Journal of Microbiology

Review

Metabolite-mediated mechanisms linking the urinary microbiome to bladder cancer: Thu Anh Trần, Ho Young Lee, Hae Woong Choi; J. Microbiol. 2025;63(11):e2509001. Published online November 30, 2025; DOI: https://doi.org/10.71150/jm.2509001

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Abstract PDF: Bladder cancer is the most common malignancy of the urinary tract and is a major health burden globally. Recent advances in microbiome research have revealed that the urinary tract harbors a resident microbial community, overturning the long-held belief in its sterility. Increasing evidence suggests that microbial dysbiosis and microbially derived metabolites contribute to bladder cancer carcinogenesis, progression, and therapeutic responses. Distinct microbial signatures have been observed in bladder cancer patients, with notable differences across disease stages and between primary and recurrent cases. Mechanistic studies have demonstrated that microbe-associated metabolites and toxins can drive DNA damage, chronic inflammation, extracellular matrix remodeling, and epithelial–mesenchymal transition. In addition, biofilm formation allows bacteria to evade immune responses and promotes persistent inflammation, creating a tumor-permissive niche. Beyond pathogenesis, microbial activity also influences therapeutic outcomes; for instance, some microbial pathways can inactivate frontline chemotherapy, while others generate metabolites with anti-tumor properties. Collectively, these patterns define a microbiota–metabolite–immunity axis, presenting opportunities for precision oncology. Targeting microbial pathways, profiling urinary microbiota, and harnessing beneficial metabolites offer promising advancements in biomarker discovery, prognostic refinement, and the development of novel therapeutic strategies for bladder cancer.

Journal Articles

The Gut Microbiota Mediates the Protective Effects of Spironolactone on Myocardial Infarction: Lu Li, Jian-Yong Sun, Yu-Lin Li, Shi-Wei Zhu, Sheng-Zhong Duan; J. Microbiol. 2024;62(10):883-895. Published online September 3, 2024; DOI: https://doi.org/10.1007/s12275-024-00164-7

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Myocardial infarction (MI) is a type of cardiovascular disease that influences millions of human beings worldwide and has a great rate of mortality and morbidity. Spironolactone has been used as a critical drug for the treatment of cardiac failure and it ameliorates cardiac dysfunction post-MI. Despite these findings, whether there is a relationship between the therapeutic effects of spironolactone and the gut microorganism after MI has not been determined. In our research, we used male C57BL/6 J mice to explore whether the gut microbiota mediates the beneficial function of spironolactone after myocardial infarction. We demonstrated that deletion of the gut microbiota eliminated the beneficial function of spironolactone in MI mice, displaying exacerbated cardiac dysfunction, cardiac infarct size. In addition, the gut microbiota was altered by spironolactone after sham or MI operation in mice. We also used male C57BL/6 J mice to investigate the function of a probiotic in the myocardial infarction. In summary, our findings reveal a precious role of the gut flora in the therapeutic function of spironolactone on MI.

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Probiotics and Prebiotics in Post-Myocardial Infarction Rehabilitation: Mechanisms, Benefits, and Future Directions
Georgy Leonov, Elena Livantsova, Yurgita Varaeva, Antonina Starodubova
Current Nutrition Reports.2025;[Epub] CrossRef
Research Trends and Hotspots of Gut Microbiota and Its Metabolites in Cardiovascular Diseases: A Bibliometric Analysis
Kaixuan Zhang, Yajun Shi, Lirong Peng, Xiaofei Zhang, Nanbo Zheng, Jiajing Xin, Junbo Zou, Fei Luan
Journal of Multidisciplinary Healthcare.2025; Volume 18: 5125. CrossRef
Insights into the role of gut microbiota modulation in the management of various cardiovascular diseases: A new approach for improving the efficacy of current cardiovascular medications
Lamiaa A. Ahmed, Khaled F. Al-Massri
European Journal of Pharmacology.2025; 1007: 178210. CrossRef
The role of the gut microbiota in the onset and progression of heart failure: insights into epigenetic mechanisms and aging
Giulia Matacchione, Francesco Piacenza, Lorenzo Pimpini, Yuri Rosati, Serena Marcozzi
Clinical Epigenetics.2024;[Epub] CrossRef

Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil: Abhilash Bhattacharjee, Anil Kumar Singh; J. Microbiol. 2024;62(7):511-523. Published online June 21, 2024; DOI: https://doi.org/10.1007/s12275-024-00129-w

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Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing & analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.

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First Case of Respiratory Infection in Rabbits Caused by Alcaligenes faecalis in Romania
Vlad Iorgoni, Ionica Iancu, Ionela Popa, Alexandru Gligor, Gabriel Orghici, Bogdan Sicoe, Corina Badea, Cristian Dreghiciu, Călin Pop, Timea Bochiș, Janos Degi, Luminita Costinar, Corina Pascu, Viorel Herman
Veterinary Sciences.2025; 12(1): 33. CrossRef

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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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)).

Citations

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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
Hepatotoxicity of imidacloprid in zebrafish and the alleviating role of 10-hydroxy-2-decenoi acid: Insights into oxidative stress, inflammation, and gut microbiota
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
Agronomy.2025; 15(7): 1578. CrossRef
SynCom‐mediated herbicide degradation activates microbial carbon metabolism in soils
Yuxiao Zhang, Jack A. Gilbert, Xuan Liu, Li Nie, Xiyuan Xu, Guifeng Gao, Lihui Lyu, Yuying Ma, Kunkun Fan, Teng Yang, Yumeng Zhang, Jiabao Zhang, Haiyan Chu
iMeta.2025;[Epub] CrossRef
Research progress of bacterial quorum sensing systems in synthetic biology applications
Boyu Luo, Tuoyu Liu, Zhi Sun, Yue Teng
Chinese Science Bulletin.2024; 69(36): 5213. CrossRef
Validation List no. 220. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef

Effects of Phosphorus‑dissolving Dark Septate Endophytes on the Growth of Blueberry: Qixin Luo , Rui Hou , Xiaojing Shang , Si Li; J. Microbiol. 2023;61(9):837-851. Published online October 5, 2023; DOI: https://doi.org/10.1007/s12275-023-00080-2

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Dark septate endophytes (DSEs) are widely distributed and improve plant growth. DSEs secrete large amounts of enzymes to mineralize insoluble phosphorus in soil and convert it into soluble phosphorus, promoting plant uptake of phosphorus. However, the effects of DSEs with phosphate-solubilizing ability on host plants need further study. In this study, phosphorusdissolving DSEs were screened for growth-promoting effects. We isolated, identified and characterized three DSE species (Thozetella neonivea, Pezicula ericae and Hyaloscyphaceae sp.) showing phosphate-solubilizing ability. The impact of single, dual or triple inoculation of DSEs on blueberry plant characteristics was studied. Their effects on colonization intensity, seedling biomass, nutrients in plants and soil, and activities of plant resistance enzymes and soil enzymes were markedly upregulated relative to the control (P < 0.05). The available phosphorus and acid phosphatase levels in different combinations were significantly increased. These findings indicate that the application of the three DSEs may be valuable in facilitating the cultivation of blueberry with a higher biomass and improved plant quality.

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Needle in a Haystack: Culturing Plant‐Beneficial Helotiales Lineages From Plant Roots
Pauline Bruyant, Jeanne Doré, Laurent Vallon, Yvan Moënne‐Loccoz, Juliana Almario
Environmental Microbiology.2025;[Epub] CrossRef
Acidomelania saccharicola sp. nov., a new species of dark septate endophytes in Helotiales, with potential of controlling Fusarium wilt of banana
Qian Nong, Yan Zhang, Yanyan Long, Yanlu Chen, Liping Qin, Shanyu Lin, Fenghua Zeng, Ling Xie
Biological Control.2025; 206: 105781. CrossRef
The Three-Dimensional Structure of the Genome of the Dark Septate Endophyte Exophiala tremulae and Its Symbiosis Effect on Alpine Meadow Plant Growth
Chu Wu, Junjie Fan, Die Hu, Honggang Sun, Guangxin Lu, Yun Wang, Yujie Yang
Journal of Fungi.2025; 11(4): 246. CrossRef
Growth-Promoting Effects of Dark Septate Endophytes Fungus Acrocalymma on Tomato (Solanum lycopersicum)
Xiaoxiao Feng, Ying Jin, Zhupeiqi Zhong, Yongli Zheng, Huiming Wu
Journal of Fungi.2025; 11(7): 510. CrossRef
Inoculation dose and strain identity shape dark septate endophyte effects on plant-soil nutrient stoichiometry in ecological restoration
Shiwei Guo, Mingyi Li, Roujia Kang, Wennian Xu, Haoji Jia, Dong Xia, Daxiang Liu
Applied Soil Ecology.2025; 216: 106523. CrossRef
Dark septate endophytes promote the growth of Cynodon dactylon under drought stress and enhance its potential for use in the ecological restoration of slopes
Haoji Jia, Qiming Geng, Mingyi Li, Ran Wang, Fuhao Wang, Yuxin Deng, Wennian Xu, Daxiang Liu
Frontiers in Plant Science.2025;[Epub] CrossRef
Diversity and Functional Roles of Root-Associated Endophytic Fungi in Two Dominant Pioneer Trees Reclaimed from a Metal Mine Slag Heap in Southwest China
Bo Bi, Yuqing Xiao, Xiaonan Xu, Qianqian Chen, Haiyan Li, Zhiwei Zhao, Tao Li
Microorganisms.2024; 12(10): 2067. CrossRef
Short-term organic fertilizer substitution increases sorghum yield by improving soil physicochemical characteristics and regulating microbial community structure
Mengen Nie, Guangqian Yue, Lei Wang, Yizhong Zhang
Frontiers in Plant Science.2024;[Epub] CrossRef

Gut Lactobacillus and Probiotics Lactobacillus lactis/rhamnosis Ameliorate Liver Fibrosis in Prevention and Treatment: Sung Min Won , Na Young Lee , Ki&# , Haripriya Gupta , Satya Priya Sharma , Kyung Hwan Kim , Byoung Kook Kim , Hyun Chae Joung , Jin Ju Jeong , Raja Ganesan , Sang Hak Han , Sang Jun Yoon , Dong Joon Kim , Ki Tae Suk; J. Microbiol. 2023;61(2):245-257. Published online February 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00014-y

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The progression and exacerbation of liver fibrosis are closely related to the gut microbiome. It is hypothesized that some probiotics may slow the progression of liver fibrosis. In human stool analysis [healthy group (n = 44) and cirrhosis group (n = 18)], difference in Lactobacillus genus between healthy group and cirrhosis group was observed. Based on human data, preventive and therapeutic effect of probiotics Lactobacillus lactis and L. rhamnosus was evaluated by using four mice fibrosis models. L. lactis and L. rhamnosus were supplied to 3,5-diethoxycarbonyl-1,4-dihydrocollidine or carbon tetrachloride-induced liver fibrosis C57BL/6 mouse model. Serum biochemical measurements, tissue staining, and mRNA expression in the liver were evaluated. The microbiome was analyzed in mouse cecal contents. In the mouse model, the effects of Lactobacillus in preventing and treating liver fibrosis were different for each microbe species. In case of L. lactis, all models showed preventive and therapeutic effects against liver fibrosis. In microbiome analysis in mouse models administered Lactobacillus, migration and changes in the ratio and composition of the gut microbial community were confirmed. L. lactis and L. rhamnosus showed preventive and therapeutic effects on the progression of liver fibrosis, suggesting that Lactobacillus intake may be a useful strategy for prevention and treatment.

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Probiotics modulation of the endotoxemic effect on the gut and liver of the lipopolysaccharide challenged mice
Gyan Babu, Banalata Mohanty
Drug and Chemical Toxicology.2025; 48(3): 627. CrossRef
Enhancing the application of probiotics in probiotic food products from the perspective of improving stress resistance by regulating cell physiological function: A review
Dingkang Wang, Ruijie Xu, Sha Liu, Xiaomin Sun, Tianxiao Zhang, Lin Shi, Youfa Wang
Food Research International.2025; 199: 115369. CrossRef
Probiotics and Cancer: Mechanistic Insights and Organ-Specific Impact
Md Faruque Ahmad, Fakhruddin Ali Ahmad, Abdulrahman A. Alsayegh, Md. Zeyaullah, Ahmad O. Babalghith, Hani Faidah, Faiyaz Ahmed, Anjum Khanam, Boshra Mozaffar, Nahla Kambal, Farkad Bantun
Biomolecules.2025; 15(6): 879. CrossRef
Integration bile acid metabolomics and gut microbiome to study the anti-liver fibrosis effects of total alkaloids of Corydalis saxicola Bunting
Qianyi Wang, MeiLing Zhang, Mingwei Meng, Zhuo Luo, Ziping Pan, Lijun Deng, Jinghua Qin, Bingjian Guo, Dan Zhu, Yanmin Zhang, Hongwei Guo, Yonghong Liang, Zhiheng Su
Chinese Medicine.2025;[Epub] CrossRef
Mucosal microbiota signatures reveal diagnostic insights in chronic liver disease
Sadık Dinçer, Yakup Ülger, Anıl Delik
BMC Gastroenterology.2025;[Epub] CrossRef
Saccharomyces cervisiae ameliorative impact combined with sulfaclozine on broiler chicken oxidative status
Nahla M. Ali, Mohamed K. Hussein, Nady Khairy Elbarbary, Zeinab-El Amgad, Enas A. Noseer
BMC Veterinary Research.2025;[Epub] CrossRef
Lactobacillus gasseri BNR17 and Limosilactobacillus fermentum ABF21069 Ameliorate High Sucrose-Induced Obesity and Fatty Liver via Exopolysaccharide Production and β-oxidation
Yu Mi Jo, Yoon Ji Son, Seul-Ah Kim, Gyu Min Lee, Chang Won Ahn, Han-Oh Park, Ji-Hyun Yun
Journal of Microbiology.2024; 62(10): 907. CrossRef
Research reviews and prospects of gut microbiota in liver cirrhosis: a bibliometric analysis (2001–2023)
Xiaofei Zhu, Ziyuan Zhou, Xiaxia Pan
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Xue Li, Xinyi Xu, Sian Tao, Yue Su, Li Wen, Dong Wang, Jibin Liu, Quansheng Feng
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Samantha Roldán-Pérez, Sara Lucía Gómez Rodríguez, José Uriel Sepúlveda-Valencia, Orlando Simón Ruiz Villadiego, María Elena Márquez Fernández, Olga I. Montoya Campuzano, Mónica María Durango-Zuleta
Heliyon.2023; 9(11): e21558. CrossRef
Agrocybe aegerita Polysaccharide Combined with Bifidobacterium lactis Bb-12 Attenuates Aging-Related Oxidative Stress and Restores Gut Microbiota
Xiaoyan Liu, Yanyu Feng, Hongmin Zhen, Lina Zhao, Hongqiang Wu, Bin Liu, Guangsen Fan, Aijun Tong
Foods.2023; 12(24): 4381. CrossRef
Probiotics and liver fibrosis: An evidence-based review of the latest research
Lin Cheng, Jianyou Shi, Haoyuan Peng, Rongsheng Tong, Yonghe Hu, Dongke Yu
Journal of Functional Foods.2023; 109: 105773. CrossRef

Characteristic alterations of gut microbiota in uncontrolled gout: Asad ul-Haq , Kyung-Ann Lee , Hoonhee Seo , Sukyung Kim , Sujin Jo , Kyung Min Ko , Su-Jin Moon , Yun Sung Kim , Jung Ran Choi , Ho-Yeon Song , Hyun-Sook Kim; J. Microbiol. 2022;60(12):1178-1190. Published online November 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2416-1

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Microbiome research has been on the rise recently for a more in-depth understanding of gout. Meanwhile, there is a need to understand the gut microbiome related to uric acid-lowering drug resistance. In this study, 16S rRNA gene-based microbiota analysis was performed for a total of 65 stool samples from 17 healthy controls and 48 febuxostat-treated gout patients (including 28 controlled subjects with decreased uric acid levels and 20 uncontrolled subjects with non-reduced uric acid levels). Alpha diversity of bacterial community decreased in the healthy control, controlled, and uncontrolled groups. In the case of beta diversity, the bacterial community was significantly different among groups (healthy control, controlled, and uncontrolled groups). Taxonomic biomarker analysis revealed the increased population of g-Bifidobacterium in healthy controls and g-Prevotella in uncontrolled patients. PCR further confirmed this result at the species level. Additionally, functional metagenomics predictions led to the exploration of various functional biomarkers, including purine metabolism. The results of this study can serve as a basis for developing potential new strategies for diagnosing and treating gout from microbiome prospects.

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Characteristics of skin microbiome associated with disease severity in systemic sclerosis
Kyung-Ann Lee, Asad Ul-Haq, Hoonhee Seo, Sujin Jo, Sukyung Kim, Ho-Yeon Song, Hyun-Sook Kim
Journal of Microbiology.2025; 63(1): e:2409018. CrossRef
Habitual coarse grain intake, gut microbiota, and hyperuricemia in individuals with or at risk of metabolic syndrome: A post-hoc analysis
Juan He, Yifei He, Junqi Li, Guoqing Ma, Yunfeng Li, Jiawen Xie, Chen He, Xinran Feng, Kaizhen Jia, Wei Li, Menghan Wang, Amei Tang, Tian Tian, Xia Liao, Weimin Li, Feng Yan, Ying Zhang, Xiaoxiao Cao, Yuelang Zhang, Nan Yang, Xin Liu, Qian Wang
Nutrition, Metabolism and Cardiovascular Diseases.2025; 35(10): 104126. CrossRef
Microbiome therapeutic PMC72 through reverse translational research in gout
Mohammed Solayman Hossain, Hoonhee Seo, Kyung-Ann Lee, Asad ul-Haq, Sukyung Kim, Sujin Jo, Md Abdur Rahim, Hanieh Tajdozian, Fatemeh Ghorbanian, Youjin Yoon, Indrajeet Barman, Md Sarower Hossen Shuvo, Hyun-Sook Kim, Ho-Yeon Song
Journal of Microbiology.2025; 63(5): e2501002. CrossRef
Interpretive prediction of hyperuricemia and gout patients via machine learning analysis of human gut microbiome
Jia-Wei Tang, Alfred Chin Yen Tay, Liang Wang
BMC Microbiology.2025;[Epub] CrossRef
Hyperuricemia and the gut microbiota: current research hotspots and future trends
Jingjing Yang, Jing Chen, Dingxiang Li, Qin Wu, Yanan Zhang, Yujia Li, Yihui Deng
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Different Prostatic Tissue Microbiomes between High- and Low-Grade Prostate Cancer Pathogenesis
Jae Heon Kim, Hoonhee Seo, Sukyung Kim, Md Abdur Rahim, Sujin Jo, Indrajeet Barman, Hanieh Tajdozian, Faezeh Sarafraz, Ho-Yeon Song, Yun Seob Song
International Journal of Molecular Sciences.2024; 25(16): 8943. CrossRef
Reassessing Gout Management through the Lens of Gut Microbiota
Jean Demarquoy, Oumaima Dehmej
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Feiyan Zhao, Zhixin Zhao, Dafu Man, Zhihong Sun, Ning Tie, Hongbin Li, Heping Zhang
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In-Young Jo, Hyung-Kwon Byeon, Myung-Jin Ban, Jae-Hong Park, Sang-Cheol Lee, Yong Kyun Won, Yun-Su Eun, Jae-Yun Kim, Na-Gyeong Yang, Sul-Hee Lee, Pyeongan Lee, Nam-Hun Heo, Sujin Jo, Hoonhee Seo, Sukyung Kim, Ho-Yeon Song, Jung-Eun Kim
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Tiago H. Zaninelli, Geovana Martelossi-Cebinelli, Telma Saraiva-Santos, Sergio M. Borghi, Victor Fattori, Rubia Casagrande, Waldiceu A. Verri
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A dynamics association study of gut barrier and microbiota in hyperuricemia
Qiulan Lv, Jun Zhou, Changyao Wang, Xiaomin Yang, Yafei Han, Quan Zhou, Ruyong Yao, Aihua Sui
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Biochemical Recurrence in Prostate Cancer Is Associated with the Composition of Lactobacillus: Microbiome Analysis of Prostatic Tissue
Jae Heon Kim, Hoonhee Seo, Sukyung Kim, Asad Ul-Haq, Md Abdur Rahim, Sujin Jo, Ho-Yeon Song, Yun Seob Song
International Journal of Molecular Sciences.2023; 24(13): 10423. CrossRef
Remote effects of kidney drug transporter OAT1 on gut microbiome composition and urate homeostasis
Vladimir S. Ermakov, Jeffry C. Granados, Sanjay K. Nigam
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Mengna Wang, Jiayao Fan, Zhaohui Huang, Dan Zhou, Xue Wang
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Asad Ul-Haq, Hoonhee Seo, Sujin Jo, Hyuna Park, Sukyung Kim, Youngkyoung Lee, Saebim Lee, Je Hoon Jeong, Ho‑Yeon Song
Polish Journal of Microbiology.2022; 71(4): 601. CrossRef

Pat- and Pta-mediated protein acetylation is required for horizontallyacquired virulence gene expression in Salmonella Typhimurium: Hyojeong Koo , Eunna Choi , Shinae Park , Eun-Jin Lee , Jung-Shin Lee; J. Microbiol. 2022;60(8):823-831. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2095-y

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Salmonella Typhimurium is a Gram-negative facultative pathogen that causes a range of diseases, from mild gastroenteritis to severe systemic infection in a variety of animal hosts. S. Typhimurium regulates virulence gene expression by a silencing mechanism using nucleoid-associated proteins such as Histone-like Nucleoid Structuring protein (H-NS) silencing. We hypothesize that the posttranslational modification, specifically protein acetylation, of proteins in gene silencing systems could affect the pathogenic gene expression of S. Typhimurium. Therefore, we created acetylation-deficient mutant by deleting two genes, pat and pta, which are involved in the protein acetylation pathway. We observed that the pat and pta deletion attenuates mouse virulence and also decreases Salmonella’s replication within macrophages. In addition, the Δpat Δpta strain showed a decreased expression of the horizontally-acquired virulence genes, mgtC, pagC, and ugtL, which are highly expressed in low Mg2+. The decreased virulence gene expression is possibly due to higher H-NS occupancy to those promoters because the pat and pta deletion increases H-NS occupancy whereas the same mutation decreases occupancy of RNA polymerase. Our results suggest that Pat- and Pta-mediated protein acetylation system promotes the expression of virulence genes by regulating the binding affinity of H-NS in S. Typhimurium.

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Reversible acetylation of ribosomal protein S1 serves as a smart switch for Salmonella to rapidly adapt to host stress
Yi-Lin Shen, Tian-Xian Liu, Lei Xu, Bang-Ce Ye, Ying Zhou
Nucleic Acids Research.2025;[Epub] CrossRef
Multi-Lasso Peptide-Based Synergistic Nanocomposite: A High-Stability, Broad-Spectrum Antimicrobial Agent with Potential for Combined Antibacterial Therapy
Yu Li, Jinyu Zhang, Ke Wei, Di Zhou, Zepeng Wang, Zhiwei Zeng, Yu Han, Weisheng Cao
ACS Nano.2024; 18(45): 31435. CrossRef

Availability of polyamines affects virulence and survival of Neisseria meningitidis: Poonam Kanojiya , Riya Joshi , Sunil D. Saroj; J. Microbiol. 2022;60(6):640-648. Published online April 18, 2022; DOI: https://doi.org/10.1007/s12275-022-1589-y

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Neisseria meningitidis is a Gram-negative human-restricted pathogen that asymptomatically resides in the human respiratory tract. Meningococcal meningitis and sepsis both are caused by N. meningitidis. The bacterium must adhere to host epithelial cells in order to colonize effectively. The factors that determine the initial attachment to the host and dispersal, are not well understood. Metabolites released by the host may aid in meningococcal colonization and dissemination. Polyamines are aliphatic polycations that assist in cell survival and proliferation. The virulence properties of N. meningitidis after exposure to polyamines were investigated. Adhesion to nasopharyngeal epithelial cells increased in the presence of spermine. Also, the relative expression of adhesin, pilE increased in the presence of spermine. Further, relative expression of ctrA, ctrB and lipB was upregulated in the presence of spermidine, indicating increased capsule formation. Upregulated capsule synthesis of N. meningitidis in the presence of spermidine allows it to survive in murine macrophages. The study suggests the importance of the extracellular pool of polyamines in promoting virulence in N. meningitidis.

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Environmental desiccation stress induces viable but non culturable state in Neisseria meningitidis
Poonam Kanojiya, Tiyasa Haldar, Sunil D. Saroj
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Prevalence and characteristics of the mcr-1 gene in retail meat samples in Zhejiang Province, China: Biao Tang , Jiang Chang , Yi Luo , Han Jiang , Canying Liu , Xingning Xiao , Xiaofeng Ji , Hua Yang; J. Microbiol. 2022;60(6):610-619. Published online March 31, 2022; DOI: https://doi.org/10.1007/s12275-022-1597-y

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Considering the serious threat to food safety and public health posed by pathogens with colistin resistance, colistin was banned as a growth promoter in 2017 in China. In recent years, the resistance rate of Escherichia coli isolated from animal intestines or feces to colistin has decreased. However, the prevalence and characteristics of the mcr-1 gene in retail meat have not been well explored. Herein, 106 mcr-1-negative and 16 mcr- 1-positive E. coli isolates were randomly recovered from 120 retail meat samples and screened using colistin. The 106 E. coli isolates showed maximum resistance to sulfafurazole (73.58%) and tetracycline (62.26%) but susceptibility to colistin (0.00%). All 16 mcr-1-positive E. coli isolates showed resistance to colistin, were extended spectrum beta-lactamase (ESBL)-positive and exhibited complex multidrug resistance (MDR). For these 16 isolates, 17 plasmid replicons and 42 antibiotic resistance genes were identified, and at least 7 antibiotic resistance genes were found in each isolate. Acquired disinfectant resistance genes were identified in 75.00% (12/16) of the isolates. Furthermore, comparative genomic and phylogenetic analysis
results
indicated that these 16 mcr-1-positive E. coli isolates and the most prevalent mcr-1-harboring IncI2 plasmid in this study were closely related to other previously reported mcr-1-positive E. coli isolates and the IncI2 plasmid, respectively, showing their wide distribution. Taken together, our findings showed that retail meat products were a crucial reservoir of mcr-1 during the colistin ban period and should be continuously monitored.

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Exploiting the antibacterial mechanism of phenazine substances from Lysobacter antibioticus 13-6 against Xanthomonas oryzae pv. oryzicola: Qi Liu , Jun Yang , Waqar Ahmed , Xiaoyan Wan , Lanfang Wei , Guanghai Ji; J. Microbiol. 2022;60(5):496-510. Published online March 31, 2022; DOI: https://doi.org/10.1007/s12275-022-1542-0

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Abstract PDF

Bacterial leaf streak caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most destructive diseases affecting rice production worldwide. In this study, we extracted and purified phenazine substances from the secondary metabolites of Lysobacter antibioticus 13-6. The bacteriostatic mechanism of phenazine substances against Xoc was investigated through physiological response and transcriptomic analysis.
Results
showed that phenazine substances affects the cell membrane permeability of Xoc, which causes cell swelling and deformation, blockage of flagellum synthesis, and imbalance of intracellular environment. The changes in intracellular environment affect the physiological and metabolic functions of Xoc, which reduces the formation of pathogenic factors and pathogenicity. Through transcriptomic analysis, we found that among differentially expressed genes, the expression of 595 genes was induced significantly (275 up-regulated and 320 down-regulated). In addition, we observed that phenazine substances affects three main functions of Xoc, i.e., transmembrane transporter activity, DNA-mediated transposition, and structural molecular activity. Phenazine substances also inhibits the potassium ion transport system that reduces Xoc resistance and induces the phosphate ion transport system to maintain the stability of the internal environment. Finally, we conclude that phenazine substances could retard cell growth and reduce the pathogenicity of Xoc by affecting cell structure and physiological metabolism. Altogether, our study highlights latest insights into the antibacterial mechanism of phenazine substances against Xoc and provides basic guidance to manage the incidence of bacterial leaf streak of rice.

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Potato tillage method is associated with soil microbial communities, soil chemical properties, and potato yield: Haiyan Ma , Chen Xie , Shunlin Zheng , Peihua Li , Hafsa Nazir Cheema , Jing Gong , Zhuqing Xiang , Juanjuan Liu , Jiahao Qin; J. Microbiol. 2022;60(2):156-166. Published online January 7, 2022; DOI: https://doi.org/10.1007/s12275-022-1060-0

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Abstract PDF

Intensive potato continuous cropping (IPCC) results in low potato yields compared with non-intensive potato continuous cropping (PCC) and potato-maize rotation (PMRC). However, it is still unclear whether the degree of potato continuous cropping obstacle is related to the soil environment formed by the previous crop. To investigate the effect of planting potatoes and planting maize after harvesting the spring potatoes on soil chemical properties and soil microbial community structure, an experiment was carried out in the same origin soil environment over a period of seven years: (a) PCC, i.e., spring planting; (b) IPCC, i.e., autumn and spring planting (IPCC); (c) PMRC, i.e., spring potatoes and summer maize (PMRC), and (d) fallow (CK). We confirmed that the potato yield under PMRC was significantly higher than that under PCC and IPCC. Under IPCC, soil total phosphorus content was significantly higher than other treatments, whereas ammonium nitrogen content was the lowest. Compared with PCC and IPCC, PMRC had a higher ammonium nitrogen content and lower total phosphorus content. The significantly different fungal taxa in IPCC (Glomerellales, Plectosphaerella, Thelebolales) may threaten the health of the plant and positive correlated with soil total phosphorus, while other microbial taxa in PMRC (Bacillales, Polythrincium, Helotiales) can mainly promotes plant nitrogen uptake and protects plants against diseases. The PMRC-promoting taxa were positively correlated with the ammonium nitrogen content and negative correlated with soil total phosphorus content. In summary, the cropping systems might have affected potato yields by changed soil microorganism community structures – especially fungal community structures – and by the chemical properties of the soils that also depends on microbes.

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Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists: Jihoon Jo , Jooseong Oh , Chungoo Park; J. Microbiol. 2020;58(3):176-192. Published online February 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9525-5

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Abstract PDF

Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted (“shotgun”) sequencing of all (“meta”) microbial genomes (“genomic”) present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.

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Setup of a scientific computing environment for computational biology: Simulation of a genome-scale metabolic model of Escherichia coli as an example: Junhyeok Jeon , Hyun Uk Kim; J. Microbiol. 2020;58(3):227-234. Published online February 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9516-6

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Computational analysis of biological data is becoming increasingly important, especially in this era of big data. Computational analysis of biological data allows efficiently deriving biological insights for given data, and sometimes even counterintuitive ones that may challenge the existing knowledge. Among experimental researchers without any prior exposure to computer programming, computational analysis of biological data has often been considered to be a task reserved for computational biologists. However, thanks to the increasing availability of user-friendly computational resources, experimental researchers can now easily access computational resources, including a scientific computing environment and packages necessary for data analysis. In this regard, we here describe the process of accessing Jupyter Notebook, the most popular Python coding environment, to conduct computational biology. Python is currently a mainstream programming language for biology and biotechnology. In particular, Anaconda and Google Colaboratory are introduced as two representative options to easily launch Jupyter Notebook. Finally, a Python package COBRApy is demonstrated as an example to simulate 1) specific growth rate of Escherichia coli as well as compounds consumed or generated under a minimal medium with glucose as a sole carbon source, and 2) theoretical production yield of succinic acid, an industrially important chemical, using E. coli. This protocol should serve as a guide for further extended computational analyses of biological data for experimental researchers without computational background.

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Rhizocompartments and environmental factors affect microbial composition and variation in native plants: Myung-Suk Kang , Moonsuk Hur , Soo-Je Park; J. Microbiol. 2019;57(7):550-561. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8646-1

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Molecular analysis based on large-scale sequencing of the plant microbiota has revealed complex relationships between plants and microbial communities, and environmental factors such as soil type can influence these relationships. However, most studies on root-associated microbial communities have focused on model plants such as Arabidopsis, rice or crops. Herein, we examined the microbiota of rhizocompartments of two native plants, Sedum takesimense Nakai and Campanula takesimana Nakai, using archaeal and bacterial 16S rRNA gene amplicon profiling, and assessed relationships between environmental factors and microbial community composition. We identified 390 bacterial genera, including known plant-associated genera such as Pseudomonas, Flavobacterium, Bradyrhizobium and Rhizobium, and uncharacterized clades such as DA101 that might be important in root-associated microbial communities in bulk soil. Unexpectedly, Nitrososphaera clade members were abundant, indicating functional association with roots. Soil texture/type has a greater impact on microbial community composition in rhizocompartments than chemical factors. Our results provide fundamental knowledge on microbial diversity, community and correlations with environmental factors, and expand our understanding of the microbiota in rhizocompartments of native plants.

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Review

[MINIREVIEW] Interdependence between iron acquisition and biofilm formation in Pseudomonas aeruginosa: Donghoon Kang , Natalia V. Kirienko; J. Microbiol. 2018;56(7):449-457. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8114-3

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Bacterial biofilms remain a persistent threat to human healthcare due to their role in the development of antimicrobial resistance. To combat multi-drug resistant pathogens, it is crucial to enhance our understanding of not only the regulation of biofilm formation, but also its contribution to bacterial virulence. Iron acquisition lies at the crux of these two subjects. In this review, we discuss the role of iron acquisition in biofilm formation and how hosts impede this mechanism to defend against pathogens. We also discuss recent findings that suggest that biofilm formation can also have the reciprocal effect, influencing siderophore production and iron sequestration.

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Journal Article

Bacillus ferrooxidans sp. nov., an iron(II)-oxidizing bacterium isolated from paddy soil: Guo-Wei Zhou , Xiao-Ru Yang , Jian-Qiang Su , Bang-Xiao Zheng , Yong-Guan Zhu; J. Microbiol. 2018;56(7):472-477. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-7543-3

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Abstract PDF

An endospore-forming bacterium, designated YT-3T, was isolated from a paddy soil in Yingtan, Jiangxi, China. Cells of strain YT-3T were Gram-positive, rod-shaped, facultative anaerobic, catalase, and oxidase positive. The optimum growth temperature and pH were 30°C (ranged from 15 to 50°C) and 6.5–7.0 (ranged from 3 to 11), respectively. Analysis of the 16S rRNA gene sequence showed that strain YT-3T was affiliated to the genus Bacillus and displayed the highest similarity to that of Bacillus drentensis JCM 21707T (98.3%), followed by B. ginsengisoli JCM 17335T (97.8%) and B. fumarioli JCM 21708T (97.0%). The similarity of rpoB gene sequence between strain YT-3T and B. drentensis JCM 21707T, B. ginsengisoli JCM 17335T and B. fumarioli JCM 21708T was 80.4%, 81.5%, and 82.1%, respectively. The genomic DNA G + C content was 44.9 mol%. The predominant respiratory quinone was Menaquinone-7, and meso-diaminopimelic acid was present in the peptidoglycan layer of cell wall. The major fatty acids were C15:0 anteiso (36.2%), C14:0 iso (19.6%), C15:0 iso (17.4%), and C16:0 iso (9.8%). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipids, and ammoniac phospholipids. The DNA-DNA hybridization values between isolate YT-3T and B. drentensis (JCM 21707T), B. ginsengisoli (JCM 17335T), and B. fumarioli (JCM 21708T) were 36.3%, 30.3%, and 25.3%, respectively. On the basis of physiological, genetic and biochemical data, strain YT-3T represented a novel species of the genus Bacillus, for which the name Bacillus ferrooxidans sp. nov was proposed. The type strain is YT-3T (= KCTC 33875T = CCTCC AB 2017049T).

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Review

MINIREVIEW] Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications: Kyoung-Soon Jang , Young Hwan Kim; J. Microbiol. 2018;56(4):209-216. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7457-0

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Abstract PDF

Advances in mass spectrometry have enabled the investigation of various biological systems by directly analyzing diverse sets of biomolecules (i.e., proteins, lipids, and carbohydrates), thus making a significant impact on the life sciences field. Over the past decade, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely utilized as a rapid and reliable method for the identification of microorganisms. MALDI-TOF MS has come into widespread use despite its relatively low resolving power (full width at half maximum, FWHM: < 5,000) and its incompatibility with tandem MS analysis, features with which other high-resolution mass spectrometers are equipped. Microbial identification is achieved by searching databases containing mass spectra of peptides and proteins extracted from microorganisms of interest, using scoring algorithms to match analyzed spectra with reference spectra. In this paper, we give a brief overview of the diverse applications of rapid and robust MALDI-TOF MS-based techniques for microbial identification in a variety of fields, such as clinical diagnosis and environmental and food monitoring. We also describe the fundamental principles of MALDI-TOF MS. The general specifications of the two major MS-based microbial identification systems available in the global market (BioTyper® and VITEK® MS Plus) and the distribution of these instruments in Republic of Korea are also discussed. The current review provides an understanding of this emerging microbial identification and classification technology and will help bacteriologists and cell biologists take advantage of this powerful technique.

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Journal Articles

Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments: Shiling Zheng , Bingchen Wang , Fanghua Liu , Oumei Wang; J. Microbiol. 2017;55(11):862-870. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7104-1

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Abstract PDF

Minerals that contain ferric iron, such as amorphous Fe(III) oxides (A), can inhibit methanogenesis by competitively accepting electrons. In contrast, ferric iron reduced products, such as magnetite (M), can function as electrical conductors to stimulate methanogenesis, however, the processes and effects of magnetite production and transformation in the methanogenic consortia are not yet known. Here we compare the effects on methanogenesis of amorphous Fe (III) oxides (A) and magnetite (M) with ethanol as the electron donor. RNAbased terminal restriction fragment length polymorphism with a clone library was used to analyse both bacterial and archaeal communities. Iron (III)-reducing bacteria including Geobacteraceae and methanogens such as Methanosarcina were enriched in iron oxide-supplemented enrichment cultures for two generations with ethanol as the electron donor. The enrichment cultures with A and non-Fe (N) dominated by the active bacteria belong to Veillonellaceae, and archaea belong to Methanoregulaceae and Methanobacteriaceae, Methanosarcinaceae (Methanosarcina mazei), respectively. While the enrichment cultures with M, dominated by the archaea belong to Methanosarcinaceae (Methanosarcina barkeri). The
results
also showed that methanogenesis was accelerated in the transferred cultures with ethanol as the electron donor during magnetite production from A reduction. Powder X-ray diffraction analysis indicated that magnetite was generated from microbial reduction of A and M was transformed into siderite and vivianite with ethanol as the electron donor. Our data showed the processes and effects of magnetite production and transformation in the methanogenic consortia, suggesting that significantly different effects of iron minerals on microbial methanogenesis in the iron-rich coastal riverine environment were present.

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NMR-based metabolomics reveals the metabolite profiles of Vibrio parahaemolyticus under ferric iron stimulation: Jun Zhou , Chenyang Lu , Dijun Zhang , Chennv Ma , Xiurong Su; J. Microbiol. 2017;55(8):628-634. Published online July 28, 2017; DOI: https://doi.org/10.1007/s12275-017-6551-z

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Vibrio parahaemolyticus is a halophilic bacterium endemic to coastal areas, and its pathogenicity has caused widespread seafood poisoning. In our previous research, the protein expression of V. parahaemolyticus in Fe3+ medium was determined using isobaric tags for relative and absolute quantitation (iTRAQ). Here, nuclear magnetic resonance (NMR) was used to detect changes in the V. parahaemolyticus metabolome. NMR spectra were obtained using methanol-water extracts of intracellular metabolites from V. parahaemolyticus under various culture conditions, and 62 metabolites were identified, including serine, arginine, alanine, ornithine, tryptophan, glutamine, malate, NAD+, NADP+, oxypurinol, xanthosine, dCTP, uracil, thymine, hypoxanthine, and betaine. Among these, 21 metabolites were up-regulated after the stimulation of the cells by ferric iron, and 9 metabolites were down-regulated. These metabolites are involved in amino acid and protein synthesis, energy metabolism, DNA and RNA synthesis and osmolality. Based on these results, we conclude that Fe3+ influences the metabolite profiles of V. parahaemolyticus.

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Nocardioides suum sp. nov. isolated from the air environment in an indoor pig farm: Siwon Lee , Wonseok Lee , Hyen-Mi Chung , Sangjung Park; J. Microbiol. 2017;55(6):417-420. Published online April 20, 2017; DOI: https://doi.org/10.1007/s12275-017-6313-y

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A bacterial strain PBT33-2T was isolated from the air environ-ment in an indoor pig farm. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PBT33-2T be-longed to the genus Nocardioides in the phylum Actinobac-teria, and was most closely related to Nocardioides daphnia D287T in a maximum-likelihood and neighbor-joining phy-logenetic trees. Strain PBT33-2T shared 95.3% sequence iden-tity with N. daphnia D287T. However, the highest sequence similarity was shown with N. sediminis MSL-01T (96.0%). It had less than 96.0% sequence identities with other type spe-cies of the genus Nocardioides. Strain PBT-33-2T grew at 15–45°C (optimum 20–35°C), pH 5.0–11.0 (optimum pH 7.0) and 0–4.0% (w/v) NaCl (optimum 0%). The major fatty acid and quinone were iso-C16:0 and MK-8, and the DNA G+C content of strain PBT33-2T was 69.3 mol%. On the basis of poly-phasic results, strain PBT33-2T represents a novel spe-cies of the genus Nocardioides, for which the name Nocar-dioides suum sp. nov. is proposed. Its type strain is PBT33-2T (=KCTC 39558T =DSM 102833T).

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Potential use of lactic acid bacteria Leuconostoc mesenteroides as a probiotic for the removal of Pb(II) toxicity: Young-Joo Yi , Jeong-Muk Lim , Suna Gu , Wan-Kyu Lee , Eunyoung Oh , Sang-Myeong Lee , Byung-Taek Oh; J. Microbiol. 2017;55(4):296-303. Published online March 31, 2017; DOI: https://doi.org/10.1007/s12275-017-6642-x

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It has been demonstrated that certain lactic acid bacteria (LAB) can sequester metal ions by binding them to their surfaces. In the present study, lead (Pb)-resistant LAB were isolated from kimchi, a Korean fermented food. A total of 96 different LAB strains were isolated, and 52 strains showed lead resistance. Among them, an LAB strain-96 (L-96) iden-tified as Leuconostoc mesenteroides showed remarkable Pb resistance and removal capacity. The maximum adsorption capacity of this strain calculated using the Langmuir isotherm was 60.6 mg Pb/g. In an in vivo experiment, young male mice were provided with water (A), Pb-water (B), or Pb-water+ L-96 (C) during puberty. Lower glutamate oxaloacetate trans-aminase (GOT) and glutamate pyruvate transaminase (GPT) levels in Pb-exposed male mice that received strain L-96 as a probiotic were suggestive of reduced hepatotoxicity. More-over, feces from mice treated with L-96 contained more Pb than feces from untreated mice. Increased Pb elimination likely reduced internal accumulation, and this hypothesis was supported by significantly lower Pb concentrations in kid-neys and testes of the mice treated with strain L-96. The mo-tility and ATP content of epididymal spermatozoa were par-tially restored if strain L-96 was administered. In conclusion, isolated L-96 LAB had lead-biosorption activity and effi-ciently detoxified lead-poisoned male mice, resulting in re-covering male reproductive function. These results suggest the potential use of LAB as a probiotic to protect humans from the adverse effects of Pb exposure.

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A New record of four Penicillium species isolated from Agarum clathratum in Korea: Myung Soo Park , Seobihn Lee , Young Woon Lim; J. Microbiol. 2017;55(4):237-246. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6405-8

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Agarum clathratum, brown algae, play important ecological roles in marine ecosystem, but can cause secondary environ-ment pollution when they pile up on the beach. In order to resolve the environment problem by A. clathratum, we focus to isolate and identify Penicillium because many species are well known to produce extracellular enzymes. A total of 32 Penicillium strains were isolated from A. clathratum sam-ples that collected from 13 sites along the mid-east coast of Korea in summer. They were identified based on morpho-logical characters and phylogenetic analysis using β-tubulin DNA sequences as well as a combined dataset of β-tubulin and calmodulin. A total of 32 strains were isolated and they were identified to 13 Penicillium species. The commonly iso-lated species were Penicillium citrinum, P. roseomaculatum, and Penicillium sp. Among 13 Penicillium species, four spe-cies – P. bilaiae, P. cremeogriseum, P. madriti, and P. rose-omaculatum – have not been previously recorded in Korea. For these four new species records to Korea, we provide mor-phological characteristics of each strain.

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The Pseudomonas aeruginosa extracellular secondary metabolite, Paerucumarin, chelates iron and is not localized to extracellular membrane vesicles: Uzma Qaisar , Cassandra J. Kruczek , Muhammed Azeem , Nasir Javaid , Jane A. Colmer-Hamood , Abdul N. Hamood; J. Microbiol. 2016;54(8):573-581. Published online August 2, 2016; DOI: https://doi.org/10.1007/s12275-016-5645-3

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Proteins encoded by the Pseudomonas aeruginosa pvcA-D operon synthesize a novel isonitrile functionalized cumarin termed paerucumarin. The pvcA-D operon enhances the expression of the P. aeruginosa fimbrial chaperone/usher pathway (cup) genes and this effect is mediated through paerucumarin. Whether pvcA-D and/or paerucumarin affect the expression of other P. aeruginosa genes is not known. In this study, we examined the effect of a mutation in pvcA-D operon the global transcriptome of the P. aeruginosa strain PAO1- UW. The mutation reduced the expression of several ironcontrolled genes including pvdS, which is essential for the expression of the pyoverdine genes. Additional transcriptional studies showed that the pvcA-D operon is not regulated by iron. Exogenously added paerucumarin enhanced pyoverdine production and pvdS expression in PAO1-UW. Iron-chelation experiments revealed that purified paerucumarin chelates iron. However, exogenously added paerucumarin significantly reduced the growth of a P. aeruginosa mutant defective in pyoverdine and pyochelin production. In contrast to other secondary metabolite, Pseudomonas quinolone signal (PQS), paerucumarin is not localized to the P. aeruginosa membrane vesicles. These results suggest that paerucumarin enhances the expression of iron-controlled genes by chelating iron within the P. aeruginosa extracellular environment. Although paerucumarin chelates iron, it does not function as a siderophore. Unlike PQS, paerucumarin is not associated with the P. aeruginosa cell envelope.

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Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings: Ui-Gi Min , So-Jeong Kim , Heeji Hong , Song-Gun Kim , Joo-Han Gwak , Man-Young Jung , Jong-Geol Kim , Jeong-Geol Na , Sung-Keun Rhee; J. Microbiol. 2016;54(6):413-419. Published online May 27, 2016; DOI: https://doi.org/10.1007/s12275-016-6086-8

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A strictly anaerobic bacterium, strain B5T, was isolated from sediment of an abandoned coal mine in Taebaek, Republic of Korea. Cells of strain B5T were non-spore-forming, straight, Gram-positive rods. The optimum pH and temperature for growth were pH 7.0 and 30°C, respectively, while the strain was able to grow within pH and temperature ranges of 5.5– 7.5 and 25–45°C, respectively. Growth of strain B5T was observed at NaCl concentrations of 0 to 6.0% (w/v) with an optimum at 3.0–4.0% (w/v). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and three unknown polar lipids. Strain B5T grew anaerobically by reducing nitrate, nitrite, ferric-citrate, ferric-nitrilotriacetate, elemental sulfur, thiosulfate, and anthraquinone- 2-sulfonate in the presence of proteinaceous compounds, organic acids, and carbohydrates as electron donors. The isolate was not able to grow by fermentation. Strain B5T did not grow under aerobic or microaerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B5T is most closely related to the genus Tepidibacillus (T. fermentans STGHT; 96.3%) and Vulcanibacillus (V. modesticaldus BRT; 94.6%). The genomic DNA G+C content (36.9 mol%) of strain B5T was higher than those of T. fermentans STGHT (34.8 mol%) and V. modesticaldus BRT (34.5 mol%). Based on its phenotypic, chemotaxonomic, and phylogenetic properties, we describe a new species of a novel genus Calculibacillus, represented by strain B5T (=KCTC 15397T =JCM 19989T), for which we propose the name Calculibacillus koreensis gen. nov., sp. nov.

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Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives
Sharareh Harirchi, Taner Sar, Mohaddaseh Ramezani, Habibu Aliyu, Zahra Etemadifar, Seyed Ali Nojoumi, Fatemeh Yazdian, Mukesh Kumar Awasthi, Mohammad J. Taherzadeh
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Gut Pathogens.2017;[Epub] CrossRef

Review

MINIREVIEW] Hydroxylation of methane through component interactions in soluble methane monooxygenases: Seung Jae Lee; J. Microbiol. 2016;54(4):277-282. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5642-6

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Methane hydroxylation through methane monooxygenases (MMOs) is a key aspect due to their control of the carbon cycle in the ecology system and recent applications of methane gas in the field of bioenergy and bioremediation. Methanotropic bacteria perform a specific microbial conversion from methane, one of the most stable carbon compounds, to methanol through elaborate mechanisms. MMOs express particulate methane monooxygenase (pMMO) in most strains and soluble methane monooxygenase (sMMO) under copper-limited conditions. The mechanisms of MMO have been widely studied from sMMO belonging to the bacterial multicomponent monooxygenase (BMM) superfamily. This enzyme has diiron active sites where different types of hydrocarbons are oxidized through orchestrated hydroxylase, regulatory and reductase components for precise control of hydrocarbons, oxygen, protons, and electrons. Recent advances in biophysical studies, including structural and enzymatic achievements for sMMO, have explained component interactions, substrate pathways, and intermediates of sMMO. In this account, oxidation of methane in sMMO is discussed with recent progress that is critical for understanding the microbial applications of C-H activation in one-carbon substrates.

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Research Support, Non-U.S. Gov't

Studies on seasonal dynamics of soil-higher fungal communities in Mongolian oak-dominant Gwangneung forest in Korea: Chang Sun Kim , Jong Woo Nam , Jong Won Jo , Sang-Yong Kim , Jae-Gu Han , Min Woo Hyun , Gi-Ho Sung , Sang-Kuk Han; J. Microbiol. 2016;54(1):14-22. Published online January 5, 2016; DOI: https://doi.org/10.1007/s12275-016-5521-1

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We surveyed macrofungi biweekly at defined plots from April to December in 2014, in the Mongolian oak-dominant forest, Gwangneung Forest, Pochen-si, Korea, and analyzed a soilhigher fungal diversity during four seasons (represented by April, August, October, and December). Based on morphological observation of collected specimens, the collected macrofungi were classified into 2 phyla 3 classes 7 orders, 14 families, 21 genera, and 33 species (36 specimens). DNA-based community analyses indicated that soil-higher fungi were classified into 2 phyla, 18 classes, 49 orders, 101 families, and 155 genera (83,360 sequence reads), defined herein as 155 genus-level operational taxonomic units (GOTUs). In the present study, we evaluated and discussed the fungal diversity in seasonal dynamics and soil layers based on collected macrofungi and pyrosequencing data while considering environmental parameters (pH, exchangeable K, T-P, NH4+, NO3-, OM, WR, TOC, and T-N). Moreover, principal components analysis (PCA) showed distinct clusters of the GOTU assemblage associated with the seasons.

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MINIREVIEW] Stress responses in Streptococcus species and their effects on the host: Cuong Thach Nguyen , Sang-Sang Park , Dong-Kwon Rhee; J. Microbiol. 2015;53(11):741-749. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5432-6

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Abstract

Streptococci cause a variety of diseases, such as dental caries, pharyngitis, meningitis, pneumonia, bacteremia, endocarditis, erysipelas, and necrotizing fasciitis. The natural niche of this genus of bacteria ranges from the mouth and nasopharynx to the skin, indicating that the bacteria will inevitably be subjected to environmental changes during invasion into the host, where it is exposed to the host immune system. Thus, the Streptococcus-host interaction determines whether bacteria are cleared by the host’s defenses or whether they survive after invasion to cause serious diseases. If this interaction was to be deciphered, it could aid in the development of novel preventive and therapeutic agents. Streptococcus species possess many virulent factors, such as peroxidases and heat-shock proteins (HSPs), which play key roles in protecting the bacteria from hostile host environments. This review will discuss insights into the mechanism(s) by which streptococci adapt to host environments. Additionally, we will address how streptococcal infections trigger host stress responses; however, the mechanism by which bacterial components modulate host stress responses remains largely unknown.

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MINIREVIEW] The cAMP/protein kinase A signaling pathway in pathogenic basidiomycete fungi: Connections with iron homeostasis: Jaehyuk Choi , Won Hee Jung , James W. Kronstad; J. Microbiol. 2015;53(9):579-587. Published online August 1, 2015; DOI: https://doi.org/10.1007/s12275-015-5247-5

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Abstract PDF

A number of pathogenic species of basidiomycete fungi are either life-threatening pathogens of humans or major economic pests for crop production. Sensing the host is a key aspect of pathogen proliferation during disease, and signal transduction pathways are critically important for detecting environmental conditions and facilitating adaptation. This review focuses on the contributions of the cAMP/protein kinase A (PKA) signaling pathway in Cryptococcus neoformans, a species that causes meningitis in humans, and Ustilago maydis, a model phytopathogen that causes a smut disease on maize. Environmental sensing by the cAMP/PKA pathway regulates the production of key virulence traits in C. neoformans including the polysaccharide capsule and melanin. For U. maydis, the pathway controls the dimorphic transition from budding growth to the filamentous cell type required for proliferation in plant tissue. We discuss recent advances in identifying new components of the cAMP/PKA pathway in these pathogens and highlight an emerging theme that pathway signaling influences iron acquisition.

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Research Support, Non-U.S. Gov'ts

Cyclic AMP-Receptor Protein Activates Aerobactin Receptor IutA Expression in Vibrio vulnificus: Choon-Mee Kim , Seong-Jung Kim , Sung-Heui Shin; J. Microbiol. 2012;50(2):320-325. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-2056-y

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Abstract PDF: The ferrophilic bacterium Vibrio vulnificus can utilize the siderophore aerobactin of Escherichia coli for iron acquisition via its specific receptor IutA. This siderophore piracy by V. vulnificus may contribute to its survival and proliferation, especially in mixed bacterial environments. In this study, we examined the effects of glucose, cyclic AMP (cAMP), and cAMP-receptor protein (Crp) on iutA expression in V. vulnificus. Glucose dose-dependently repressed iutA expression. A mutation in cya encoding adenylate cyclase required for cAMP synthesis severely repressed iutA expression, and this change was recovered by in trans complementing cya or the addition of exogenous cAMP. Furthermore, a mutation in crp encoding Crp severely repressed iutA expression, and this change was recovered by complementing crp. Accordingly, glucose deprivation under iron-limited conditions is an environmental signal for iutA expression, and Crp functions as an activator that regulates iutA expression in response to glucose availability.

Molecular Analysis of Spatial Variation of Iron-Reducing Bacteria in Riverine Alluvial Aquifers of the Mankyeong River: So-Jeong Kim , Dong-Chan Koh , Soo-Je Park , In-Tae Cha , Joong-Wook Park , Jong-Hwa Na , Yul Roh , Kyung-Seok Ko , Kangjoo Kim , Sung-Keun Rhee; J. Microbiol. 2012;50(2):207-217. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1342-z

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Abstract PDF

Alluvial aquifers are one of the mainwater resources in many countries. Iron reduction in alluvial aquifers is often a major anaerobic process involved in bioremediation or causing problems, including the release of As trapped in Fe(III) oxide. We investigated the distribution of potential iron-reducing bacteria (IRB) in riverine alluvial aquifers (B1, B3, and B6 sites) at the Mankyeong River, Republic of Korea. Inactive iron reduction zones, the diversity and abundance of IRB can be examined using a clone library and quantitative PCR analysis of 16S rRNA genes. Geobacter spp. are potential IRB in the iron-reducing zone at the B6 (9 m) site, where high Fe(II) and arsenic (As) concentrations were observed. At the B3 (16 m) site, where low iron reduction activity was predicted, a dominant clone (10.6%) was 99% identical in 16S rRNA gene sequence with Rhodoferax ferrireducens. Although a major clone belonging to Clostridium spp. was found, possible IRB candidates could not be unambiguously determined at the B1 (18 m) site. Acanonical correspondence analysis demonstrated that, among potential IRB, only the Geobacteraceae were well correlated with Fe(II) and As concentrations. Our results indicate high environmental heterogeneity, and thus high spatial variability, in thedistribution of potential IRB in the riverine alluvial aquifersnear the Mankyeong River.

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Environmental Microbiology.2014; 16(1): 189. CrossRef
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Effects of Phosphate Addition on Biofilm Bacterial Communities and Water Quality in Annular Reactors Equipped with Stainless Steel and Ductile Cast Iron Pipes: Hyun-Jung Jang , Young-June Choi , Hee-Myong Ro , Jong-Ok Ka; J. Microbiol. 2012;50(1):17-28. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1040-x

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Abstract PDF: The impact of orthophosphate addition on biofilm formation and water quality was studied in corrosion-resistant stainless steel (STS) pipe and corrosion-susceptible ductile cast iron (DCI) pipe using cultivation and culture-independent approaches. Sample coupons of DCI pipe and STS pipe were installed in annular reactors, which were operated for 9 months under hydraulic conditions similar to a domestic plumbing system. Addition of 5 mg/L of phosphate to the plumbing systems, under low residual chlorine conditions, promoted a more significant growth of biofilm and led to a greater rate reduction of disinfection by-products in DCI pipe than in STS pipe. While the level of THMs (trihalomethanes) increased under conditions of low biofilm concentration, the levels of HAAs (halo acetic acids) and CH (chloral hydrate) decreased in all cases in proportion to the amount of biofilm. It was also observed that chloroform, the main species of THM, was not readily decomposed biologically and decomposition was not proportional to the biofilm concentration; however, it was easily biodegraded after the addition of phosphate. Analysis of the 16S rDNA sequences of 102 biofilm isolates revealed that Proteobacteria (50%) was the most frequently detected phylum, followed by Firmicutes (10%) and Actinobacteria (2%), with 37% of the bacteria unclassified. Bradyrhizobium was the dominant genus on corroded DCI pipe, while Sphingomonas was predominant on non-corroded STS pipe. Methylobacterium and Afipia were detected only in the reactor without added phosphate. PCR-DGGE analysis showed that the diversity of species in biofilm tended to increase when phosphate was added regardless of the pipe material, indicating that phosphate addition upset the biological stability in the plumbing systems.

Research Support, U.S. Gov't, Non-P.H.S.

NOTE] The Helicobacter pylori Ferric Uptake Regulator (Fur) Is Essential for Growth Under Sodium Chloride Stress: Hanan Gancz , D. Scott Merrell; J. Microbiol. 2011;49(2):294-298. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0396-7

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Abstract PDF

Epidemiological data and animal models indicate that Helicobacter pylori and dietary NaCl have a synergistic ill effect on gastric maladies. Here we show that the Ferric Uptake Regulator (Fur), which is a crucial regulatory factor required for H. pylori colonization, is essential for growth in the presence of high NaCl concentrations. Moreover, we demonstrate that the transcriptional response induced by sodium chloride stress exhibits similarities to that seen under iron depletion.

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High salt condition alters LPS synthesis and induces the emergence of drug resistance mutations in Helicobacter pylori
Hongming Huang, Huang Yang, Shunhang Feng, Xiaoyan Zhang, Chu Chen, Hongyu Yan, Rui Li, Mengxin Liu, Juan Lin, Yancheng Wen, Feifei She, Anne-Catrin Uhlemann
Antimicrobial Agents and Chemotherapy.2024;[Epub] CrossRef
A Positively Selected fur -R88H Mutation Enhances Helicobacter pylori Fitness in a High-Salt Environment and Alters Fur-Dependent Regulation of Gene Expression
John T. Loh, Emily L. Struttmann, Natalie Favret, M. Lorena Harvey, Suman B. Pakala, Abha Chopra, Mark S. McClain, Timothy L. Cover, Denise Monack
Infection and Immunity.2023;[Epub] CrossRef
Metal binding and oligomerization properties of FurC (PerR) from Anabaena sp. PCC7120: an additional layer of regulation?
Cristina Sarasa-Buisan, Etienne Emonot, Marta Martínez-Júlvez, Emma Sevilla, Adrián Velázquez-Campoy, Serge Crouzy, M Teresa Bes, Isabelle Michaud-Soret, María F Fillat
Metallomics.2022;[Epub] CrossRef
Insights into the Orchestration of Gene Transcription Regulators in Helicobacter pylori
Andrea Vannini, Davide Roncarati, Federico D’Agostino, Federico Antoniciello, Vincenzo Scarlato
International Journal of Molecular Sciences.2022; 23(22): 13688. CrossRef
Interplay between Amoxicillin Resistance and Osmotic Stress in Helicobacter pylori
Ian H. Windham, D. Scott Merrell, George O’Toole
Journal of Bacteriology.2022;[Epub] CrossRef
Transcriptional response to metal starvation in the emerging pathogen Mycoplasma genitalium is mediated by Fur-dependent and –independent regulatory pathways
Carlos Martínez-Torró, Sergi Torres-Puig, Marta Monge, Lucía Sánchez-Alba, Miguel González-Martín, Marina Marcos-Silva, Alex Perálvarez-Marín, Francesc Canals, Enrique Querol, Jaume Piñol, Oscar Q. Pich
Emerging Microbes & Infections.2020; 9(1): 5. CrossRef
High-Salt Conditions Alter Transcription of Helicobacter pylori Genes Encoding Outer Membrane Proteins
John T. Loh, Amber C. Beckett, Matthew B. Scholz, Timothy L. Cover, Vincent B. Young
Infection and Immunity.2018;[Epub] CrossRef
Bismuth-Induced Inactivation of Ferric Uptake Regulator from Helicobacter pylori
Xiaojun He, Xiangwen Liao, Hongyan Li, Wei Xia, Hongzhe Sun
Inorganic Chemistry.2017; 56(24): 15041. CrossRef
Characterization of Key Helicobacter pylori Regulators Identifies a Role for ArsRS in Biofilm Formation
Stephanie L. Servetas, Beth M. Carpenter, Kathryn P. Haley, Jeremy J. Gilbreath, Jennifer A. Gaddy, D. Scott Merrell, T. J. Silhavy
Journal of Bacteriology.2016; 198(18): 2536. CrossRef
Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses
Amira Suriaty Yaakop, Kok-Gan Chan, Robson Ee, Yan Lue Lim, Siew-Kim Lee, Fazilah Abd Manan, Kian Mau Goh
Scientific Reports.2016;[Epub] CrossRef
Helicobacter pylori Adaptation In Vivo in Response to a High-Salt Diet
John T. Loh, Jennifer A. Gaddy, Holly M. Scott Algood, Silvana Gaudieri, Simon Mallal, Timothy L. Cover, S. R. Blanke
Infection and Immunity.2015; 83(12): 4871. CrossRef
Global Microarray Analysis of Alkaliphilic Halotolerant Bacterium Bacillus sp. N16-5 Salt Stress Adaptation
Liang Yin, Yanfen Xue, Yanhe Ma, Marie-Joelle Virolle
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A. Metris, S. M. George, F. Mulholland, A. T. Carter, J. Baranyi, J. Björkroth
Applied and Environmental Microbiology.2014; 80(15): 4745. CrossRef
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Patrick M. Chong, Tarah Lynch, Stuart McCorrister, Pamela Kibsey, Mark Miller, Denise Gravel, Garrett R. Westmacott, Michael R. Mulvey, Axel Cloeckaert
PLoS ONE.2014; 9(1): e82622. CrossRef
Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution
Aifen Zhou, Edward Baidoo, Zhili He, Aindrila Mukhopadhyay, Jason K Baumohl, Peter Benke, Marcin P Joachimiak, Ming Xie, Rong Song, Adam P Arkin, Terry C Hazen, Jay D Keasling, Judy D Wall, David A Stahl, Jizhong Zhou
The ISME Journal.2013; 7(9): 1790. CrossRef
Crosstalk between Helicobacter pylori and Gastric Epithelial Cells Is Impaired by Docosahexaenoic Acid
Marta Correia, Valérie Michel, Hugo Osório, Meriem El Ghachi, Mathilde Bonis, Ivo G. Boneca, Hilde De Reuse, António A. Matos, Pascal Lenormand, Raquel Seruca, Ceu Figueiredo, Jose Carlos Machado, Eliette Touati, Georgina L. Hold
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The Ferric Uptake Regulator of Helicobacter Pylori : a Critical Player in the Battle for Iron and Colonization of the Stomach
Oscar Q Pich, D Scott Merrell
Future Microbiology.2013; 8(6): 725. CrossRef
Detailed analysis of Helicobacter pylori Fur‐regulated promoters reveals a Fur box core sequence and novel Fur‐regulated genes
Oscar Q. Pich, Beth M. Carpenter, Jeremy J. Gilbreath, D. Scott Merrell
Molecular Microbiology.2012; 84(5): 921. CrossRef
Analysis of Helicobacter pylori cagA Promoter Elements Required for Salt-Induced Upregulation of CagA Expression
John T. Loh, David B. Friedman, M. Blanca Piazuelo, Luis E. Bravo, Keith T. Wilson, Richard M. Peek, Pelayo Correa, Timothy L. Cover, S. R. Blanke
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Journal Article

Oceanicoccus sagamiensis gen. nov., sp. nov., a Gammaproteobacterium Isolated from Sea Water of Sagami Bay in Japan: Sanghwa Park , Kazuhiro Kogure , Akira Yokota; J. Microbiol. 2011;49(2):233-237. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0368-y

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Abstract PDF: A gram-negative, motile, coccoid- and amorphous-shaped, non-pigmented chemoheterotrophic bacterium, designated strain PZ-5T, was isolated from sea water of Sagami Bay in Japan and subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate could be affiliated with the class Gammaproteobacteria. Strain PZ-5T showed below 93.9% similarity with validly published bacteria and demonstrated the highest sequence similarity to Dasania marina KOPRI 20902T (93.9%). Strain PZ-5T formed a monophyletic group with D. marina KOPRI 20902T. The DNA G+C content of strain PZ-5T was 49.8 mol%. The major isoprenoid quinone was Q-8 and redominant cellular fatty acids were C15:0 ISO 2OH (19%), C16:1 ω7c (17.4%), C17:1 ω8c (16.2%), C11:0 3OH (7.5%), and C15:1 ω8c (6.5%). Based on evidence from a polyphasic taxonomical study, it was concluded that the strain should be classified as representing a new genus and species of the class Gammaproteobacteria, for which the name Oceanicoccus sagamiensis gen. nov., sp. nov., (type strain PZ-5T =NBRC 107125T =KCTC 23278T) is proposed.

Research Support, Non-U.S. Gov'ts

Seasonal Abundance and Distribution of Vibrio Species in the Treated Effluents of Wastewater Treatment Facilities in Suburban and Urban Communities of Eastern Cape Province, South Africa: Etinosa O. Igbinosa , Chikwelu L. Obi , Anthony I. Okoh; J. Microbiol. 2011;49(2):224-232. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0227-x

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Abstract PDF: We assessed the seasonal abundance and distribution of Vibrio species as well as some selected environmental parameters in the treated effluents of two wastewater treatment plants (WWTP), one each located in a suburban and urban community of Eastern Cape Province, South Africa. Vibrio population density ranged from 2.1×101 to 4.36×104 CFU/ml in the suburban community and from 2.80×101 to 1.80×105 CFU/ml in the urban community. Vibrio species associated with 180 μm, 60 μm, and 20 μm plankton sizes were observed at densities of 0-1.36×103 CFU/ml, 0-8.40×102 CFU/ml, and 0-6.80×102 CFU/ml, respectively at the suburban community’s WWTP. In the urban community, observed densities of culturable Vibrio were 0-2.80×102 CFU/ml (180 μm), 0-6.60×102 CFU/ml (60 μm), and 0-1.80×103 CFU/ml (20 μm). The abundance of free-living Vibrio species ranged from 0 to 1.0×102 and 1.0×103 CFU/ml in the suburban and urban communities’ WWTPs, respectively. Molecular confirmation of the presumptive Vibrio isolates revealed the presence of V. fluvialis (41.38%), V. vulnificus (34.48%), and V. parahaemolyticus (24.14%) in the suburban community effluents. In the urban community molecular confirmation revealed that the same species were present at slightly different percentages, V. fluvialis (40%), V. vulnificus (36%), and V. parahaemolyticus (24%). There was no significant correlation between Vibrio abundance and season, either as free-living or planktonassociated entities, but Vibrio species abundance was positively correlated with temperature (r=0.565; p<0.01), salinity, and dissolved oxygen (p<0.05). Turbidity and pH showed significant seasonal variation (p<0.05) across the seasons in both locations. This study underscores the potential of WWTPs to be sources of Vibrio pathogens in the watershed of suburban and urban communities in South Africa.

Iron Homeostasis in Brucella abortus: the Role of Bacterioferritin: Marta A. Almirón , Rodolfo A. Ugalde; J. Microbiol. 2010;48(5):668-673. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0145-3

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Brucella abortus is the etiological agent of bovine brucellosis, an infectious disease of humans and cattle. Its pathogenesis is mainly based on its ability to survive and multiply inside macrophages. It has been demonstrated that if B. abortus ferrochelatase cannot incorporate iron into protoporphyrin IX to synthesize heme, the intracellular replication and virulence in mice is highly attenuated. Therefore, it can be hypothesized that the unavailability of iron could lead to the same attenuation in B. abortus pathogenicity. Thus, the purpose of this work was to obtain a B. abortus derivative unable to keep an internal iron pool and test its ability to replicate under iron limitation. To achieve this, we searched for iron-storage proteins in the genome of brucellae and found bacterioferritin (Bfr) as the sole ferritin encoded. Then, a B. abortus bfr mutant was built up and its capacity to store iron and replicate under iron limitation was investigated. Results indicated that B. abortus Bfr accounts for 70% of the intracellular iron content. Under iron limitation, the bfr mutant suffered from enhanced iron restriction with respect to wild type according to its growth retardation pattern, enhanced sensitivity to oxidative stress, accelerated production of siderophores, and altered expression of membrane proteins. Nonetheless, the bfr mutant was able to adapt and replicate even inside eukaryotic cells, indicating that B. abortus responds to internal iron starvation before sensing external iron availability. This suggests an active role of Bfr in controlling iron homeostasis through the availability of Bfr-bound iron.

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Brucellosis: Bacteriology, pathogenesis, epidemiology and role of the metallophores in virulence: a review
Ghassan Ghssein, Zeinab Ezzeddine, Sima Tokajian, Charbel Al Khoury, Hussein Kobeissy, Jose-Noel Ibrahim, Christelle Iskandar, Hussein F. Hassan
Frontiers in Cellular and Infection Microbiology.2025;[Epub] CrossRef
The Pseudogene BMEA_B0173 Deficiency in Brucella melitensis Contributes to M-epitope Formation and Potentiates Virulence in a Mice Infection Model
Ge Zhang, Hao Dong, Yu Feng, Hui Jiang, Tonglei Wu, Jiali Sun, Xin Wang, Minghe Liu, Xiaowei Peng, Yinghui Zhang, Xiaoqian Zhang, Liangquan Zhu, Jiabo Ding, Xingjia Shen
Current Microbiology.2022;[Epub] CrossRef
The Irr and RirA Proteins Participate in a Complex Regulatory Circuit and Act in Concert To Modulate Bacterioferritin Expression in Ensifer meliloti 1021
Daniela Costa, Vanesa Amarelle, Claudio Valverde, Mark R. O'Brian, Elena Fabiano, Robert M. Kelly
Applied and Environmental Microbiology.2017;[Epub] CrossRef
Transcriptome Analysis of the Intracellular Facultative Pathogen Piscirickettsia salmonis: Expression of Putative Groups of Genes Associated with Virulence and Iron Metabolism
Alvaro Machuca, Victor Martinez, James E Samuel
PLOS ONE.2016; 11(12): e0168855. CrossRef
Role and regulation of ferritin-like proteins in iron homeostasis and oxidative stress survival of Caulobacter crescentus
Ivan Gonçalves de Castro Ferreira, Mirian Molnar Rodrigues, José Freire da Silva Neto, Ricardo Ruiz Mazzon, Marilis do Valle Marques
BioMetals.2016; 29(5): 851. CrossRef
Quantitative analysis of the Brucella suis proteome reveals metabolic adaptation to long-term nutrient starvation
Sascha Al Dahouk, Véronique Jubier-Maurin, Heinrich Neubauer, Stephan Köhler
BMC Microbiology.2013; 13(1): 199. CrossRef
Adaptation of Salmonella enterica Hadar under static magnetic field: effects on outer membrane protein pattern
Sarra Snoussi, Alya El May, Laurent Coquet, Philippe Chan, Thierry Jouenne, Ahmed Landoulsi, Emmanuelle DÉ
Proteome Science.2012;[Epub] CrossRef
Iron Storage Proteins Are Essential for the Survival and Pathogenesis of Mycobacterium tuberculosis in THP-1 Macrophages and the Guinea Pig Model of Infection
P. Vineel Reddy, Rupangi Verma Puri, Aparna Khera, Anil K. Tyagi
Journal of Bacteriology.2012; 194(3): 567. CrossRef
Metal acquisition and virulence inBrucella
R. Martin Roop
Animal Health Research Reviews.2012; 13(1): 10. CrossRef

Journal Article

Characterization of Cultivated Fungi Isolated from Grape Marc Wastes Through the Use of Amplified rDNA Restriction Analysis and Sequencing: Spyridon Ntougias , Nektarios Kavroulakis , Kalliope K. Papadopoulou , Constantinos Ehaliotis , Georgios I. Zervakis; J. Microbiol. 2010;48(3):297-306. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-9193-y

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Microbial assessment of grape marc wastes, the residual solid by-product of the wine-industry, was performed by identifying phylogenetically the fungal culturable diversity in order to evaluate environmental and disposal safety issues and to discuss ecological considerations of applications on agricultural land. Fungal spores in grape marc were estimated to 4.7×106 per g dry weight. Fifty six fungal isolates were classified into eight operational taxonomic units (OTUs) following amplified ribosomal DNA restriction analysis (ARDRA) and colony morphology. Based on 18S rRNA gene and 5.8S rRNA gene-ITS sequencing, the isolates representing OTUs #1, #2, #3, and #4, which comprised 44.6%, 26.8%, 12.5%, and 5.3%, respectively, of the number of the total isolates, were identified as Aspergillus fumigatus, Bionectria ochroleuca, Haematonectria haematococca, and Trichosporon mycotoxinivorans. The isolates of OTU#5 demonstrated high phylogenetic affinity with Penicillium spp., while members of OTUs #6 and #7 were closer linked with Geotrichum candidum var. citri-aurantii and Mycocladus corymbifer, respectively (95.4 and 97.9% similarities in respect to their 5.8S rRNA gene-ITS sequences). The OTU#8 with a single isolate was related with Aspergillus strains. It appears that most of the fungal isolates are associated with the initial raw material. Despite the fact that some of the species identified may potentially act as pathogens, measures such as the avoidance of maintaining large and unprocessed quantities of grape marc wastes in premises without adequate aeration, together with its suitable biological treatment (e.g., composting) prior to any agriculture-related application, could eliminate any pertinent health risks.

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High impact biowastes from South European agro-industries as feedstock for second-generation biorefineries
Alberto Scoma, Stefano Rebecchi, Lorenzo Bertin, Fabio Fava
Critical Reviews in Biotechnology.2016; 36(1): 175. CrossRef
Microbial community structure and disposal issues of table olive wastewaters generated from the fermentation of the olive cultivar ‘Kalamon’
Marina Papadelli, Spyridon Ntougias
Annals of Microbiology.2014; 64(4): 1483. CrossRef
Dynamics of Panax ginseng Rhizospheric Soil Microbial Community and Their Metabolic Function
Yong Li, YiXin Ying, WanLong Ding, Shilin Chen
Evidence-Based Complementary and Alternative Medicine.2014;[Epub] CrossRef
Two Trichosporon species isolated from Central-European mygalomorph spiders (Araneae: Mygalomorphae)
Petr Heneberg, Milan Řezáč
Antonie van Leeuwenhoek.2013; 103(4): 713. CrossRef
Characterization of Soil Bacterial Communities in Rhizospheric and Nonrhizospheric Soil of Panax ginseng
Yi Xin Ying, Wan Long Ding, Yong Li
Biochemical Genetics.2012; 50(11-12): 848. CrossRef

Research Support, N.I.H., Extramural

Helicobacter pylori apo-Fur Regulation Appears Unconserved Across Species: Shana Miles , Beth M. Carpenter , Hanan Gancz , D. Scott Merrell; J. Microbiol. 2010;48(3):378-386. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-0022-0

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Abstract PDF: The Ferric Uptake Regulator (Fur) is a transcriptional regulator that is conserved across a broad number of bacterial species and has been shown to regulate expression of iron uptake and storage genes. Additionally, Fur has been shown to be an important colonization factor of the gastric pathogen Helicobacter pylori. In H. pylori, Fur-dependent regulation appears to be unique in that Fur is able to act as a transcriptional repressor when bound to iron as well as in its iron free (apo) form. To date, apo-regulation has not been identified in any other bacterium. To determine whether Fur from other species has the capacity for aporegulation, we investigated the ability of Fur from Escherichia coli, Campylobacter jejuni, Desulfovibrio vulgaris Hildenborough, Pseudomonas aeruginosa, and Vibrio cholerae to complement both iron-bound and apo-Fur regulation within the context of a H. pylori fur mutant. We found that while some Fur species (E. coli, C. jejuni, and V. cholerae) complemented iron-bound regulation, apo-regulation was unable to be complemented by any of the examined species. These data suggest that despite the conservation among bacterial Fur proteins, H. pylori Fur contains unique structure/function features that make it novel in comparison to Fur from other species.

Research Support, Non-U.S. Gov'ts

Experimental and Computational Characterization of the Ferric Uptake Regulator from Aliivibrio salmonicida (Vibrio salmonicida): Hege Lynum Pedersen , Rafi Ahmad , Ellen Kristin Riise , Hanna-Kirsti Schrøder Leiros , Stefan Hauglid , Sigrun Espelid , Bjørn Olav Brandsdal , Ingar Leiros , Nils-Peder Willassen , Peik Haugen; J. Microbiol. 2010;48(2):174-183. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-9199-5

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Abstract PDF: The Ferric uptake regulator (Fur) is a global transcription factor that affects expression of bacterial genes in an iron-dependent fashion. Although the Fur protein and its iron-responsive regulon are well studied, there are still important questions that remain to be answered. For example, the consensus Fur binding site also known as the “Fur box” is under debate, and it is still unclear which Fur residues directly interact with the DNA. Our long-term goal is to dissect the biological roles of Fur in the development of the disease cold-water vibriosis, which is caused by the psychrophilic bacteria Aliivibrio salmonicida (also known as Vibrio salmonicida). Here, we have used experimental and computational methods to characterise the Fur protein from A. salmonicida (AS-Fur). Electrophoretic mobility shift assays show that AS-Fur binds to the recently proposed vibrio Fur box consensus in addition to nine promoter regions that contain Fur boxes. Binding appears to be dependent on the number of Fur boxes, and the predicted “strength” of Fur boxes. Finally, structure modeling and molecular dynamics simulations provide new insights into potential AS-Fur–DNA interactions.

Effect of Iron on Cytolysin A Expression in Salmonella enterica serovar Typhi: Jinghua Cui , Honghua Piao , Shen Jin , Hee Sam Na , Yeongjin Hong , Hyon E Choy , Phil Youl Ryu; J. Microbiol. 2009;47(4):479-485. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-009-0039-4

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Abstract PDF: Previously, a novel protein ClyA (Cytolysin A) has been identified in Escherichia coli K-12, Salmonella enterica serovars Typhi and Paratyphi A and Shigella. Salmonella spp. synthesize substantial amounts of ClyA upon infection of the human host, although the mechanism by which ClyA is induced in vivo is unclear. Since environmental signals could control the expression of virulence determinants, ClyA expression in S. Typhi Ty2 was tested by Western blotting in the presence of normal pooled human serum (NPS). The level of ClyA expression increased in the presence of NPS in a concentration-dependent manner. RPMI 1640 medium similarly induced ClyA expression. ClyA expression was inversely proportional to the concentration of iron in RPMI medium. Therefore, we speculated that iron inhibited the expression of ClyA in S. Typhi Ty2, and free iron depletion may be one of the causes of S. Typhi-mediated induction of ClyA in vivo. Transcription from a clyA-lacZ fusion gene decreased as iron concentration increased, but not as significantly as the ClyA protein expression. It is concluded that the regulatory effect of iron on clyA expression is mainly at translational level.

The Ecology of Vibrio vulnificus, Vibrio cholerae, and Vibrio parahaemolyticus in North Carolina Estuaries: Karen Dyer Blackwell , James D. Oliver; J. Microbiol. 2008;46(2):146-153. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0216-2

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While numerous studies have characterized the distribution and/or ecology of various pathogenic Vibrio spp., here we have simultaneously examined several estuarine sites for Vibrio vulnificus, V. cholerae, and V. parahaemolyticus. For a one year period, waters and sediment were monitored for the presence of these <br>three pathogens at six different sites on the east coast of North Carolina in the United States. All three pathogens, identified using colony hybridization and PCR methods, occurred in these estuarine environments, although V. cholerae occurred only infrequently and at very low levels. Seventeen chemical, physical, and biological parameters were investigated, including salinity, water temperature, turbidity, dissolved oxygen, levels of various inorganic nutrients and dissolved organic carbon, as well as total vibrios, total coliforms, and E. coli. We found each of the Vibrio spp. in water and sediment to correlate to several of these environmental measurements, with water temperature and total Vibrio levels correlating highly (P<0.0001) with occurrence of the three pathogens. Thus, these two parameters may represent simple assays for characterizing the potential public health hazard of estuarine waters.

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Brett A. Froelich, Tiffany C. Williams, Rachel T. Noble, James D. Oliver
Applied and Environmental Microbiology.2012; 78(11): 3885. CrossRef
Ecology of Vibrio parahaemolyticus and Vibrio vulnificus in the Coastal and Estuarine Waters of Louisiana, Maryland, Mississippi, and Washington (United States)
Crystal N. Johnson, John C. Bowers, Kimberly J. Griffitt, Vanessa Molina, Rachel W. Clostio, Shaofeng Pei, Edward Laws, Rohinee N. Paranjpye, Mark S. Strom, Arlene Chen, Nur A. Hasan, Anwar Huq, Nicholas F. Noriea, D. Jay Grimes, Rita R. Colwell
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Sonja Oberbeckmann, Antje Wichels, Karen H. Wiltshire, Gunnar Gerdts
Antonie van Leeuwenhoek.2011; 100(2): 291. CrossRef
Temporal and Spatial Variability in Culturable Pathogenic Vibrio spp. in Lake Pontchartrain, Louisiana, following Hurricanes Katrina and Rita
Olivia D. Nigro, Aixin Hou, Gayatri Vithanage, Roger S. Fujioka, Grieg F. Steward
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Effect of fur on pyrC Gene Expression: Sangho Chai , Chang Kyu Song , Seong Kwun Kim , Jun Ho Park , Sechan Wee; J. Microbiol. 2007;45(6):583-589.; DOI: https://doi.org/2604 [pii]

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Abstract PDF: The promoter region of pyrC (dihydroorotase) gene of Escherichia coli was shown to have Fur protein binding properties by gel retardation assay. In vivo regulation of the pyrC expression was studied by measuring dihydroorotase activity and beta-galactosidase level in the fur+ and fur- genetic background. The expression of chromosomal dihydroorotase activity and beta-galactosidase activity of pyrC-lacZ fusion plasmid was repressed to about 30% and 17%, respectively in the fur+ strain compared to those in the fur- strain. Divalent ions such as Fe2+ and Zn2+ were not required for the repression. PyrC expression was also reduced to one half by 1 mM uracil. The effect of uracil was independent on the fur gene.

Source Environment Feature Related Phylogenetic Distribution Pattern of Anoxygenic Photosynthetic Bacteria as Revealed by pufM Analysis: Yonghui Zeng , Nianzhi Jiao; J. Microbiol. 2007;45(3):205-212.; DOI: https://doi.org/2541 [pii]

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Abstract PDF: Anoxygenic photosynthesis, performed primarily by anoxygenic photosynthetic bacteria (APB), has been supposed to arise on Earth more than 3 billion years ago. The long established APB are distributed in almost every corner where light can reach. However, the relationship between APB phylogeny and source environments has been largely unexplored. Here we retrieved the pufM sequences and related source information of 89 pufM containing species from the public database. Phylogenetic analysis revealed that horizontal gene transfer (HGT) most likely occurred within 11 out of a total 21 pufM subgroups, not only among species within the same class but also among species of different phyla or subphyla. A clear source environment feature related phylogenetic distribution pattern was observed, with all species from oxic habitats and those from anoxic habitats clustering into independent subgroups, respectively. HGT among ancient APB and subsequent long term evolution and adaptation to separated niches may have contributed to the coupling of environment and pufM phylogeny.

Vibrio vulnificus Metalloprotease VvpE has no Direct Effect on Iron-uptake from Human Hemoglobin: Hui-Yu Sun , Song-Iy Han , Mi-Hwa Choi , Seong-Jung Kim , Choon-Mee Kim , Sung-Heui Shin; J. Microbiol. 2006;44(5):537-547.; DOI: https://doi.org/2443 [pii]

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Abstract PDF: This study was designed to determine whether or not Vibrio vulnificus metalloprotease VvpE can promote iron uptake via the proteolytic cleavage of human hemoglobin. We found that V. vulnificus utilized hemoglobin as an iron source more efficiently via the vulnibactin-mediated iron-uptake system than via the HupA-mediated iron-uptake system and, of the proteases produced by V. vulnificus, VvpE was found to be the only protease capable of destroying hemoglobin. However, VvpE expression, on both the transcriptional and protein levels, was suppressed in iron-limited media. However, vvpE transcription, but not extracellular VvpE production, was reactivated by the addition of hemoglobin or inorganic iron into iron-limited media. Moreover, vvpE transcription began only in the late growth phase when V. vulnificus had already consumed most of the iron for growth. In addition, neither vvpE mutation nor in trans vvpE complementation affected the ability of V. vulnificus to acquire iron or to grow in iron-limited media or in cirrhotic ascites containing hemoglobin. Hemoglobin added into iron-limited media was not destroyed, but gradually formed an insoluble aggregate during culture; this aggregation of hemoglobin occurred regardless of vvpE mutation or complementation. These results indicate that VvpE is not required for efficient iron uptake from hemoglobin. On the contrary, hemoglobin or iron is required for efficient vvpE transcription. In addition, a discrepancy exists between vvpE transcription and extracellular VvpE production in iron-limited media containing inorganic iron or hemoglobin, which suggests that additional unknown posttranscriptional events may be involved in the extracellular production of VvpE.

Characterization, Cloning and Expression of the Ferritin Gene from the Korean Polychaete, Periserrula leucophryna: Byeong Ryong Jeong , Su-Mi Chung , Nam Joo Baek , Kwang Bon Koo , Hyung Suk Baik , Han-Seung Joo , Chung-Soon Chang , Jang Won Choi; J. Microbiol. 2006;44(1):54-63.; DOI: https://doi.org/2336 [pii]

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Abstract PDF: Ferritin is a major eukaryotic protein and in humans is the protein of iron storage. A partial gene fragment of ferritin (255 bp) taken from the total RNA of Periserrula leucophryna, was amplified by RT-PCR using oligonucleotide primers designed from the conserved metal binding domain of eukaryotic ferritin and confirmed by DNA sequencing. Using the 32P-labeled partial ferritin cDNA fragment, 28 different clones were obtained by the screening of the P. leucophryna cDNA library prepared in the Uni-ZAP XR vector, sequenced and characterized. The longest clone was named the PLF (Periserrula leucophryna ferritin) gene and the nucleotide and amino acid sequences of this novel gene were deposited in the GenBank databases with accession numbers DQ207752 and ABA55730, respectively. The entire cDNA of PLF clone was 1109 bp (CDS: 129-653), including a coding nucleotide sequence of 525 bp, a 5''-untranslated region of 128 bp, and a 3''-noncoding region of 456 bp. The 5''-UTR contains a putative iron responsive element (IRE) sequence. Ferritin has an open reading frame encoding a polypeptide of 174 amino acids including a hydrophobic signal peptide of 17 amino acids. The predicted molecular weights of the immature and mature ferritin were calculated to be 20.3 kDa and 18.2 kDa, respectively. The region encoding the mature ferritin was subcloned into the pT7-7 expression vector after PCR amplification using the designed primers and included the initiation and termination codons; the recombinant clones were expressed in E. coli BL21(DE3) or E. coli BL21(DE3)pLysE. SDS-PAGE and western blot analysis showed that a ferritin of approximately 18 kDa (mature form) was produced and that by iron staining in native PAGE, it is likely that the recombinant ferritin is correctly folded and assembled into a homopolymer composed of a single subunit.

Staphylococcus aureus Siderophore-Mediated Iron-Acquisition System Plays a Dominant and Essential Role in the Utilization of Transferrin-Bound Iron: Ra-Young Park , Hui-Yu Sun , Mi-Hwa Choi , Young-Hoon Bai , Sung-Heui Shin; J. Microbiol. 2005;43(2):183-190.; DOI: https://doi.org/2163 [pii]

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Abstract PDF: Staphylococcus aureus is known to be capable of utilizing transferrin-bound iron, via both siderophore- and transferrin-binding protein (named IsdA)-mediated iron-acquisition systems. This study was designed in order to determine which iron-acquisition system plays the essential or dominant role with respect to the acquisition of iron from human transferrin, in the growth of S. aureus. Holotransferrin (HT) and partially iron-saturated transferrin (PT), but not apotransferrin (AT), were found to stimulate the growth of S. aureus. S. aureus consumed most of the transferrin-bound iron during the exponential growth phase. Extracellular proteases were not, however, involved in the liberation of iron from transferrin. Transferrin-binding to the washed whole cells via IsdA was not observed during the culture. The expression of IsdA was observed only in the deferrated media with AT, but not in the media supplemented with PT or HT. In contrast, siderophores were definitely produced in the deferrated media with PT and HT, as well as in the media supplemented with AT. The siderophores proved to have the ability to remove iron directly from transferrin, but the washed whole cells expressing IsdA did not. In the bioassay, the growth of S. aureus on transferrin-bound iron was stimulated by the siderophores alone. These results demonstrate that the siderophore-mediated iron-acquisition system plays a dominant and essential role in the uptake of iron from transferrin, whereas the IsdA-mediated iron-acquisition system may play only an ancillary role in the uptake of iron from transferrin.

Growth of Staphylococcus aureus with Defective Siderophore Production in Human Peritoneal Dialysate Solution: Ra-Young Park , Hui-Yu Sun , Mi-Hwa Choi , Young-Hoon Bae , Sung-Heui Shin; J. Microbiol. 2005;43(1):54-61.; DOI: https://doi.org/2137 [pii]

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Abstract PDF: In this study, we attempted to determine the effects of iron-availability and the activity of the bacterial iron-uptake system (IUS) on the growth of Staphylococcus aureus in human peritoneal dialysate (HPD) solution. A streptonigrin-resistant S. aureus (SRSA) strain, isolated from S. aureus ATCC 6538, exhibited defective siderophore production, thereby resulting in ineffective uptake of iron from low iron-saturated transferrin. The growth of both strains was stimulated in HPD solution supplemented with FeCl_3 and holotransferrin, but growth was inhibited in HPD solution which had been supplemented with apotransferrin and dipyridyl. The SRSA strain grew less robustly than did its parental strain in both iron-supplemented HPD solution and regular HPD solution. These results indicate that iron-availability and siderophore-mediated IUS activity in particular, the ability to produce siderophores and thus capture iron from low iron-saturated transferrin play critical roles in the growth of S. aureus in HPD solution. Our results also indicated that the possibility of using iron chelators as therapeutic or preventive agents warrants further evaluation.

Journal Article

Growth and Physiological Properties of Wild Type and Mutants of Halomonas subglaciescola DH-1 in Saline Environment: Hye Jeong Ryu , Yoo Jung Jeong , Doo Hyun Park; J. Microbiol. 2004;42(3):174-180.; DOI: https://doi.org/2093 [pii]

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Abstract PDF: A halophilic bacterium was isolated from fermented seafood. The 16S rDNA sequence identity between the isolate and Halomonas subglaciescola AJ306801 was above 95%. The isolate that did not grow in the condition without NaCl or in the condition with other sodium (Na^+) or chloride ions (Cl^-) instead of NaCl was named H. subglaciescola DH-1. Two mutants capable of growing without NaCl were obtained by random mutagenesis, of which their total soluble protein profiles were compared with those of the wild type by two-dimensional electrophoresis. The external compatible solutes (betaine and choline) and cell extract of the wild type did not function as osmoprotectants, and these parameters within the mutants did not enhance their growth in the saline environment. In the proton translocation test, rapid acidification of the reactant was not detected for the wild type, but it was detected for the mutant in the condition without NaCl. From these results, we derived the hypothesis that NaCl may be absolutely required for the energy metabolism of H. subglaciescola DH-1 but not for its osmoregulation, and the mutants may have another modified proton translocation system that is independent of NaCl, except for those mutants with an NaCl-dependent system.

Effects of Hydrogen Ions on Aquatic Microbial Populations in Korea: Ahn, Young Beom , Cho, Hong Bum , Choi, Yong Keel; J. Microbiol. 1995;33(3):184-190.

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Abstract PDF: From July 1994 to March 1995, eighteen variables of physico-chemical factors including heavy metals, and of bacteria in the four reservoirs of Kyonggi-Do were investigated to examine the effects of acidic precipitation to bacterial population. The pH range in the study area is from 6.56 to 10.24, which also showed seasonal change extensively compared to other factors. The correlation analysis showed that pH has a significant positive correlation (mean 79%) with the microbial populations in Wangsong reservoir. By multiple regression analysis on all of the seasons and stations, good explanation was obtained for the variation in total direct count of bacteria (71% and 88%, respectively), and the plate count of heterotrophic bacteria (76% and 88%, respectively). In the surface water of Wansong reservoir, the variation of total count of bacteria was affected by the S/O (soluble sugar/total organic matter ratio) value and the pH, and that of the plate count of heterotrophic bacteria was explained as 63% by pH. However, in other stations they were explained by the NO₂, total organic matter (TOM), soluble sugar (SS), temperature, and dissolved oxygen as 21~91%. On the basis of the results, the bacterial populations on the media at pH 3.0, 4.0, 5.0, 6.0 and 7.0 were compared to determine the effects of acidic proceeding. All the colonies grew the best on the media of pH 7.0, but started to decrease from pH 5.0.

Identification of hemolysin as one of the important virulent factors in vibrio anguillarum V7: Choe, Young Chool , Jeong, Ga Jin; J. Microbiol. 1995;33(4):283-288.

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Abstract PDF: We have identified hemolysin rendering virulency of Vibrio anguilarum grown at 23℃ which was evaluated on human RBCs. Hemolysin itself was separated as a single band on non-denaturing gel electrophoresis. Vibrio hemolysin was destroyed by trypsin and proteinase K and was heat labile. Optimal pH for activity was around pH 6 while pI of the molecule was recognized as 5.7, with relative distance (R_f) on non-denaturing gel was 0.7. Addition of EDTA and FeCI₃drew the possibility that the production of hemolysin was mainly induced to overcome iron deficiency inside host animals upon infection.

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