja Valverde-Pérez, Omid Tavakoli, Irini Angelidaki
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Thinesh Selvaratnam, Shaseevarajan Sivanantharajah, Kirusha Sriram
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Harnessing MicroRNAs and CRISPR to enhance biofuel production in microalgae
Dariga K. Kirbayeva, Altynay Y. Shayakhmetova, Bekzhan D. Kossalbayev, Assemgul K. Sadvakasova, Meruyert O. Bauenova
International Journal of Hydrogen Energy.2025; 157: 150399. CrossRef
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Lactobacillus acidophilus KBL409 Ameliorates Atopic Dermatitis in a Mouse Model: Woon-ki Kim , You Jin Jang , SungJun Park , Sung-gyu Min , Heeun Kwon , Min Jung Jo , GwangPyo Ko; J. Microbiol. 2024;62(2):91-99. Published online February 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00104-5

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Abstract PDF

Atopic dermatitis (AD) is a chronic inflammatory skin disease with repeated exacerbations of eczema and pruritus. Probiotics can prevent or treat AD appropriately via modulation of immune responses and gut microbiota. In this study, we evaluated effects of Lactobacillus acidophilus (L. acidophilus) KBL409 using a house dust mite (Dermatophagoides farinae)-induced in vivo AD model. Oral administration of L. acidophilus KBL409 significantly reduced dermatitis scores and decreased infiltration of immune cells in skin tissues. L. acidophilus KBL409 reduced in serum immunoglobulin E and mRNA levels of T helper (Th)1 (Interferon-γ), Th2 (Interleukin [IL]-4, IL-5, IL-13, and IL-31), and Th17 (IL-17A) cytokines in skin tissues. The anti-inflammatory cytokine IL-10 was increased and Foxp3 expression was up-regulated in AD-induced mice with L. acidophilus KBL409. Furthermore, L. acidophilus KBL409 significantly modulated gut microbiota and concentrations of short-chain fatty acids and amino acids, which could explain its effects on AD. Our results suggest that L. acidophilus KBL409 is the potential probiotic for AD treatment by modulating of immune responses and gut microbiota of host.

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The gut-skin axis: a bi-directional, microbiota-driven relationship with therapeutic potential
Maira Jimenez-Sanchez, Larissa S. Celiberto, Hyungjun Yang, Ho Pan Sham, Bruce A. Vallance
Gut Microbes.2025;[Epub] CrossRef
Probiotics ameliorate atopic dermatitis by modulating the dysbiosis of the gut microbiota in dogs
Hyokeun Song, Seung-Hyun Mun, Dae-Woong Han, Jung-Hun Kang, Jae-Uk An, Cheol-Yong Hwang, Seongbeom Cho
BMC Microbiology.2025;[Epub] CrossRef
The effect of daily oral probiotic and postbiotic supplementation on the canine skin microbiota: Insights from culture‐dependent and long‐read 16S rRNA gene sequencing methods
Letitia Grant, Manijeh Mohammadi Dehcheshmeh, Esmaeil Ebrahimie, Aliakbar Khabiri, Tania Veltman, Michael Shipstone, Darren J. Trott
Veterinary Dermatology.2025; 36(5): 581. CrossRef
The efficacy of Akkermansia muciniphila YGMCC2602-derived postbiotics in skin repair
Zhili He, Wenfang Song, Shichang Zhang, Minlei Zhao, Fan Wang, Shanshan He, Xiaochi Jie, Qi Gao, Jianguo Chen
Journal of Functional Foods.2025; 131: 106950. CrossRef
Differential modulation of post-antibiotic colonization resistance to Clostridioides difficile by two probiotic Lactobacillus strains
Matthew H. Foley, Arthur S. McMillan, Sarah O'Flaherty, Rajani Thanissery, Molly E. Vanhoy, Mary Gracen Fuller, Rodolphe Barrangou, Casey M. Theriot, Jacques Ravel
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Innovative microbial strategies in atopic dermatitis
Jingtai Ma, Yiting Fang, Jinxing Hu, Shiqi Li, Lilian Zeng, Siyi Chen, Zhifeng Li, Ruiling Meng, Xingfen Yang, Fenglin Zhang, Guiyuan Ji, Peihua Liao, Liang Chen, Wei Wu
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Pedro Brivaldo Viana da Silva, Thiécla Katiane Osvaldt Rosales, João Paulo Fabi
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Microbiota Modulation as an Approach to Prevent the Use of Antimicrobials Associated with Canine Atopic Dermatitis
Tânia Lagoa, Luís Martins, Maria Cristina Queiroga
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The Skin Histopathology of Pro- and Parabiotics in a Mouse Model of Atopic Dermatitis
Hun Hwan Kim, Se Hyo Jeong, Min Yeong Park, Pritam Bhagwan Bhosale, Abuyaseer Abusaliya, Jeong Doo Heo, Hyun Wook Kim, Je Kyung Seong, Tae Yang Kim, Jeong Woo Park, Byeong Soo Kim, Gon Sup Kim
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Sung Jae Jang, Eun Jung Jo, Cheonghoon Lee, Bo-Ram Cho, Yun Jeong Shin, Jun Soo Song, Woon-Ki Kim, Nanhee Lee, Hyungjin Lee, SungJun Park, GwangPyo Ko
Probiotics and Antimicrobial Proteins.2024;[Epub] CrossRef

miR-135b Aggravates Fusobacterium nucleatum-Induced Cisplatin Resistance in Colorectal Cancer by Targeting KLF13: Wei Zeng , Jia Pan , Guannan Ye; J. Microbiol. 2024;62(2):63-73. Published online February 24, 2024; DOI: https://doi.org/10.1007/s12275-023-00100-1

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Cisplatin resistance is the main cause of colorectal cancer (CRC) treatment failure, and the cause has been reported to be related to Fusobacterium nucleatum (Fn) infection. In this study, we explored the role of Fn in regulating cisplatin resistance of CRC cells and its underlying mechanism involved. The mRNA and protein expressions were examined by qRT-PCR and western blot. Cell proliferation and cell apoptosis were assessed using CCK8 and flow cytometry assays, respectively. Dual-luciferase reporter gene assay was adopted to analyze the molecular interactions. Herein, our results revealed that Fn abundance and miR-135b expression were markedly elevated in CRC tissues, with a favorable association between the two. Moreover, Fn infection could increase miR-135b expression via a concentration-dependent manner, and it also enhanced cell proliferation but reduced apoptosis and cisplatin sensitivity by upregulating miR-135b. Moreover, KLF13 was proved as a downstream target of miR-135b, of which overexpression greatly diminished the promoting effect of miR-135b or Fn-mediated cisplatin resistance in CRC cells. In addition, it was observed that upstream 2.5 kb fragment of miR-135b promoter could be interacted by β-catenin/TCF4 complex, which was proved as an effector signaling of Fn. LF3, a blocker of β-catenin/TCF4 complex, was confirmed to diminish the promoting role of Fn on miR-135b expression. Thus, it could be concluded that Fn activated miR-135b expression through TCF4/β-catenin complex, thereby inhibiting KLF13 expression and promoting cisplatin resistance in CRC.

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miR-135b: A key role in cancer biology and therapeutic targets
Yingchun Shao, Shuangshuang Zhang, Yuxin Pan, Zhan Peng, Yinying Dong
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Dezhi Yan, Qingliu He, Chunjian Wang, Tian Li, Xueping Yi, Haisheng Yu, Wenfei Wu, Hanyun Yang, Wenzhao Wang, Liang Ma
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Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale: Allan de Carvalho, Marcia Giambiagi-deMarval, Ciro César Rossi; J. Microbiol. 2024;62(9):775-784. Published online July 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00156-7

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Abstract PDF

Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.

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Review

Metabolic Interaction Between Host and the Gut Microbiota During High‑Fat Diet‑Induced Colorectal Cancer: Chaeeun Lee, Seungrin Lee, Woongjae Yoo; J. Microbiol. 2024;62(3):153-165. Published online April 16, 2024; DOI: https://doi.org/10.1007/s12275-024-00123-2

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Abstract PDF

Colorectal cancer (CRC) is the second-highest cause of cancer-associated mortality among both men and women worldwide. One of the risk factors for CRC is obesity, which is correlated with a high-fat diet prevalent in Western dietary habits. The association between an obesogenic high-fat diet and CRC has been established for several decades; however, the mechanisms by which a high-fat diet increases the risk of CRC remain unclear. Recent studies indicate that gut microbiota strongly infuence the pathogenesis of both high-fat diet-induced obesity and CRC. The gut microbiota is composed of hundreds of bacterial species, some of which are implicated in CRC. In particular, the expansion of facultative anaerobic Enterobacteriaceae, which is considered a microbial signature of intestinal microbiota functional imbalance (dysbiosis), is associated with both high-fat diet-induced obesity and CRC. Here, we review the interaction between the gut microbiome and its metabolic byproducts in the context of colorectal cancer (CRC) during high-fat diet-induced obesity. In addition, we will cover how a high-fat diet can drive the expansion of genotoxin-producing Escherichia coli by altering intestinal epithelial cell metabolism during gut infammation conditions.

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Journal Article

Quorum Quenching Potential of Reyranella sp. Isolated from Riverside Soil and Description of Reyranella humidisoli sp. nov.: Dong Hyeon Lee, Seung Bum Kim; J. Microbiol. 2024;62(6):449-461. Published online May 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00131-2

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Abstract PDF

Quorum quenching refers to any mechanism that inhibits quorum sensing processes. In this study, quorum quenching activity among bacteria inhabiting riverside soil was screened, and a novel Gram-stain-negative, rod shaped bacterial strain designated MMS21-HV4-11(T), which showed the highest level of quorum quenching activity, was isolated and subjected to further analysis. Strain MMS21-HV4-11(T) could be assigned to the genus Reyranella of Alphaproteobacteria based on the 16S rRNA gene sequence, as the strain shared 98.74% sequence similarity with Reyranella aquatilis seoho-37(T), and then 97.87% and 97.80% sequence similarity with Reyranella soli KIS14-15(T) and Reyranella massiliensis 521(T), respectively. The decomposed N-acyl homoserine lactone was restored at high concentrations under acidic conditions, implying that lactonase and other enzyme(s) are responsible for quorum quenching. The genome analysis indicated that strain MMS21-HV4-11(T) had two candidate genes for lactonase and one for acylase, and expected protein structures were confirmed. In the quorum sensing inhibition assay using a plant pathogen Pectobacterium carotovorum KACC 14888, development of soft rot was significantly inhibited by strain MMS21-HV4-11(T). Besides, the swarming motility by Pseudomonas aeruginosa PA14 was significantly inhibited in the presence of strain MMS21-HV4-11(T). Since the isolate did not display direct antibacterial activity against either of these species, the inhibition was certainly due to quorum quenching activity. In an extended study with the type strains of all known species of Reyranella, all strains were capable of degrading N-acyl homoserine lactones (AHLs), thus showing quorum quenching potential at the genus level. This is the first study on the quorum quenching potential and enzymes responsible in Reyranella. In addition, MMS21-HV4-11(T) could be recognized as a new species through taxonomic characterization, for which the name Reyranella humidisoli sp. nov. is proposed (type strain = MMS21-HV4-11( T) = KCTC 82780( T) = LMG 32365(T)).

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Study of N-acyl homoserine lactone (AHL) degradation potential of bacteria isolated from environmental samples and their impact on quorum sensing regulated biofilm formation of Pseudomonas aeruginosa
Anju Tomy, Rakesh Yasarla
Journal of Environmental Chemical Engineering.2025; 13(2): 115974. CrossRef
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Yujing Tang, Yandong Zhan, Shuangshuang Gao, Ting Li, Hongzhuan Xuan
Journal of Hazardous Materials.2025; 494: 138695. CrossRef
Description of Humidisolicoccus flavus gen. nov., sp. nov., a novel actinobacterium isolated from riverside soil
Da Chan Kim, Seung Bum Kim
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
The Causative Agent of Soft Rot in Plants, the Phytopathogenic Bacterium Pectobacterium carotovorum subsp. carotovorum: A Brief Description and an Overview of Methods to Control It
Alla I. Perfileva, Elena I. Strekalovskaya, Nadezhda V. Klushina, Igor V. Gorbenko, Konstantin V. Krutovsky
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Boyu Luo, Tuoyu Liu, Zhi Sun, Yue Teng
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Reviews

Fecal Microbiota Transplantation: Indications, Methods, and Challenges.: Jee Young Lee, Yehwon Kim, Jiyoun Kim, Jiyeun Kate Kim; J. Microbiol. 2024;62(12):1057-1074. Published online November 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00184-3

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Abstract PDF

Over the past two decades, as the importance of gut microbiota to human health has become widely known, attempts have been made to treat diseases by correcting dysbiosis of gut microbiota through fecal microbiota transplantation (FMT). Apart from current knowledge of gut microbiota, FMT to treat disease has a long history, from the treatment of food poisoning in the fourth century to the treatment of Clostridioides difficile infections in the twentieth century. In 2013, FMT was recognized as a standard treatment for recurrent C. difficile because it consistently showed high efficacy. Though recurrent C. difficile is the only disease internationally recognized for FMT efficacy, FMT has been tested for other diseases and shown some promising preliminary results. Different FMT methods have been developed using various formulations and administration routes. Despite advances in FMT, some issues remain to be resolved, such as donor screening, manufacturing protocols, and unknown components in the fecal microbiota. In this review, we discuss the mechanisms, clinical indications, methods, and challenges of current FMT. We also discuss the development of alternative therapies to overcome the challenges of FMT.

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Fecal Microbiota Transplantation (FMT) in Clostridium difficile Infection: A Paradigm Shift in Gastrointestinal Microbiome Modulation
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The Microbiome Matters: Its Impact on Cancer Development and Therapeutic Responses: In‑Young Chung, Jihyun Kim, Ara Koh; J. Microbiol. 2024;62(3):137-152. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00110-7

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Abstract PDF

In the evolving landscape of cancer research, the human microbiome emerges as a pivotal determinant reshaping our understanding of tumorigenesis and therapeutic responses. Advanced sequencing technologies have uncovered a vibrant microbial community not confned to the gut but thriving within tumor tissues. Comprising bacteria, viruses, and fungi, this diverse microbiota displays distinct signatures across various cancers, with most research primarily focusing on bacteria. The correlations between specifc microbial taxa within diferent cancer types underscore their pivotal roles in driving tumorigenesis and infuencing therapeutic responses, particularly in chemotherapy and immunotherapy. This review amalgamates recent discoveries, emphasizing the translocation of the oral microbiome to the gut as a potential marker for microbiome dysbiosis across diverse cancer types and delves into potential mechanisms contributing to cancer promotion. Furthermore, it highlights the adverse efects of the microbiome on cancer development while exploring its potential in fortifying strategies for cancer prevention and treatment.

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