Journal of Microbiology

Journal Articles

Activity of Lactobacillus crispatus isolated from vaginal microbiota against Mycobacterium tuberculosis: Youngkyoung Lee , Hoonhee Seo , Sukyung Kim Abdur Rahim , Youjin Yoon , Jehee Jung , Saebim Lee , Chang Beom Ryu , Ho-Yeon Song; J. Microbiol. 2021;59(11):1019-1030. Published online November 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1332-0

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Tuberculosis, an infectious disease, is caused by Mycobacterium tuberculosis. It remains a significant public health issue around the globe, causing about 1.8 million deaths every year. Drug-resistant M. tuberculosis, including multi-drug-resistant (MDR), extremely-drug-resistant (XDR), and totally drugresistant (TDR) M. tuberculosis, continues to be a threat to public health. In the case of antibiotic-resistant tuberculosis, the treatment effect of conventional antibiotics is low. Side effects caused by high doses over a long period are causing severe problems. To overcome these problems, there is an urgent need to develop a new anti-tuberculosis drug that is different from the existing compound-based antibiotics. Probiotics are defined as live microorganisms conferring health benefits. They can be potential therapeutic agents in this context as the effectiveness of probiotics against different infectious diseases has been well established. Here, we report that Lactobacillus crispatus PMC201 shows a promising effect on tuberculosis isolated from vaginal fluids of healthy Korean women. Lactobacillus crispatus PMC201 reduced M. tuberculosis H37Rv under co-culture conditions in broth and reduced M. tuberculosis H37Rv and XDR M. tuberculosis in macrophages. Lactobacillus crispatus PMC201 was not toxic to a guinea pig model and did not induce dysbiosis in a human intestinal microbial ecosystem simulator. Taken together, these
results
indicate that L. crispatus PMC201 can be a promising alternative drug candidate in the current tuberculosis drug regime. Further study is warranted to assess the in vivo efficacy and confirm the mode of action of L. crispatus PMC201.

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Exploring the potential of Lactocaseibacillus rhamnosus PMC203 in inducing autophagy to reduce the burden of Mycobacterium tuberculosis
Md Abdur Rahim, Hoonhee Seo, Sukyung Kim, Indrajeet Barman, Fatemeh Ghorbanian, Mohammed Solayman Hossain, Md Sarower Hossen Shuvo, Saebim Lee, Ho-Yeon Song
Medical Microbiology and Immunology.2024;[Epub] CrossRef
Efficacy of lyophilized Lactobacillus sakei as a potential candidate for preventing carbapenem-resistant Klebsiella infection
Hanieh Tajdozian, Hoonhee Seo, Yoonkyoung Jeong, Fatemeh Ghorbanian, Chae-eun Park, Faezeh Sarafraz, Md Abdur Rahim, Youngkyoung Lee, Sukyung Kim, Saebim Lee, Jung-Hyun Ju, Chul-Ho Kim, Ho-Yeon Song
Annals of Microbiology.2024;[Epub] CrossRef
Identification of Probiotic Strains with Anti-Tuberculosis Activity and Their Characterization as Potential Therapeutic Agents
Mohammed Solayman Hossain, Hoonhee Seo, Md Abdur Rahim, Md Sarower Hossen Shuvo, Indrajeet Barman, Hokyoung Kim, Jinhyeon An, Sukyung Kim, Ho-Yeon Song
Journal of Bacteriology and Virology.2024; 54(4): 325. CrossRef
The gut and lung microbiota in pulmonary tuberculosis: susceptibility, function, and new insights into treatment
Qiqi Zhuo, Xianyi Zhang, Kehong Zhang, Chan Chen, Zhen Huang, Yuzhong Xu
Expert Review of Anti-infective Therapy.2023; 21(12): 1355. CrossRef
Host microbiome in tuberculosis: disease, treatment, and immunity perspectives
Archana Pant, Bhabatosh Das, Gopalakrishnan Aneeshkumar Arimbasseri
Frontiers in Microbiology.2023;[Epub] CrossRef
Antibiotic Resistance to Mycobacterium tuberculosis and Potential Use of Natural and Biological Products as Alternative Anti-Mycobacterial Agents
Roberto Arrigoni, Andrea Ballini, Skender Topi, Lucrezia Bottalico, Emilio Jirillo, Luigi Santacroce
Antibiotics.2022; 11(10): 1431. CrossRef
In Vivo Efficacy of Bacillus velezensis Isolated from Korean Gochang Bokbunja Vinegar against Carbapenem-Resistant Klebsiella pneumoniae Infections
Fatemeh Ghorbanian, Hoonhee Seo, Hanieh Tajdozian, Youngkyoung Lee, MD Abdur Rahim, Sukyung Kim, Il-Yun Jung, Saebim Lee, Ho-Yeon Song
Polish Journal of Microbiology.2022; 71(4): 553. CrossRef

Zinc-binding domain mediates pleiotropic functions of Yvh1 in Cryptococcus neoformans: Jae-Hyung Jin , Myung Kyung Choi , Hyun-Soo Cho , Yong-Sun Bahn; J. Microbiol. 2021;59(7):658-665. Published online July 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1287-1

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Abstract: Yvh1 is a dual-specificity phosphatase (DUSP) that is evolutionarily conserved in eukaryotes, including yeasts and humans. Yvh1 is involved in the vegetative growth, differentiation, and virulence of animal and plant fungal pathogens. All Yvh1 orthologs have a conserved DUSP catalytic domain at the N-terminus and a zinc-binding (ZB) domain with two zinc fingers (ZFs) at the C-terminus. Although the DUSP domain is implicated in the regulation of MAPK signaling in humans, only the ZB domain is essential for most cellular functions of Yvh1 in fungi. This study aimed to analyze the functions of the DUSP and ZB domains of Yvh1 in the human fungal pathogen Cryptococcus neoformans, whose Yvh1 (CnYvh1) contains a DUSP domain at the C-terminus and a ZB domain at the N-terminus. Notably, CnYvh1 has an extended internal domain between the two ZF motifs in the ZB domain. To elucidate the function of each domain, we constructed individual domain deletions and swapping strains by complementing the yvh1Δ mutant with wild-type (WT) or mutated YVH1 alleles and examined their Yvh1-dependent phenotypes, including growth under varying stress conditions, mating, and virulence factor production. Here, we found that the complementation of the yvh1Δ mutant with the mutated YVH1 alleles having two ZFs of the ZB domain, but not the DUSP and extended internal domains, restored the WT phenotypic traits in the yvh1Δ mutant. In conclusion, the ZB domain, but not the N-terminal DUSP domain, plays a pivotal role in the pathobiological functions of cryptococcal Yvh1.

Comprehensive analysis of fungal diversity and enzyme activity in nuruk, a Korean fermenting starter, for acquiring useful fungi: Emily Carroll , Tran Ngoc Trinh , Hokyoung Son , Yin-Won Lee , Jeong-Ah Seo; J. Microbiol. 2017;55(5):357-365. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7114-z

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Abstract

Nuruk is a fermenting starter that is involved in the pro-duction of alcoholic beverages, and has been used in South Korea for a very long time. To analyze the fungal diversity, we collected a total of 59 nuruk samples from several com-panies and persons in 2013 to 2014, and obtained 364 iso-lates. All of the single isolated fungi were identified, both morphologically and molecularly, based on the sequences of ribosomal RNA gene [18S, ITS1-5.8S-ITS2, and 26S (D1/D2 region)]. In 46 nuruk samples out of 59 (78%), Saccharo-mycopsis fibuligera, a dimorphic yeast, was most frequently isolated. Among the filamentous fungi, Aspergillus and Lich-theimia were found in more than 50% of the samples with lower colony forming unit (CFU/g of sample) than those of yeasts. The yeasts S. fibuligera and Wickerhamomyces ano-malus were counted with maximum 1.3 – 1.8 × 108 CFU/g. Among Mucorales fungi, Lichtheimia and Mucor were iso-lated in much higher numbers than Rhizopus and Rhizo-mucor. Overall, the home-made nuruks tend to contain more diverse filamentous fungi than the commercial nuruks. To acquire industrially useful filamentous fungi and yeasts, we analyzed the enzyme activities of α-amylase, glucoamylase and acid protease associated with brewing properties for 131 strains. Aspergillus oryzae and S. fibuligera had high α- and glucoamylase activities and most isolates of Lichtheimia ramosa had high acid protease activity. For further applica-tions, 27 fungal strains were chosen based on isolation fre-quencies from nuruk, and the ability to produce useful en-zyme.

Citations

Citations to this article as recorded by

Review: Rhizopus sp. beyond tempeh. An Occidental approach to mold-based fermentations
José María Martín-Miguélez, Jordi Bross, Diego Prado, Esther Merino, Ramón Perisé Moré, Julián Otero, Andoni Luis Aduriz, Josué Delgado
International Journal of Gastronomy and Food Science.2025; 39: 101090. CrossRef
In silico evaluation of the potential allergenicity of a fungal biomass from Rhizomucor pusillus for use as a novel food ingredient
Kevin Scaife, Steve L. Taylor, Lucie Pařenicová, Richard E. Goodman, Trung D. Vo, Elisa Leune, Mohamed Abdelmoteleb, Yvonne Dommels
Regulatory Toxicology and Pharmacology.2024; 150: 105629. CrossRef
Human Health Benefits and Microbial Consortium of Stevia Fermented with Barley Nuruk
Hyun-Ju Han, Min Nyeong Ko, Chan Seong Shin, Chang-Gu Hyun
Fermentation.2024; 10(7): 330. CrossRef
Stabilization of jiuyao quality for huangjiu brewing by fortifying functional strains based on core microbial community analysis
Ying Zhu, Shuangping Liu, Donglin Ma, Yuezheng Xu, Chen Yang, Jian Mao
Food Bioscience.2023; 52: 102370. CrossRef
In silico and in vitro safety assessment of a fungal biomass from Rhizomucor pusillus for use as a novel food ingredient
Kevin Scaife, Trung D. Vo, Yvonne Dommels, Elisa Leune, Kaj Albermann, Lucie Pařenicová
Food and Chemical Toxicology.2023; 179: 113972. CrossRef
Effects of saccharification agents on the microbial and metabolic profiles of Korean rice wine (makgeolli)
Jeongmin Cha, Seong-Eun Park, Eun-Ju Kim, Seung-Ho Seo, Kwang-Moon Cho, Sun Jae Kwon, Mee-Hyun Lee, Hong-Seok Son
Food Research International.2023; 172: 113367. CrossRef
Unraveling multifunction of low-temperature Daqu in simultaneous saccharification and fermentation of Chinese light aroma type liquor
Yifu Zheng, Feng Liang, Yi Wu, Shibo Ban, Heqiang Huang, Yan Xu, Xuliang Wang, Qun Wu
International Journal of Food Microbiology.2023; 397: 110202. CrossRef
Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products
Da Min Jeong, Hyeon Jin Kim, Min-Seung Jeon, Su Jin Yoo, Hye Yun Moon, Eun-joo Jeon, Che Ok Jeon, Seong-il Eyun, Hyun Ah Kang
FEMS Yeast Research.2023;[Epub] CrossRef
Enzymatic Hydrolysis of Tenebrio molitor (Mealworm) Using Nuruk Extract Concentrate and an Evaluation of Its Nutritional, Functional, and Sensory Properties
Legesse Shiferaw Chewaka, Chan Soon Park, Youn-Soo Cha, Kebede Taye Desta, Bo-Ram Park
Foods.2023; 12(11): 2188. CrossRef
The differences in carbohydrate utilization ability between six rounds of Sauce-flavor Daqu
Qi Zhu, Liangqiang Chen, Zheng Peng, Qiaoling Zhang, Wanqiu Huang, Fan Yang, Guocheng Du, Juan Zhang, Li Wang
Food Research International.2023; 163: 112184. CrossRef
Amylolytic Fungi in the Ethnic Beer Starter “emao” and Their Beer-Producing Attributes
Nitesh Boro, Diganta Narzary
Frontiers in Sustainable Food Systems.2022;[Epub] CrossRef
Enzyme activity of Aspergillus section Nigri strains isolated from the Korean fermentation starter, nuruk
Eunji Jeong, Jeong-Ah Seo
Journal of Microbiology.2022; 60(10): 998. CrossRef
Probiotic properties of lactic acid bacteria isolated from traditionally prepared dry starters of the Eastern Himalayas
Pooja Pradhan, Jyoti Prakash Tamang
World Journal of Microbiology and Biotechnology.2021;[Epub] CrossRef
Fermentation profiling of rice wine produced by Aspergillus oryzae KSS2 and Rhizopus oryzae KJJ39 newly isolated from Korean fermentation starter
Minjoo Kim, Jeong-Ah Seo
Applied Biological Chemistry.2021;[Epub] CrossRef
Integrated genomic and transcriptomic analysis reveals unique mechanisms for high osmotolerance and halotolerance in Hyphopichia yeast
Dong Wook Lee, Chang Pyo Hong, Eun Jung Thak, Sin‐Gi Park, Choong Hwan Lee, Jae Yun Lim, Jeong‐Ah Seo, Hyun Ah Kang
Environmental Microbiology.2021; 23(7): 3499. CrossRef
pH Changes Have a Profound Effect on Gene Expression, Hydrolytic Enzyme Production, and Dimorphism in Saccharomycopsis fibuligera
Mohamed El-Agamy Farh, Najib Abdellaoui, Jeong-Ah Seo
Frontiers in Microbiology.2021;[Epub] CrossRef
Saccharomycopsis fibuligera in liquor production: A review
Zai-Bin Xie, Kai-Zheng Zhang, Zhen-Hui Kang, Jian-Gang Yang
European Food Research and Technology.2021; 247(7): 1569. CrossRef
Diversity of Filamentous Fungi Isolated From Some Amylase and Alcohol-Producing Starters of India
Anu Anupma, Jyoti Prakash Tamang
Frontiers in Microbiology.2020;[Epub] CrossRef
Isolation and Identification of Fungi with Glucoamylase Activity from Loog-pang-khao-mak (A Thai Traditional Fermentation Starter)
Nawaphorn Roongrojmongkhon, Nattawut Rungjindamai, Tipachai Vatanavicharn, Duangjai Ochaikul
Journal of Pure and Applied Microbiology.2020; 14(1): 233. CrossRef
Natural Occurrence of Aflatoxigenic Aspergillus Species and Aflatoxins in Traditional Korean Fermentation Starters, Meju and Nuruk
So Young Woo, Sang Yoo Lee, Fei Tian, A-Yeong Jeong, Cha Nee Yoo, Seung Yoon Kang, Hyang Sook Chun
Journal of Food Hygiene and Safety.2020; 35(5): 438. CrossRef
Characterisation of physicochemical properties, flavour components and microbial community in Chinese Guojing roasted sesame-like flavourDaqu
Guangsen Fan, Yihua Du, Zhilei Fu, Min Chen, Zhou Wang, Pengxiao Liu, Xiuting Li
Journal of the Institute of Brewing.2020; 126(1): 105. CrossRef
Composition and Metabolic Functions of the Microbiome in Fermented Grain during Light-Flavor Baijiu Fermentation
Xiaoning Huang, Yi Fan, Ting Lu, Jiamu Kang, Xiaona Pang, Beizhong Han, Jingyu Chen
Microorganisms.2020; 8(9): 1281. CrossRef
Comprehensive analysis of different grades of roasted-sesame-like flavored Daqu
Guangsen Fan, Zhilei Fu, Chao Teng, Qiuhua Wu, Pengxiao Liu, Ran Yang, Karim a H M Minhazul, Xiuting Li
International Journal of Food Properties.2019; 22(1): 1205. CrossRef
A script for initiating molecular biology studies with non-conventional yeasts based on Saccharomycopsis schoenii
Yeseren Kayacan, Adam Griffiths, Jürgen Wendland
Microbiological Research.2019; 229: 126342. CrossRef
Designation of rice cake starters for fermented rice products with desired characteristics and fast fermentation
Jaruporn Rakmai, Benjamas Cheirsilp, Sirasit Srinuanpan
Journal of Food Science and Technology.2019; 56(6): 3014. CrossRef
Overexpression of RAD51 Enables PCR-Based Gene Targeting in Lager Yeast
Beatrice Bernardi, Yeseren Kayacan, Madina Akan, Jürgen Wendland
Microorganisms.2019; 7(7): 192. CrossRef
Expansion of a Telomeric FLO/ALS-Like Sequence Gene Family in Saccharomycopsis fermentans
Beatrice Bernardi, Yeseren Kayacan, Jürgen Wendland
Frontiers in Genetics.2018;[Epub] CrossRef
Comparison of volatile and non-volatile metabolites in rice wine fermented by Koji inoculated with Saccharomycopsis fibuligera and Aspergillus oryzae
Eun Yeong Son, Sang Mi Lee, Minjoo Kim, Jeong-Ah Seo, Young-Suk Kim
Food Research International.2018; 109: 596. CrossRef
Bioformation of Volatile and Nonvolatile Metabolites by Saccharomycopsis fibuligera KJJ81 Cultivated under Different Conditions—Carbon Sources and Cultivation Times
Sang Mi Lee, Ji Hye Jung, Jeong-Ah Seo, Young-Suk Kim
Molecules.2018; 23(11): 2762. CrossRef

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

The Impacts of Excessive Nitrogen Additions on Enzyme Activities and Nutrient Leaching in Two Contrasting Forest Soils: Haryun Kim , Hojeong Kang; J. Microbiol. 2011;49(3):369-375. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0421-x

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Abstract: Nitrogen (N) deposition has increased dramatically worldwide, which may affect forest soils in various ways. In this study, we conducted a short-term manipulation experiment of N addition on two types of forest soils (urban and rural soils) found in Korea. N addition significantly decreased phenol oxidase activities in urban soil samples; however, it did not affect those in rural soils. Furthermore, N addition did not change β-glucosidase and N-acetylglucosaminidase activities, except for β-glucosidase activities in the O layer of rural soils. Changes in microbial biomass and general activity (dehydrogenase activity) were not induced by N addition, except for dehydrogenase in the A layer of urban soils. Although N addition did not change the extractable soil nutrients, organic matter, and water contents significantly, it enhanced nutrient leaching and resulted in lower pH leachate. These results suggest that excessive N addition to forest soils may induce nutrient leaching in the long-term. Overall results of our study also suggest that N addition may induce retardation of organic matter decomposition in soils; however, such a response may depend on the intensity of previous exposure to N deposition.

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

Functional Shifts in Unvegetated, Perhumid, Recently-Deglaciated Soils Do Not Correlate with Shifts in Soil Bacterial Community Composition: Sarah R. Sattin , Cory C. Cleveland , Eran Hood , Sasha C. Reed , Andrew J. King , Steven K. Schmidt , Michael S. Robeson , Nataly Ascarrunz , Diana R. Nemergut; J. Microbiol. 2009;47(6):673-681. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0194-7

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Abstract: Past work in recently deglaciated soils demonstrates that microbial communities undergo shifts prior to plant colonization. To date, most studies have focused on relatively ‘long’ chronosequences with the ability to sample plant-free sites over at least 50 years of development. However, some recently deglaciated soils feature rapid plant colonization and questions remain about the relative rate of change in the microbial community in the unvegetated soils of these chronosequences. Thus, we investigated the forelands of the Mendenhall Glacier near Juneau, AK, USA, where plants rapidly establish. We collected unvegetated samples representing soils that had been ice-free for 0, 1, 4, and 8 years. Total nitrogen (N) ranged from 0.00~0.14 mg/g soil, soil organic carbon pools ranged from 0.6~2.3 mg/g soil, and both decreased in concentration between the 0 and 4 yr soils. Biologically available phosphorus (P) and pH underwent similar dynamics. However, both pH and available P increased in the 8 yr soils. Nitrogen fixation was nearly undetectable in the most recently exposed soils, and increased in the 8 yr soils to ~5 ng N fixed/cm2/h, a trend that was matched by the activity of the soil N-cycling enzymes urease and β-1,4-N-acetyl-glucosaminidase. 16S rRNA gene clone libraries revealed no significant differences between the 0 and 8 yr soils; however, 8 yr soils featured the presence of cyanobacteria, a division wholly absent from the 0 yr soils. Taken together, our results suggest that microbes are consuming allochtonous organic matter sources in the most recently exposed soils. Once this carbon source is depleted, a competitive advantage may be ceded to microbes not reliant on in situ nutrient sources.

Review

Effects of Elevated Atmospheric CO_2 Concentrations on Soil Microorganisms: Chris Freeman , Seon-Young Kim , Seung-Hoon Lee , Hojeong Kang; J. Microbiol. 2004;42(4):267-277.; DOI: https://doi.org/2111 [pii]

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Abstract: Effects of elevated CO_2 on soil microorganisms are known to be mediated by various interactions with plants, for which such effects are relatively poorly documented. In this review, we summarize and synthesize results from studies assessing impacts of elevated CO_2 on soil ecosystems, focusing primarily on plants and a variety the of microbial processes. The processes considered include changes in microbial biomass of C and N, microbial number, respiration rates, organic matter decomposition, soil enzyme activities, microbial community composition, and functional groups of bacteria mediating trace gas emission such as methane and nitrous oxide. Elevated CO_2 in atmosphere may enhance certain microbial processes such as CH_4 emission from wetlands due to enhanced carbon supply from plants. However, responses of extracellular enzyme activities and microbial community structure are still controversy, because interferences with other factors such as the types of plants, nutrient availabilitial in soil, soil types, analysis methods, and types of CO_2 fumigation systems are not fully understood.

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