Journal of Microbiology

Reviews

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

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

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Strong inhibitory effects of Desmodesmus sp. on Microcystis blooms: Potential as a biological control agent in aquaculture
Bo Yang, Yuhua Li, Zihan Wang, Zhiguang Yue, Junqi Wen, Xueqin Zhao, Hu Zhang, Xianfeng Wang, Xiufen Wang, Man Zhang
Aquaculture Reports.2025; 40: 102579. CrossRef
Field-scale artificial floating islands reduces cyanotoxin from residential raw sewage treatment basin
Zhaozhe Chen, Jiyoung Lee, Molly Mills, Abigail Volk, Ozeas S. Costa
Ecological Engineering.2025; 212: 107543. CrossRef
Artificial Intelligence-Based Microfluidic Platform for Detecting Contaminants in Water: A Review
Yihao Zhang, Jiaxuan Li, Yu Zhou, Xu Zhang, Xianhua Liu
Sensors.2024; 24(13): 4350. CrossRef
Alleviation of H2O2 toxicity by extracellular catalases in the phycosphere of Microcystis aeruginosa
Yerim Park, Wonjae Kim, Yeji Cha, Minkyung Kim, Woojun Park
Harmful Algae.2024; 137: 102680. CrossRef
Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems
Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park
Journal of Microbiology.2024; 62(11): 933. CrossRef
Laboratory-Simulated Inhibitory Effects of the Floating-Bed Plants on Microcystis aeruginosa and Their Microbial Communities’ Responses to Microcystins
Shuwen Zhang, Yuanpu Sha, Yuanyuan Tang, Longjie Li, Feihu Wang, Jing Dong, Xuejun Li, Yunni Gao, Xiaofei Gao, Huatao Yuan, Jingxiao Zhang
Microorganisms.2024; 12(10): 2035. CrossRef
Host-Associated Microbiome
Woo Jun Sul
Journal of Microbiology.2024; 62(3): 135. CrossRef

Coordinated regulation of interferon and inflammasome signaling pathways by SARS-CoV-2 proteins: Na-Eun Kim , Yoon-Jae Song; J. Microbiol. 2022;60(3):300-307. Published online January 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1502-8

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Abstract

Type I and III interferons (IFNs) and the nucleotide-binding domain (NBD) leucine-rich repeat (LRR)-containing receptor (NLR) family pyrin domain containing 3 (NLRP3) inflammasome play pivotal roles in the pathogenesis of SARS-CoV-2. While optimal IFN and inflammasome responses are essential for limiting SARS-CoV-2 infection, aberrant activation of these innate immune responses is associated with COVID-19 pathogenesis. In this review, we focus our discussion on recent findings on SARS-CoV-2-induced type I and III IFNs and NLRP3 inflammasome responses and the viral proteins regulating these mechanisms.

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E. A. Krieger, O. V. Samodova, O. A. Svitich, R. V. Samoilikov, E. A. Meremianina, L. V. Ivanova, N. A. Bebyakova, E. N. Ilina, A. V. Pavlenko, Yu. I. Esin, A. L. Arkhipova, S. N. Kovalchuk, A. V. Kudryavtsev
Russian Journal of Infection and Immunity.2024; 13(6): 1027. CrossRef
SARS-CoV-2 ORF8 as a Modulator of Cytokine Induction: Evidence and Search for Molecular Mechanisms
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Viruses.2024; 16(1): 161. CrossRef
Sensing of viral lung infections by cGAS-STING
Lei Fang, Michael Roth
Exploration of Immunology.2022; : 303. CrossRef
Two years of COVID-19 pandemic: where are we now?
Jinjong Myoung
Journal of Microbiology.2022; 60(3): 235. CrossRef
The Potential of Purinergic Signaling to Thwart Viruses Including SARS-CoV-2
Davide Ferrari, Michele Rubini, Jorge S. Burns
Frontiers in Immunology.2022;[Epub] CrossRef

Journal Articles

Geographic diversity in Helicobacter pylori oipA genotype between Korean and United States isolates: Aeryun Kim , Jing Lai , D. Scott Merrell , Ji-Hye Kim , Hanfu Su , Jeong-Heon Cha; J. Microbiol. 2021;59(12):1125-1132. Published online October 31, 2021; DOI: https://doi.org/10.1007/s12275-021-1450-8

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Abstract

Helicobacter pylori outer membrane inflammatory protein A (OipA) was originally named for its role in inducing inflammation in the host, as evidenced by high mucosal IL-8 levels. Expression of OipA is regulated by phase variation of a CT dinucleotide-repeat located in the 5􍿁􀁇region of the gene. However, little is known about OipA geographic diversity across isolates. To address this gap, we conducted a large-scale molecular epidemiologic analysis using H. pylori clinical isolates obtained from two geographically distinct populations: Korea and the United States (US). Most Korean isolates (98.7%) possessed two copies of oipA located at two specific loci (A and B) while all US isolates contained only one copy of oipA at locus A. Furthermore, most Korean oipA (94.8%) possessed three or less CT repeats while most US oipA (96.6%) contained five or more CT repeats. Among the two copies, all Korean H. pylori possessed at least one oipA ‘on’ phase variant while the single copy of oipA in US isolates showed 56.2% ‘on’ and 43.8% ‘off.’ Thus, host differences seem to have driven geographic diversification of H. pylori across these populations such that OipA expression in US isolates is still regulated by phase variation with 5 or more CT repeats, while Korean isolates always express OipA; duplication of the oipA combined with a reduction of CT repeats to three or less ensures continued expression. En masse, these findings suggest that diversity in the oipA gene copy number, CT repeats, and phase variation among H. pylori from different populations may confer a benefit in adaptation to particular host populations.

Citations

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Pathogenicity and virulence of Helicobacter pylori : A paradigm of chronic infection
Marguerite Clyne, Tadhg Ó Cróinín
Virulence.2025;[Epub] CrossRef
Genetic diversity of the oipA gene among Helicobacter pylori isolates and clinical outcome in Vietnam
Thi Hong Nhung Thai, Hong Phong Nguyen, Thi Hai Yen Nguyen, Thi Be Hai Nguyen, Thai Hoa Nguyen, Thi Mai Ngan Nguyen, Thi Minh Thi Ha
Infection, Genetics and Evolution.2023; 112: 105438. CrossRef
Characterization of East-Asian Helicobacter pylori encoding Western EPIYA-ABC CagA
Kavinda Tissera, Myeong-A Kim, Jing Lai, Sacheera Angulmaduwa, Aeryun Kim, D. Scott Merrell, Ji-Hye Kim, Hanfu Su, Jeong-Heon Cha
Journal of Microbiology.2022; 60(2): 207. CrossRef

Pedobacter aquicola sp. nov., isolated from freshwater: Yochan Joung , Hye-jin Jang , Miri Park , Jaeho Song , Jang-Cheon Cho; J. Microbiol. 2018;56(7):478-484. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-7499-3

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Abstract

A non-motile, pink-pigmented bacterial strain designated IMCC25679T, was isolated from freshwater Lake Chungju of Korea. Phylogenetic trees based on 16S rRNA gene sequences showed that the strain IMCC25679T formed a lineage within the genus Pedobacter. The strain IMCC25679T was closely related to Pedobacter daechungensis Dae 13T (96.4% sequence similarity), Pedobacter rivuli HME8457T (95.3%) and Pedobacter lentus DS-40T (94.3%). The major fatty acids of IMCC- 25679T were iso-C15:0, iso-C16:0 and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE), an unidentified sphingolipid (SL), an unidentified aminolipid (AL) and three unidentified polar lipids (PL). The DNA G + C content of IMCC25679T was 32.2 mol%. Based on the evidence presented in this study, the strain IMCC25679T represents a novel species within the genus Pedobacter, with the proposed name Pedobacter aquicola, sp. nov. The type strain is IMCC25679T (= KACC 19486T = NBRC113131T).

Citations

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Genome-Based Classification of Pedobacter albus sp. nov. and Pedobacter flavus sp. nov. Isolated from Soil
Nhan Le Thi Tuyet, Jaisoo Kim
Diversity.2024; 16(5): 292. CrossRef
Pedobacter rhodius sp. nov. and Pedobacter punctiformis sp. nov., isolated from soil
Haejin Woo, Geeta Chhetri, Inhyup Kim, Yoonseop So, Sunho Park, Yonghee Jung, Taegun Seo
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Screening of potential microbial markers for lung cancer using metagenomic sequencing
Qiang Chen, Kai Hou, Mingze Tang, Shuo Ying, Xiaoyun Zhao, Guanhua Li, Jianhui Pan, Xiaomin He, Han Xia, Yuechuan Li, Zheng Lou, Li Zhang
Cancer Medicine.2023; 12(6): 7127. CrossRef
Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water
Le Tran Tien Chau, Yong-Seok Kim, Chang-Jun Cha
Antonie van Leeuwenhoek.2022; 115(3): 445. CrossRef
Pedobacter riviphilus sp. nov., isolated from stream sediment
Hong Sik Im, Yochan Joung, Sang-Seob Lee
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Complete Genome Sequence of Pedobacter sp. PAMC26386 and Their Low Temperature Application in Arabinose-containing Polysaccharides Degradation
Cya-Yong Cho, So-Ra Han, Tae-Jin Oh
Current Microbiology.2021; 78(3): 944. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4043. CrossRef
Pedobacter indicus sp. nov., isolated from deep-sea sediment
Xiao-yan He, Na Li, Xiu-lan Chen, Yu-zhong Zhang, Xi-ying Zhang, Xiao-yan Song
Antonie van Leeuwenhoek.2020; 113(3): 357. CrossRef
Leeia aquatica sp. nov., isolated from freshwater
Jaeho Song, Yochan Joung, Shan-Hui Li, Juchan Hwang, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology .2020; 70(11): 5848. CrossRef
Sphingobacterium chungjuense sp. nov., isolated from a freshwater lake
Jaeho Song, Yochan Joung, Shan-Hui Li, Juchan Hwang, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology .2020; 70(12): 6126. CrossRef
Rhodoferax lacus sp. nov., isolated from a large freshwater lake
Miri Park, Jaeho Song, Gi Gyun Nam, Jang-Cheon Cho
International Journal of Systematic and Evolutionary Microbiology .2019; 69(10): 3135. CrossRef

Review

MINIREVIEW] Toxin-producing Cyanobacteria in Freshwater: A Review of the Problems, Impact on Drinking Water Safety, and Efforts for Protecting Public Health: Melissa Y. Cheung , Song Liang , Jiyoung Lee; J. Microbiol. 2013;51(1):1-10. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2549-3

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Abstract: Cyanobacteria have adapted to survive in a variety of environments and have been found globally. Toxin-producing cyanobacterial harmful algal blooms (CHABs) have been increasing in frequency worldwide and pose a threat to drinking and recreational water. In this study, the prevalence, impact of CHABs and mitigation efforts were reviewed, focusing on the Lake Erie region and Ohio’s inland lakes that have been impacted heavily as an example so that the findings can be transferrable to other parts of the world that face the similar problems due to the CHABs in their freshwater environments. This paper provides a basic introduction to CHABs and their toxins as well as an overview of public health implications including exposure routes, health effects, and drinking water issues, algal bloom advisory practices in Ohio, toxin measurements results in Ohio public water supplies, and mitigation efforts.

Journal Articles

Flavobacterium cheonhonense sp. nov., Isolated from a Freshwater Reservoir: Siwon Lee , Jung-Hwan Oh , Hang-Yeon Weon , Tae-Young Ahn; J. Microbiol. 2012;50(4):562-566. Published online July 21, 2012; DOI: https://doi.org/10.1007/s12275-012-1229-z

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Abstract: A novel bacterium, designated strain ARSA-15T, was isolated from a freshwater sample collected from the Cheonho reservoir, Cheonan, Republic of Korea. The isolate was deepyellow pigment, Gram-negative, rod-shaped, non-motile, and catalase- and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Flavobacterium, and shared less than 97% sequence similarity with recognized Flavobacterium species. The novel species was able to grow at 10–37°C, pH 6.5–10.0, and in 0–0.5% (w/v) NaCl concentrations. Chemotaxonomically, iso-C15:1, iso-C15:0, and iso-C16:0 were observed to be the predominant cellular fatty acid, and menaquinone-6 (MK-6) was the predominant respiratory quinone. The major polar lipid patterns of strain ARSA-19T was phosphatidylethanolamine, unknown aminolipid (AL1 and AL2), and unidentified polar lipids (L1, L2, and L3). The genomic DNA G+C content of the isolate was 39.2 mol%. On the basis of polyphasic approach, strain ARSA-15T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium cheonhonense sp. nov. is proposed. The type strain is ARSA-15T (=KACC 14967T =KCTC 23180T =JCM 17064T).

NOTE] Arenimonas aquaticum sp. nov., a Member of the Gammaproteobacterium, Isolated from a Freshwater Reservoir: A-Ram Kim , Siwon Lee , Kyudong Han , Tae-Young Ahn; J. Microbiol. 2012;50(2):354-358. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1301-8

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Abstract: A novel bacterial strain, designated NA-09T, was isolated from a freshwater sample collected from the Cheonho reservoir, Republic of Korea. Colonies were creamy-white pigmented, translucent, and circular with convex shape. The isolate was Gram-staining negative, strictly aerobic, motile, and rod-shaped. The 16S rRNA gene sequence analysis revealed that strain NA-09T belonged to the genus Arenimonas and showed the highest sequence similarities with Arenimonas malthae CC-JY-1T (95.4%), A. oryziterrae YC6267T (94.9%), A. composti P2-12-1T (94.8%), and A. donghaensis H03-R19T (94.1%). The major fatty acids were iso-C16:0 (20.8%), iso-C15:0 (16.9%), summed feature 1 (13.2%), and iso-C16:1ω7c alcohol (10.2%). The major isoprenoid quinone of the isolate was ubiquionone-8. On the basis of the data from the polyphasic characterization, the strain NA-09T represents a novel species, for which the name Arenimonas aquaticum sp. nov. is proposed (type strain NA-09T =KACC 14663T =NBRC 106550T).

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

Host Species as a Strong Determinant of the Intestinal Microbiota of Fish Larvae: Xuemei Li , Yuhe Yu , Weisong Feng , Qingyun Yan , Yingchun Gong; J. Microbiol. 2012;50(1):29-37. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1340-1

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Abstract

We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized using rank-abundance plots fitted with linear regression models.
Results
showed that the intestinal bacterial evenness was significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal eukaryotic microorganisms were almost identical.

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Stratified Distribution of Nutrients and Extremophile Biota within Freshwater Ice Covering the Surface of Lake Baikal: Nina A. Bondarenko , Olga I. Belykh , Ludmila P. Golobokova , Olga V. Artemyeva , Natalia F. Logacheva , Irina V. Tikhonova , Irina A. Lipko , Tatyana Ya. Kostornova , Valentina V. Parfenova , Tamara V. Khodzher , Young-Gun Zo; J. Microbiol. 2012;50(1):8-16. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1251-1

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Abstract: Biological entities and gradients of selected chemicals within the seemingly barren ice layers covering Lake Baikal were investigated. Ice cores 40–68 cm long were obtained from inshore and offshore sites of Southern Lake Baikal during the cold period of a year (March-April) in 2007 and 2008. In microscopic observations of the melted ice, both algae and bacteria were found in considerable numbers (>103 cells/L and >104 cells/ml, respectively). Among all organisms found, diatom was generally the most predominant taxon in the ice. Interestingly, both planktonic and benthic algae were present in considerable numbers (2–4×104 cells/L). Dominant phototrophic picoplankton were comprised of small green algae of various taxa and cyanobacteria of Synechococcus and Cyanobium. The bacterial community consisted mostly of short rod and cocci cells, either freeliving or aggregated. Large numbers of yeast-like cells and actinomycete mycelium were also observed. Concentrations of silica, phosphorus, and nitrate were low by an order of magnitude where biota was abundant. The profile of the ice could be interpreted as vertical stratification of nutrients and biomass due to biological activities. Therefore, the organisms in the ice were regarded to maintain high activity while thriving under freezing conditions. Based on the results, it was concluded that the freshwater ice covering the surface of Lake Baikal is considerably populated by extremophilic microorganisms that actively metabolize and form a detritus food chain in the unique large freshwater ecosystem of Lake Baikal.

Flavobacterium koreense sp. nov., Flavobacterium chungnamense sp. nov., and Flavobacterium cheonanense sp. nov., Isolated from a Freshwater Reservoir: Siwon Lee , Hang-Yeon Weon , Soo-Jin Kim , Tae-Young Ahn; J. Microbiol. 2011;49(3):387-392. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0382-0

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Abstract: Taxonomic studies were performed on three strains isolated from Cheonho reservoir in Cheonan, Korea. The isolates were Gram-negative, aerobic, rod-shaped, non-motile, catalase-positive, and oxidase-positive. Colonies on solid media were cream-yellow, smooth, shiny, and circular. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these strains belong to the genus Flavobacterium. The strains shared 98.6-99.4% sequence similarity with each other and showed less than 97% similarity with members of the genus Flavobacterium with validly published names. The DNA-DNA hybridization results confirmed the separate genomic status of strains ARSA-42T, ARSA-103T, and ARSA-108T. The isolates contained menaquinone-6 as the predominant menaquinone and iso-C15:0, iso-C15:0 3-OH, iso-C15:1 G, and iso-C16:0 3-OH as the major fatty acids. The genomic DNA G+C content of the isolates were 31.4-33.2 mol%. According to the phenotypic and genotypic data, these organisms are classified as representative of three novel species in the genus Flavobacterium, and the name Flavobacterium koreense sp. nov. (strain ARSA-42T =KCTC 23182T =JCM 17066T =KACC 14969T), Flavobacterium chungnamense sp. nov. (strain ARSA-103T =KCTC 23183T =JCM 17068T =KACC 14971T), and Flavobacterium cheonanense sp. nov. (strain ARSA-108T =KCTC 23184T =JCM 17069T =KACC 14972T) are proposed.

Published Erratum

Erratum to: Protective and Pathogenic Role of Humoral Responses in COVID‑19: Uni Park , Nam-Hyuk Cho; J. Microbiol. 2023;61(7):713-713.; DOI: https://doi.org/10.1007/s12275-023-00058-0

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