Journal of Microbiology

Meta-Analysis

Proposal of a health gut microbiome index based on a meta-analysis of Korean and global population datasets: Hyun-Seok Oh , Uigi Min , Hyejin Jang , Namil Kim , Jeongmin Lim , Mauricio Chalita , Jongsik Chun; J. Microbiol. 2022;60(5):533-549. Published online March 31, 2022; DOI: https://doi.org/10.1007/s12275-022-1526-0

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The disruption of the human gut microbiota has been linked to host health conditions, including various diseases. However, no reliable index for measuring and predicting a healthy microbiome is currently available. Here, the sequencing data of 1,663 Koreans were obtained from three independent studies. Furthermore, we pooled 3,490 samples from public databases and analyzed a total of 5,153 fecal samples. First, we analyzed Korean gut microbiome covariates to determine the influence of lifestyle on variation in the gut microbiota. Next, patterns of microbiota variations across geographical locations and disease statuses were confirmed using a global cohort and disease data. Based on comprehensive comparative analysis, we were able to define three enterotypes among Korean cohorts, namely, Prevotella type, Bacteroides type, and outlier type. By a thorough categorization of dysbiosis and the evaluation of microbial characteristics using multiple datasets, we identified a wide spectrum of accuracy levels in classifying health and disease states. Using the observed microbiome patterns, we devised an index named the gut microbiome index (GMI) that could consistently predict health conditions from human gut microbiome data. Compared to ecological metrics, the microbial marker index, and machine learning approaches, GMI distinguished between healthy and non-healthy individuals with a higher accuracy across various datasets. Thus, this study proposes a potential index to measure health status of gut microbiome that is verified from multiethnic data of various diseases, and we expect this model to facilitate further clinical application of gut microbiota data in future.

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A comparison of the prevalence of respiratory pathogens and opportunistic respiratory pathogenic profile of ‘clean’ and ‘unclean’ removable dental prostheses
Tong Wah Lim, Shi Huang, Yufeng Zhang, Michael Francis Burrow, Colman McGrath
Journal of Dentistry.2024; 145: 104968. CrossRef
Characterization of pathogenic microbiome on removable prostheses with different levels of cleanliness using 2bRAD-M metagenomic sequencing
Tong Wah Lim, Shi Huang, Yuesong Jiang, Yufeng Zhang, Michael Francis Burrow, Colman McGrath
Journal of Oral Microbiology.2024;[Epub] CrossRef
Gut microbial signatures in clinically stable ulcerative colitis according to the mucosal state and associated symptoms
Soyoung Kim, Yeonjae Jung, Seung Bum Lee, Hyun‐Seok Oh, Sung Noh Hong
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Difference in gut microbial dysbiotic patterns between body-first and brain-first Parkinson's disease
Don Gueu Park, Woorim Kang, In-Ja Shin, Mauricio Chalita, Hyun-Seok Oh, Dong-Wook Hyun, Hyun Kim, Jongsik Chun, Young-Sil An, Eun Jeong Lee, Jung Han Yoon
Neurobiology of Disease.2024; 201: 106655. CrossRef
Should Routine Diagnostics Implement Gut Microbiota Analysis?
Giuseppe Guido Maria Scarlata, Ludovico Abenavoli
The International Journal of Gastroenterology and Hepatology Diseases.2024;[Epub] CrossRef
Feasibility study for a fully decentralized clinical trial in participants with functional constipation symptoms
Ki Young Huh, Woo Kyung Chung, Jiyeon Park, SeungHwan Lee, Min‐Gul Kim, Jaeseong Oh, Kyung‐Sang Yu
Clinical and Translational Science.2023; 16(11): 2177. CrossRef
Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health
Car Reen Kok, Devin Rose, Robert Hutkins
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Effects of the multidomain intervention with nutritional supplements on cognition and gut microbiome in early symptomatic Alzheimer’s disease: a randomized controlled trial
Eun Hye Lee, Geon Ha Kim, Hee Kyung Park, Hae Jin Kang, Yoo Kyoung Park, Hye Ah Lee, Chang Hyung Hong, So Young Moon, Woorim Kang, Hyun-Seok Oh, Hai-Jeon Yoon, Seong Hye Choi, Jee Hyang Jeong
Frontiers in Aging Neuroscience.2023;[Epub] CrossRef
Fecal microbial signatures of healthy Han individuals from three bio-geographical zones in Guangdong
Litao Huang, Liting Deng, Changhui Liu, Enping Huang, Xiaolong Han, Cheng Xiao, Xiaomin Liang, Huilin Sun, Chao Liu, Ling Chen
Frontiers in Microbiology.2022;[Epub] CrossRef

Journal Articles

Description of Microbacterium luteum sp. nov., Microbacterium cremeum sp. nov., and Microbacterium atlanticum sp. nov., three novel C50 carotenoid producing bacteria: Fuquan Xie , Siwen Niu , Xihuang Lin , Shengxiang Pei , Li Jiang , Yun Tian , Gaiyun Zhang; J. Microbiol. 2021;59(10):886-897. Published online September 7, 2021; DOI: https://doi.org/10.1007/s12275-021-1186-5

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Abstract

We have identified three Microbacterium strains, A18JL200T, NY27T, and WY121T, that produce C50 carotenoids. Taxonomy shows they represent three novel species. These strains shared < 98.5% 16S rRNA gene sequence identity with each other and were closely related to Microbacterium aquimaris JCM 15625T, Microbacterium yannicii JCM 18959T, Microbacterium ureisolvens CFH S00084T, and Microbacterium hibisci CCTCC AB 2016180T. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) showed differences among the three strains and from their closest relatives, with values ranging from 20.4% to 34.6% and 75.5% to 87.6%, respectively. These values are below the threshold for species discrimination. Both morphology and physiology also differed from those of phylogenetically related Microbacterium species, supporting that they are indeed novel species. These strains produce C50 carotenoids (mainly decaprenoxanthin). Among the three novel species, A18JL200T had the highest total yield in carotenoids (6.1 mg/L or 1.2 mg/g dry cell weight). Unusual dual isoprenoid biosynthetic pathways (methylerythritol phosphate and mevalonate pathways) were annotated for strain A18JL200T. In summary, we found strains of the genus Microbacterium that are potential producers of C50 carotenoids, but their genome has to be investigated further.

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Chlamydomonas reinhardtii and Microbacterium forte sp. nov., a mutualistic association that favors sustainable hydrogen production
Neda Fakhimi, María Jesus Torres, Emilio Fernández, Aurora Galván, Alexandra Dubini, David González-Ballester
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Discovery of a new bacterium, Microbacterium betulae sp. nov., in birch wood associated with hypersensitivity pneumonitis in woodworkers
Mariola Paściak, Krzysztof J. Pawlik, Dariusz Martynowski, Łukasz Łaczmański, Jarosław Ciekot, Bogumiła Szponar, Angelina Wójcik‐Fatla, Barbara Mackiewicz, Ewelina Farian, Grażyna Cholewa, Alicja Cholewa, Jacek Dutkiewicz
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Jian Xiao, Tian Liang, Shangdong Yang, Hongwei Tan
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Jun Ren, Junhao Shen, Thi Duc Thai, Min-gyun Kim, Seung Ho Lee, Wonseop Lim, Dokyun Na
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Maria Linden, Alexander Flegler, Michelle M. Feuereisen, Fabian Weber, André Lipski, Andreas Schieber
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Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium
Soon Dong Lee, Hong Lim Yang, In Seop Kim
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Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions
Mark Milhaven, Cyril J. Versoza, Aman Garg, Lindsey Cai, Sanjana Cherian, Kamalei Johnson, Kevin Salas Perez, Madison Blanco, Jackelyn Lobatos, Corinne Mitra, Maria Strasser, Susanne P. Pfeifer
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Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef

The quorum sensing regulator OpaR is a repressor of polar flagellum genes in Vibrio parahaemolyticus: Renfei Lu , Junfang Sun , Yue Qiu , Miaomiao Zhang , Xingfan Xue , Xue Li , Wenhui Yang , Dongsheng Zhou , Lingfei Hu , Yiquan Zhang; J. Microbiol. 2021;59(7):651-657. Published online June 1, 2021; DOI: https://doi.org/10.1007/s12275-021-0629-3

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Abstract

Vibrio parahaemolyticus possesses two types of flagella: a single polar flagellum (Pof) for swimming and the peritrichous lateral flagella (Laf) for swarming. Expression of Laf genes has previously been reported to be regulated by the quorum sensing (QS) regulators AphA and OpaR. In the present study, we showed that OpaR, the QS regulator at high cell density (HCD), acted as a negative regulator of swimming motility and the transcription of Pof genes in V. parahaemolyticus. OpaR bound to the promoter-proximal DNA regions of flgAMN, flgMN, and flgBCDEFGHIJ within the Pof gene loci to repress their transcription, whereas it negatively regulates the transcription of flgKL-flaC in an indirect manner. Thus, this work investigated how QS regulated the swimming motility via direct action of its master regulator OpaR on the transcription of Pof genes in V. parahaemolyticus.

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Yue Zhou, Jingyang Chang, Feng Li, Mei He, Rui Li, Yaqin Hou, Yiquan Zhang, Renfei Lu, Ming Yang
Current Microbiology.2025;[Epub] CrossRef
GefB, a GGDEF domain-containing protein, affects motility and biofilm formation of Vibrio parahaemolyticus and is regulated by quorum sensing regulators
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VPA0198, a GGDEF domain-containing protein, affects the motility and biofilm formation of Vibrio parahaemolyticus and is regulated by quorum sensing associated regulators
Yining Zhou, Jingyang Chang, Miaomiao Zhang, Xue Li, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Bin Ni, Renfei Lu, Yiquan Zhang
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Identification of an LysR family transcriptional regulator that activates motility and flagellar gene expression in Vibrio parahaemolyticus
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The LuxO-OpaR quorum-sensing cascade differentially controls Vibriophage VP882 lysis-lysogeny decision making in liquid and on surfaces
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CalR Inhibits the Swimming Motility and Polar Flagellar Gene Expression in Vibrio parahaemolyticus
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Transcriptomic Profiles of Vibrio parahaemolyticus During Biofilm Formation
Yiquan Zhang, Tingting Zhang, Yue Qiu, Miaomiao Zhang, Xiuhui Lu, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Bo Gao, Renfei Lu
Current Microbiology.2023;[Epub] CrossRef
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F. Javier Vazquez-Armenta, M. Olivia Aros-Corrales, M. Lizeth Alvarez-Ainza, A. Thalia Bernal-Mercado, J. Fernando Ayala-Zavala, Adrian Ochoa-Leyva, A. Alexis Lopez-Zavala
F1000Research.2023; 12: 1256. CrossRef
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Quorum sensing and QsvR tightly control the transcription of vpa0607 encoding an active RNase II-type protein in Vibrio parahaemolyticus
Yiquan Zhang, Xingfan Xue, Fengjun Sun, Xue Li, Miaomiao Zhang, Qimin Wu, Tingting Zhang, Xi Luo, Renfei Lu
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QsvR represses the transcription of polar flagellum genes in Vibrio parahaemolyticus
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Masa-aki Yoshida, Takuma Tanabe, Hideo Akiyoshi, Makoto Kawamukai
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Nur Afiqah Md Yusof, Siti Aisyah Razali, Azyyati Mohd Padzil, Benjamin Yii Chung Lau, Syarul Nataqain Baharum, Nor Azlan Nor Muhammad, Nurul Hanun Ahmad Raston, Chou Min Chong, Natrah Fatin Mohd Ikhsan, Magdalena Lenny Situmorang, Low Chen Fei
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Comparative genomic analysis of selenium utilization traits in different marine environments: Muhammad Farukh; J. Microbiol. 2020;58(2):113-122. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9250-0

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Abstract

Selenium (Se) is an essential trace element for many organisms, which is required in the biosynthesis of proteins with selenocysteine, tRNAs with selenouridine, and certain enzymes with Se as a cofactor. Recent large-scale metagenomics projects provide a unique opportunity for studying the global trends of Se utilization in marine environments. Here, we analyzed samples from different marine microbial communities, revealed by the Tara Oceans project, to characterize the Se utilization traits. We found that the selenophosphate synthetase gene, which defines the overall Se utilization, and Se utilization traits are present in all samples. Regions with samples rich and poor in Se utilization traits were categorized. From the analysis of environmental factors, the mesopelagic zone and high temperature (> 15°C) of water are favorable, while geographical location has little influence on Se utilization. All Se utilization traits showed a relatively independent occurrence. The taxonomic classification of Se traits shows that most of the sequences corresponding to Se utilization traits belong to the phylum Proteobacteria. Overall, our study provides useful insights into the general features of Se utilization in ocean samples and may help to understand the evolutionary dynamics of Se utilization in different marine environments.

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The selenophosphate synthetase family: A review
Bruno Manta, Nadezhda E Makarova, Marco Mariotti
Free Radical Biology and Medicine.2022; 192: 63. CrossRef
Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective
Yan Zhang, Jiao Jin, Biyan Huang, Huimin Ying, Jie He, Liang Jiang
Biomolecules.2022; 12(7): 917. CrossRef
Uses of Selenium Nanoparticles in the Plant Production
Iqra Bano, Sylvie Skalickova, Hira Sajjad, Jiri Skladanka, Pavel Horky
Agronomy.2021; 11(11): 2229. CrossRef

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

Distinct Patterns of Marine Bacterial Communities in the South and North Pacific Oceans: Sung-Suk Suh , Mirye Park , Jinik Hwang , Sukchan Lee , Youngjae Chung , Taek-Kyun Lee; J. Microbiol. 2014;52(10):834-841. Published online October 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4287-6

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Abstract

The study of oceanic microbial communities is crucial for our understanding of the role of microbes in terms of biomass, diversity and ecosystem function. In this study, 16S rRNA gene tag pyrosequencing was used to investigate change in bacterial community structure between summer and winter water masses from Gosung Bay in the South Sea of Korea and Chuuk in Micronesia, located in the North and South Pacific Oceans, respectively. Summer and winter sampling from each water mass revealed highly diverse bacterial communities, containing ~900 Operational Taxonomic Units (OTUs). The microbial distribution and highly heterogeneous composition observed at both sampling sites were different from those of most macroorganisms. The bacterial communities in the seawater at both sites were most abundant in Proteobacteria during the summer in Gosung and in Bacterioidetes during the winter. The proportion of Cyanobacteria was higher in summer than in winter in Chuuk and similar in Gosung. Additionally, the microbial community during summer in Gosung was significantly different from other communities observed based on the unweighted UniFrac distance. These data suggest that in both oceanic areas sampled, the bacterial communities had distinct distribution patterns with spatially- and temporally-heterogeneous distributions.

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Metavirome Profiling and Dynamics of the DNA Viral Community in Seawater in Chuuk State, Federated States of Micronesia
Seung Won Jung, Kang Eun Kim, Hyun-Jung Kim, Taek-Kyun Lee
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The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean
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Yafei Wang, Hongmei Lin, Ranran Huang, Weidong Zhai
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Characterization of bacterial community structure in two alcyonacean soft corals (Litophyton sp. and Sinularia sp.) from Chuuk, Micronesia
Joon Sang Park, Jeonghoon Han, Sung-Suk Suh, Hyun-Jung Kim, Taek-Kyun Lee, Seung Won Jung
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Zhao-Yu Jiang, Fu-Lin Sun
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Abundance and community composition of bacterioplankton in the Northern South China Sea during winter: geographic position and water layer influences
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Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean
Yuan-Yuan Li, Xiao-Huang Chen, Zhang-Xian Xie, Dong-Xu Li, Peng-Fei Wu, Ling-Fen Kong, Lin Lin, Shuh-Ji Kao, Da-Zhi Wang
Frontiers in Microbiology.2018;[Epub] CrossRef
Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea
Jin Zhou, Xiao Song, Chun-Yun Zhang, Guo-Fu Chen, Yong-Min Lao, Hui Jin, Zhong-Hua Cai
Microbial Ecology.2018; 76(3): 592. CrossRef
A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean
Jing Wang, Jinjun Kan, Laura Borecki, Xiaodong Zhang, Dongxiao Wang, Jun Sun
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Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea
Sung-Suk Suh, Mirye Park, Jinik Hwang, Eui-Joon Kil, Seung Won Jung, Sukchan Lee, Taek-Kyun Lee, Torsten Thomas
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Effect of Fumarate Reducing Bacteria on In Vitro Rumen Fermentation, Methane Mitigation and Microbial Diversity: Lovelia Mamuad , Seon Ho Kim , Chang Dae Jeong , Yeon Jae Choi , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2014;52(2):120-128. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3518-1

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Abstract

The metabolic pathways involved in hydrogen (H2) production, utilization and the activity of methanogens are the important factors that should be considered in controlling methane (CH4) emissions by ruminants. H2 as one of the major substrate for CH4 production is therefore should be controlled. One of the strategies on reducing CH4 is through the use of hydrogenotrophic microorganisms such as fumarate reducing bacteria. This study determined the effect of fumarate reducing bacteria, Mitsuokella jalaludinii, supplementation on in vitro rumen fermentation, CH4 production, diversity and quantity. M. jalaludinii significantly reduced CH4 at 48 and 72 h of incubation and significantly increased succinate at 24 h. Although not significantly different, propionate was found to be highest in treatment containing M. jalaludinii at 12 and 48 h of incubation. These results suggest that supplementation of fumarate reducing bacteria to ruminal fermentation reduces CH4 production and quantity, increases succinate and changes the rumen microbial diversity.

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Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield
Qiushuang Li, Zhiyuan Ma, Jiabin Huo, Xiumin Zhang, Rong Wang, Shizhe Zhang, Jinzhen Jiao, Xiyang Dong, Peter H Janssen, Emilio M Ungerfeld, Chris Greening, Zhiliang Tan, Min Wang
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Keith W. Savin, Peter J. Moate, S. R. O. Williams, Carolyn Bath, Joanne Hemsworth, Jianghui Wang, Doris Ram, Jody Zawadzki, Simone Rochfort, Benjamin G. Cocks, James E. Wells
PLOS ONE.2022; 17(5): e0268157. CrossRef
Effect of Autochthonous Nepalese Fruits on Nutrient Degradation, Fermentation Kinetics, Total Gas Production, and Methane Production in In-Vitro Rumen Fermentation
Rajan Dhakal, Manuel Gonzalez Ronquillo, Einar Vargas-Bello-Pérez, Hanne Helene Hansen
Animals.2022; 12(17): 2199. CrossRef
Reducing Enteric Methanogenesis through Alternate Hydrogen Sinks in the Rumen
Prasanta Kumar Choudhury, Rajashree Jena, Sudhir Kumar Tomar, Anil Kumar Puniya
Methane.2022; 1(4): 320. CrossRef
Methane Emissions Regulated by Microbial Community Response to the Addition of Monensin and Fumarate in Different Substrates
Dan Xue, Huai Chen, Xiaolin Luo
Applied Sciences.2021; 11(14): 6282. CrossRef
Different milk replacers alter growth performance and rumen bacterial diversity of dairy bull calves
Yangdong Zhang, Jing Cheng, Nan Zheng, Yuanqing Zhang, Di Jin
Livestock Science.2020; 231: 103862. CrossRef
Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions
Emilio M. Ungerfeld
Frontiers in Microbiology.2020;[Epub] CrossRef
Rumen fermentation and microbial community composition influenced by live Enterococcus faecium supplementation
Lovelia L. Mamuad, Seon Ho Kim, Ashraf A. Biswas, Zhongtang Yu, Kwang-Keun Cho, Sang-Bum Kim, Kichoon Lee, Sang Suk Lee
AMB Express.2019;[Epub] CrossRef
Advanced estimation and mitigation strategies: a cumulative approach to enteric methane abatement from ruminants
Mahfuzul Islam, Sang-Suk Lee
Journal of Animal Science and Technology.2019; 61(3): 122. CrossRef
Recent insight and future techniques to enhance rumen fermentation in dairy goats
Lovelia L. Mamuad, Sung Sill Lee, Sang Suk Lee
Asian-Australasian Journal of Animal Sciences.2019; 32(8): 1321. CrossRef
Effects of illite supplementation on in vitro and in vivo rumen fermentation, microbial population and methane emission of Hanwoo steers fed high concentrate diets
Ashraf A. Biswas, Sung‐Sill Lee, Lovelia L. Mamuad, Seon‐Ho Kim, Yeon‐Jae Choi, Chanhee Lee, Kichoon Lee, Gui‐Seck Bae, Sang‐Suk Lee
Animal Science Journal.2018; 89(1): 114. CrossRef
Effect of different concentrate diet levels on rumen fluid inoculum used for determination of in vitro rumen fermentation, methane concentration, and methanogen abundance and diversity
Seon-Ho Kim, Lovelia L. Mamuad, Eun-Joong Kim, Ha-Guyn Sung, Gui-Seck Bae, Kwang-Keun Cho, Chanhee Lee, Sang-Suk Lee
Italian Journal of Animal Science.2018; 17(2): 359. CrossRef
Methanobacterium formicicum as a target rumen methanogen for the development of new methane mitigation interventions: A review
P Chellapandi, M Bharathi, C Sangavai, R Prathiviraj
Veterinary and Animal Science.2018; 6: 86. CrossRef
Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau
Dan Xue, Huai Chen, Xinquan Zhao, Shixiao Xu, Linyong Hu, Tianwei Xu, Lin Jiang, Wei Zhan
Systematic and Applied Microbiology.2017; 40(4): 227. CrossRef
Increased propionate concentration inLactobacillus mucosae-fermented wet brewers grains and duringin vitrorumen fermentation
L.L. Mamuad, S.H. Kim, Y.J. Choi, A.P. Soriano, K.K. Cho, K. Lee, G.S. Bae, S.S. Lee
Journal of Applied Microbiology.2017; 123(1): 29. CrossRef
Use of Lysozyme as a Feed Additive on In vitro Rumen Fermentation and Methane Emission
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Quantification of organic acids in ruminal in vitro batch culture fermentation supplemented with fumarate using a herb mix as a substrate
J. Pisarčíková, Z. Váradyová, K. Mihaliková, S. Kišidayová, J. Plaizier
Canadian Journal of Animal Science.2016; 96(1): 60. CrossRef
Rumen fermentation and performance of Hanwoo steers fed total mixed ration with Korean rice wine residue
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Journal of Animal Science and Technology.2016;[Epub] CrossRef
Limits to Dihydrogen Incorporation into Electron Sinks Alternative to Methanogenesis in Ruminal Fermentation
Emilio M. Ungerfeld
Frontiers in Microbiology.2015;[Epub] CrossRef
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Chang-Dae Jeong, Lovelia L. Mamuad, Seon-Ho Kim, Yeon Jae Choi, Alvin P. Soriano, Kwang Keun Cho, Che-Ok Jeon, Sung Sil Lee, Sang-Suk Lee
Asian-Australasian Journal of Animal Sciences.2014; 28(1): 50. CrossRef

Molecular Detection and Genotyping of Fusarium oxysporum f. sp. psidii Isolates from Different Agro-Ecological Regions of India: Rupesh Kumar Mishra , Brajesh Kumar Pandey , Vijai Singh , Amita John Mathew , Neelam Pathak , Mohammad Zeeshan; J. Microbiol. 2013;51(4):405-412. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-2638-3

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11 Scopus

Abstract: Twenty one isolates of Fusarium oxysporum f. sp. psidii (Fop), causing a vascular wilt in guava (Psidium guajava L.), were collected from different agro-ecological regions of India. The pathogenicity test was performed in guava seedlings, where the Fop isolates were found to be highly pathogenic. All 21 isolates were confirmed as F. oxysporum f. sp. psidii by a newly developed, species-specific primer against the conserved regions of 28S rDNA and the intergenic spacer region. RAPD and PCR-RFLP were used for genotyping the isolates to determine their genetic relationships. Fifteen RAPD primers were tested, of which five primers produced prominent, polymorphic, and reproducible bands. RAPD yielded an average of 6.5 polymorphic bands per primer, with the amplified DNA fragments ranging from 200–2,000 bp in size. A dendrogram constructed from these data indicated a 22–74% level of homology. In RFLP analysis, two major bands (350 and 220 bp) were commonly present in all isolates of F. oxysporum. These findings provide new insight for rapid, specific, and sensitive disease diagnosis. However, genotyping could be useful in strain-level discrimination of isolates from different agro-ecological regions of India.

Novel and Highly Diverse Fungal Endophytes in Soybean Revealed by the Consortium of Two Different Techniques: Tiago de Souza Leite , Andréia Cnossen-Fassoni , Olinto Liparini Pereira , Eduardo Seiti Gomide Mizubuti , Elza Fernandes de Araújo , Marisa Vieira de Queiroz; J. Microbiol. 2013;51(1):56-69. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2356-x

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40 Scopus

Abstract: Fungal endophytes were isolated from the leaves of soybean cultivars in Brazil using two different isolation techniques – fragment plating and the innovative dilution-to-extinction culturing – to increase the species richness, frequency of isolates and diversity. A total of 241 morphospecies were obtained corresponding to 62 taxa that were identified by analysis of the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA). The Phylum Ascomycota predominated, representing 99% and 95.2% of isolates in the Monsoy and Conquista cultivars, respectively, whereas the Phylum Basidiomycota represented 1% and 4.8% of isolates, respectively. The genera Ampelomyces, Annulohypoxylon, Guignardia, Leptospora, Magnaporthe, Ophiognomonia, Paraconiothyrium, Phaeosphaeriopsis, Rhodotorula, Sporobolomyces, and Xylaria for the first time were isolated from soybean; this suggests that soybean harbours novel and highly diverse fungi. The yeasts genera Rhodotorula and Sporobolomyces (subphylum Pucciniomycotina) represent the Phylum Basidiomycota. The species richness was greater when both isolation techniques were used. The diversity of fungal endophytes was similar in both cultivars when the same isolation technique was used except for Hill’s index, N1. The use of ITS region sequences allowed the isolates to be grouped according to Order, Class and Phylum. Ampelomyces, Chaetomium, and Phoma glomerata are endophytic species that may play potential roles in the biological control of soybean pathogens. This study is one of the first to apply extinction-culturing to isolate fungal endophytes in plant leaves, thus contributing to the development and improvement of this technique for future studies.

NOTE] Molecular Phylogenetic Status of Korean Strain of Podosphaera xanthii, a Causal Pathogen of Powdery Mildew on Japanese Thistle (Cirsium japonicum) in Korea: Hyang Burm Lee; J. Microbiol. 2012;50(6):1075-1080. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2618-z

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Abstract: Powdery mildew diseases are sensitive to climate change and spread can be favored by increased temperature and low moisture. During 2011 to 2012, a powdery mildew disease by a Podosphaera species was observed on the leaves of Japanese thistle (Cirsium japonicum) in Korea. The initial sign of this disease included scattered superficial white mycelia on leaves. As the disease progressed, abundant necrotic black spots exhibiting chasmothecia were formed on the leaves. rDNA ITS and 28S homologies of the fungus (EML-CSPW1) showed 100% identity values with those regions from many strains of P. xanthii (syn. P. fusca) via NCBI BLASTN search.

Characterization, Metabolites and Gas Formation of Fumarate Reducing Bacteria Isolated from Korean Native Goat (Capra hircus coreanae): Lovelia L. Mamuad , Seon Ho Kim , Sung Sil Lee , Kwang Keun Cho , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2012;50(6):925-931. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2497-3

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Abstract: Fumarate reducing bacteria, able to convert fumarate to succinate, are possible to use for the methane reduction in rumen because they can compete for H2 with methanogens. In this, we isolated fumarate reducing bacteria from a rumen of Korean native goat and characterized their molecular properties [fumarate reductase A gene (frdA)], fumarate reductase activities, and productions of volatile fatty acids and gas. Eight fumarate reducing bacteria belonging to Firmicutes were isolated from rumen fluid samples of slaughtered Korean black goats and characterized their phylogenetic positions based on 16S rRNA gene sequences. PCR based analyses showed that only one strain, closely related to Mitsuokella jalaludinii, harbored frdA. The growths of M. jalaludinii and Veillonella parvula strains were tested for different media. Interestingly, M. jalaludinii grew very well in the presence of hydrogen alone, while V. parvula grew well in response of fumarate and fumarate plus hydrogen. M. jalaludinii produced higher levels of lactate (P≤0.05) than did V. parvula. Additionally, M. jalaludinii produced acetate, but not butyrate, whereas V. parvula produced butyrate, not acetate. The fumarate reductase activities of M. jalaludinii and V. parvula were 16.8 ± 0.34 and 16.9 ± 1.21 mmol NADH oxidized/min/mg of cellular N, respectively. In conclusion, this showed that M. jalaludinii can be used as an efficient methane reducing agent in rumen.

NOTE] Detection of a Unique Fibrinolytic Enzyme in Aeromonas sp. JH1: Han-Young Cho , Min Jeong Seo , Jeong Uck Park , Byoung Won Kang , Gi-Young Kim , Woo Hong Joo , Young-Choon Lee , Yong Kee Jeong; J. Microbiol. 2011;49(6):1018-1021. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1376-7

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Abstract: A fibrinolytic enzyme was found in a Gram-negative bacterium, Aeromonas sp. JH1. SDS-PAGE and fibrinzymography showed that it was a 36 kDa, monomeric protein. Of note, the enzyme was highly specific for fibrinogen molecules and the hydrolysis rate of fibrinogen subunits was highest for α, β, and γ chains in that order. The first 15 amino acids of N-terminal sequence were X-D-A-T-G-P-G-G-N-V-X-T-G-K-Y, which was distinguishable from other fibrinolytic enzymes. The optimum pH and temperature of the enzyme were approximately 8.0 and 40°C, respectively. Therefore, these results provide a fibrinolytic enzyme with potent thrombolytic activity from the Aeromonas genus.

Diversity of Endophytic Bacteria in Ginseng and Their Potential for Plant Growth Promotion: Regupathy Thamizh Vendan , Young Joon Yu , Sun Hee Lee , Young Ha Rhee; J. Microbiol. 2010;48(5):559-565. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0082-1

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176 Scopus

Abstract: Endophytic bacteria have been found in virtually every plant studied, where they colonize the internal tissues of their host plant and can form a range of different beneficial relationships. The diversity of bacterial endophytes associated with ginseng plants of varying age levels in Korea was investigated. Fifty-one colonies were isolated from the interior of ginseng stems. Although a mixed composition of endophyte communities was recovered from ginseng based on the results of 16S rDNA analysis, bacteria of the genus Bacillus and Staphylococcus dominated in 1-year-old and 4-year-old plants, respectively. Phylogenetic analysis revealed four clusters: Firmicutes, Actinobacteria, α-Proteobacteria, and γ-Proteobacteria, with Firmicutes being predominant. To evaluate the plant growth promoting activities, 18 representative isolates were selected. Amplification of nifH gene confirmed the presence of diazotrophy in only two isolates. Half of the isolates solubilized mineral phosphate. Except four, all the other endophytic isolates produced significant amounts of indole acetic acid in nutrient broth. Iron sequestering siderophore production was detected in seven isolates. Isolates E-I-3 (Bacillus megaterium), E-I-4 (Micrococcus luteus), E-I-8 (B. cereus), and E-I-20 (Lysinibacillus fusiformis) were positive for most of the plant growth promoting traits, indicating their role in growth promotion of ginseng.

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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Abstract: 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.

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

Molecular Diversity of Chrysoviruses in Korean Isolates of A New Fungal Species, Cryphonectria nitschkei: Jung-Mi Kim , Jung-Ae Kim , Jin-Ah Park , Seung-Moon Park , Byeong-Jin Cha , Moon-Sik Yang , Dae-Hyuk Kim; J. Microbiol. 2009;47(4):441-447. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-009-0206-7

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Abstract: Genetic diversity of the chrysovirus within the four fungal strains was analyzed by comparing the full- length sequences of cloned chrysoviral genes encoding the RNA-dependent RNA polymerase (RdRp) and capsid protein (CP). Because the morphological characteristics of four chrysovirus-infected Cryphonectria spp. strains were different, strain identification was conducted via sequence comparison of the internal transcribed spacers (ITSs) of the fungal rRNA gene. Phylogenic analysis of the ITS regions revealed that the four strains were closely clustered with the reference strain of Cryphonectria nitschkei, while they were more distantly related to other common Cryphonectria species, indicating that they were likely C. nitschkei. Sequence comparison among chrysoviruses from Korean C. nitschkei strains revealed that similarities of the RdRp and CP genes ranged from 98% to 100% and from 95% to 100%, respectively, at the protein level. Their corresponding nucleotide sequences showed 97% to 100% and 84% to 100% identities, respectively. Compared to RdRp, the CP gene had more divergence, suggesting the presence of genes possessing different evolutionary rates within the chrysovirus genome. Sequence comparisons with other known chrysoviruses showed that the four Korean chrysoviruses were clustered together at the next lineage level. Discovering why two strains (bs131 and bs132) containing identical ITS sequences and chrysoviruses display different phenotypes should prove interesting.

A New Dactylella Species from Orbilia alba: ZeFen Yu , YanJie Kong , Ying Zhang , Min Qiao , JianWei Guo , Ke-Qin Zhang; J. Microbiol. 2009;47(3):265-269. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0301-1

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Abstract: A new Dactylella species, Dactylella alba was isolated from the ascospores of Orbilia alba collected in Wen- shan County, Yunnan Province, China. Conidiophores were either not branched or occasionally branched, bearing divergent sterigmata on the tip with single conidium on each. Conidia were elongated ellipsoids, 1-2 septate, mostly 1 septate. By combining the ITS sequence with morphological characteristics, a new anamorphic species is described and illustrated together with its teleomorph.

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