Journal of Microbiology

Journal Articles

Increase in the genetic polymorphism of varicella-zoster virus after passaging in in vitro cell culture: Hye Rim Hwang , Seok Cheon Kim , Se Hwan Kang , Chan Hee Lee; J. Microbiol. 2019;57(11):1033-1039. Published online October 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9429-4

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Primary infections with the varicella-zoster virus (VZV) result in varicella, while latent reactivation leads to herpes zoster. Both varicella and zoster can be prevented by live attenuated vaccines. There have been reports suggesting that both clinical VZV strains and those in vaccine preparations are genetically polymorphic, containing mixtures of both wild-type and vaccine-type sequences at certain vaccine-specific sites. In this study, the genetic polymorphism of the VZV genome was examined by analyzing the frequencies of minor alleles at each nucleotide position. Next-generation sequencing of the clinical VZV strain YC02 passaged in an in vitro cell culture was used to identify genetically polymorphic sites (GPS), where the minor allele frequency (MAF) exceeded 5%. The number of GPS increased by 7.3-fold at high passages (p100) when compared to low passages (p17), although the average MAF remained similar. GPS were found in 6 open reading frames (ORFs) in p17, 35, and 54 ORFs in p60 and p100, respectively. GPS were found more frequently in the dispensable gene group than the essential gene group, but the average MAF was greater in the essential gene group. The most common two major/minor base pairs were A/g and T/c. GPS were found in all three passages at 16 positions, all located in the reiterated (R) region. The population diversity as measured by Shannon entropy increased in p60 and p100. However, the entropy remained unchanged in the R regions.

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Genetic changes in plaque-purified varicella vaccine strain Suduvax during in vitro propagation in cell culture
Hye Rim Hwang, Se Hwan Kang, Chan Hee Lee
Journal of Microbiology.2021; 59(7): 702. CrossRef
Genetic diversity through social heterosis can increase virulence in RNA viral infections and cancer progression
Saba Ebrahimi, Peter Nonacs
Royal Society Open Science.2021;[Epub] CrossRef

Exploring the oral microflora of preschool children: Wen Ren , Qun Zhang , Xuenan Liu , Shuguo Zheng , Lili Ma , Feng Chen , Tao Xu , Baohua Xu; J. Microbiol. 2017;55(7):531-537. Published online April 22, 2017; DOI: https://doi.org/10.1007/s12275-017-6474-8

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Abstract

The oral cavity is one of the most important and complicated habitats in our body and supports diverse microbial communities. In this study, we aimed to determine the bacterial diversity and composition of various oral micro-niches. Samples were collected from supragingival plaque, saliva, and tongue coating from 10 preschool children (30 samples total). 16S rRNA gene pyrosequencing dataset generated 314,639 clean reads with an average of 10,488 ± 2,787 reads per sample. The phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria were predominant, accounting for more than 90% of the total sequences. We found the highest α diversity, microbial richness, and evenness in plaque, compared with saliva and tongue coating. Plaque was also distinguished from saliva and tongue coating by phylogenetic distances (weighted UniFrac). Taxa with different relative abundances were further identified, confirming the existence of microbial differences across the three niches. Core microbiomes were defined of each niche; however, only a small proportion of operational taxonomic units (8.07%) were shared by the three niches. Coaggregation between Actinomyces spp. and Streptococcus spp. and other correlations among periodontal pathogens, such as Prevotella, Fusobacteria, Capnocytophaga, and Tannerella, were shown by a co-occurrence network. In summary, our study provides a framework of oral microbial communities in the population of preschool children as a baseline for further studies of oral diseases related to microbes.

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Salivary microbiota dysbiosis and elevated polyamine levels contribute to the severity of periodontal disease
Md Haroon Rashid, Sandhya Pavan Kumar, Resma Rajan, Anitha Mamillapalli
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A dynamic microcosm biofilm model for root carious-like lesion development: analysis of demineralization and microbiological characterization
Tamires Timm Maske, Glenda Ávila Marques, Bruna Dalongaro Fritsch, Bruna Moraes Kremer, Maximiliano Sérgio Cenci, Pabulo Henrique Rampelotto, Rodrigo Alex Arthur
Biofouling.2025; 41(5): 536. CrossRef
The tongue microbiome of young patients with chronic kidney disease and their healthy mothers
Karolin C. Hoefer, Lutz T. Weber, Anna Greta Barbe, Isabelle Graf, Stefanie Thom, Angela Nowag, Claus J. Scholz, Hilmar Wisplinghoff, Michael J. Noack, Nathalie Jazmati
Clinical Oral Investigations.2024;[Epub] CrossRef
Species-level characterization of saliva and dental plaque microbiota reveals putative bacterial and functional biomarkers of periodontal diseases in dogs
Giulia Alessandri, Federico Fontana, Leonardo Mancabelli, Chiara Tarracchini, Gabriele Andrea Lugli, Chiara Argentini, Giulia Longhi, Sonia Mirjam Rizzo, Laura Maria Vergna, Rosaria Anzalone, Alice Viappiani, Francesca Turroni, Maria Cristina Ossiprandi,
FEMS Microbiology Ecology.2024;[Epub] CrossRef
Molecular Genetic Analysis of Perioperative Colonization by Infection-Related Microorganisms in Patients Receiving Intraoral Microvascular Grafts
Henriette Louise Moellmann, Katharina Kommer, Nadia Karnatz, Klaus Pfeffer, Birgit Henrich, Majeed Rana
Journal of Clinical Medicine.2024; 13(14): 4103. CrossRef
Advances in the oral microbiota and rapid detection of oral infectious diseases
Xuan Xiao, Shangfeng Liu, Hua Deng, Yuhan Song, Liang Zhang, Zhifeng Song
Frontiers in Microbiology.2023;[Epub] CrossRef
Novel Strategies for Preventing Dysbiosis in the Oral Cavity
Mariana B Rebelo, Cláudia S Oliveira, Freni K Tavaria
Frontiers in Bioscience-Elite.2023;[Epub] CrossRef
Lactobacillus paracasei ET-22 Suppresses Dental Caries by Regulating Microbiota of Dental Plaques and Inhibiting Biofilm Formation
Meng Guo, Jianmin Wu, Weilian Hung, Zhe Sun, Wen Zhao, Hanglian Lan, Zhi Zhao, Guna Wuri, Bing Fang, Liang Zhao, Ming Zhang
Nutrients.2023; 15(15): 3316. CrossRef
Exploring Oral Microbiome in Healthy Infants and Children: A Systematic Review
Silvia D’Agostino, Elisabetta Ferrara, Giulia Valentini, Sorana Andreea Stoica, Marco Dolci
International Journal of Environmental Research and Public Health.2022; 19(18): 11403. CrossRef
Sonication versus the conventional method for evaluation of the dental microbiome: a prospective pilot study
Oliver Wagendorf, Peter Menzel, Rolf Schwarzer, Norbert Neckel, Saskia Preissner, Max Heiland, Susanne Nahles
BMC Oral Health.2022;[Epub] CrossRef
The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions
Xinyi Li, Yanmei Liu, Xingyou Yang, Chengwen Li, Zhangyong Song
Frontiers in Microbiology.2022;[Epub] CrossRef
Predominance of non-Streptococcus mutans bacteria in dental biofilm and its relation to caries progression
Doaa M. AlEraky, Marwa Madi, Maha El Tantawi, Jehan AlHumaid, Sarah Fita, Sayed AbdulAzeez, J. Francis Borgio, Fahad A. Al-Harbi, Adel S. Alagl
Saudi Journal of Biological Sciences.2021; 28(12): 7390. CrossRef
The impact of caries status on supragingival plaque and salivary microbiome in children with mixed dentition: a cross-sectional survey
Xiaoxia Yang, Lidan He, Siqi Yan, Xinyi Chen, Guoying Que
BMC Oral Health.2021;[Epub] CrossRef
Acquisition and establishment of the oral microbiota
A. M. (Marije) Kaan, Dono Kahharova, Egija Zaura, M. Curtis, R. Darveau
Periodontology 2000.2021; 86(1): 123. CrossRef
Microbiome of Saliva and Plaque in Children According to Age and Dental Caries Experience
Eungyung Lee, Suhyun Park, Sunwoo Um, Seunghoon Kim, Jaewoong Lee, Jinho Jang, Hyoung-oh Jeong, Jonghyun Shin, Jihoon Kang, Semin Lee, Taesung Jeong
Diagnostics.2021; 11(8): 1324. CrossRef
Relationship of Salivary Microbiome with the Worsening of the Periodontal Health Status in Young Adults: A 3-Year Cohort Study
Md Monirul Islam, Daisuke Ekuni, Naoki Toyama, Terumasa Kobayashi, Kohei Fujimori, Yoko Uchida, Daiki Fukuhara, Ayano Taniguchi-Tabata, Kota Kataoka, Yoshiaki Iwasaki, Manabu Morita
International Journal of Environmental Research and Public Health.2020; 17(5): 1764. CrossRef
The canine oral microbiome: variation in bacterial populations across different niches
Avika Ruparell, Taichi Inui, Ruth Staunton, Corrin Wallis, Oliver Deusch, Lucy J. Holcombe
BMC Microbiology.2020;[Epub] CrossRef
The oral microbiome and salivary proteins influence caries in children aged 6 to 8 years
Wang Chen, Qian Jiang, Guowei Yan, Deqin Yang
BMC Oral Health.2020;[Epub] CrossRef
MEDICAL AND GENETIC STUDIES OF ORAL MICROBIOMA STATUS IN CHILDREN
S. S. Ostrovska, P. G. Gerasimchuk
Bulletin of Problems Biology and Medicine.2019; 4(1): 43. CrossRef
The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human
Anthony P. Corfield
Microorganisms.2018; 6(3): 78. CrossRef
Distinctions and associations between the microbiota of saliva and supragingival plaque of permanent and deciduous teeth
Weihua Shi, Jing Tian, He Xu, Qiong Zhou, Man Qin, Kazuhiro Takemoto
PLOS ONE.2018; 13(7): e0200337. CrossRef

Review

MINIREVIEW] High-resolution imaging of the microbial cell surface: Ki Woo Kim; J. Microbiol. 2016;54(11):703-708. Published online October 29, 2016; DOI: https://doi.org/10.1007/s12275-016-6348-5

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Abstract

Microorganisms, or microbes, can function as threatening pathogens that cause disease in humans, animals, and plants; however, they also act as litter decomposers in natural ecosystems. As the outermost barrier and interface with the environment, the microbial cell surface is crucial for cell-to-cell communication and is a potential target of chemotherapeutic agents. Surface ultrastructures of microbial cells have typically been observed using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Owing to its characteristics of low-temperature specimen preparation and superb resolution (down to 1 nm), cryo-field emission SEM has revealed paired rodlets, referred to as hydrophobins, on the cell walls of bacteria and fungi. Recent technological advances in AFM have enabled high-speed live cell imaging in liquid at the nanoscale level, leading to clear visualization of celldrug interactions. Platinum-carbon replicas from freeze-fractured fungal spores have been observed using transmission electron microscopy, revealing hydrophobins with varying dimensions. In addition, AFM has been used to resolve bacteriophages in their free state and during infection of bacterial cells. Various microscopy techniques with enhanced spatial resolution, imaging speed, and versatile specimen preparation are being used to document cellular structures and events, thus addressing unanswered biological questions.

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Application of advanced bioimaging technologies in viral infections
Yu Sun, Can Cao, Yilin Peng, Xuyao Dai, Xiaoke Li, Jing Li, Tengxiao Liang, Ping Song, Yongan Ye, Jinsheng Yang, Ning Li, Ruodan Xu
Materials Today Physics.2024; 46: 101488. CrossRef
Potential role of intratumor bacteria outside the gastrointestinal tract: More than passengers
Zhu Liu, Lian‐Lian Hong, Zhi‐Qiang Ling
Cancer Medicine.2023; 12(16): 16756. CrossRef
The photothermal effect of polypyrrole modified gold nanoparticles on SKOV-3 cells using SEM and AFM
C Z Liu, Y X Huang, C R Zhao, Z B Wang
Journal of Physics: Conference Series.2021; 1777(1): 012019. CrossRef
Cell mechanics characteristics of anti-HER2 modified PPy@GNPs and its photothermal treatment of SKOV-3 cells
Chuanzhi Liu, Chunru Zhao, Yuxi Huang, Haiyan Li, Xuan Guo, Zuobin Wang
Applied Nanoscience.2021; 11(3): 911. CrossRef
Guidelines for a Morphometric Analysis of Prokaryotic and Eukaryotic Cells by Scanning Electron Microscopy
Dominika Czerwińska-Główka, Katarzyna Krukiewicz
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Using Atomic Force Microscopy To Illuminate the Biophysical Properties of Microbes
John W. Goss, Catherine B. Volle
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Evaluating Efficacy of Antimicrobial and Antifouling Materials for Urinary Tract Medical Devices: Challenges and Recommendations
Madeleine Ramstedt, Isabel A. C. Ribeiro, Helena Bujdakova, Filipe J. M. Mergulhão, Luisa Jordao, Peter Thomsen, Martin Alm, Mette Burmølle, Todorka Vladkova, Fusun Can, Meital Reches, Martijn Riool, Alexandre Barros, Rui L. Reis, Emilio Meaurio, Judith K
Macromolecular Bioscience.2019;[Epub] CrossRef
Cell biology of microbes and pharmacology of antimicrobial drugs explored by Atomic Force Microscopy
Cécile Formosa-Dague, Raphaël Emmanuel Duval, Etienne Dague
Seminars in Cell & Developmental Biology.2018; 73: 165. CrossRef
The Role of Glycans in Bacterial Adhesion to Mucosal Surfaces: How Can Single-Molecule Techniques Advance Our Understanding?
Cécile Formosa-Dague, Mickaël Castelain, Hélène Martin-Yken, Karen Dunker, Etienne Dague, Marit Sletmoen
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SEM imaging of the stimulatory response of RAW264.7 cells against Porphyromonas gingivalis using a simple technique employing new conductive materials
Chisato Takahashi, Yoshiki Umemura, Ayako Naka, Hiromitsu Yamamoto
Journal of Biomedical Materials Research Part B: Applied Biomaterials.2018; 106(3): 1280. CrossRef
A Cryosectioning Technique for the Observation of Intracellular Structures and Immunocytochemistry of Tissues in Atomic Force Microscopy (AFM)
Eiji Usukura, Akihiro Narita, Akira Yagi, Nobuaki Sakai, Yoshitsugu Uekusa, Yuka Imaoka, Shuichi Ito, Jiro Usukura
Scientific Reports.2017;[Epub] CrossRef

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

Identification of Porcine Endogenous Retrovirus (PERV) packaging sequence and development of PERV packaging viral vector system: Jiwon Choi , Hoon-mi Kim , Jong Kwang Yoon , Yeondong Cho , Hee-Jung Lee , Kang Chang Kim , Chang-Kyu Kim , Gye-Woong Kim , Young Bong Kim; J. Microbiol. 2015;53(5):348-353. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-5134-0

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Abstract

Studies of the retroviruses have focused on the specific interaction of the nucleocapsid protein with a packaging signal in the viral RNA as important for this selectivity, but the packaging signal in porcine endogenous retrovirus (PERV) has not been defined. Herein, we identified and analyzed this packaging signal in PERV and found hairpin structures with conserved tetranucleotides in their loops and nucleocapsid recognition sequences; both of which are key elements in the viral packaging signal of MLV. We evaluated packaging efficiency of sequence variants isolated from viral and proviral integrated genomes. All viral packaging sequences (Ψ) were identical, while five distinct packaging sequences were identified from proviral sources. One proviral sequence (Ψ1) was identical to that of the viral Ψ and had the highest packaging efficiency. Three variants (Ψ2, Ψ3, Ψ4) maintained key elements of the viral packaging signal, but had nucleotide replacements and consequently demonstrated reduced packaging efficiency. Despite of the same overall hairpin structure, the proviral variant (Ψ5) had only one GACG sequence in the hairpin loop and showed the lowest packaging efficiency other than ΔΨ, in which the essential packaging sequence was removed. This result, thus, defined the packaging sequences in PERV and emphasized the importance of nucleotide sequence and RNA structure in the determination of packaging efficiency. In addition, we demonstrate efficient infection and gene expression from the PERVbased viral vector, which may serve as a novel alternative to current retroviral expression systems.

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Porcine Endogenous Retrovirus (PERV) – Molecular Structure and Replication Strategy in the Context of Retroviral Infection Risk of Human Cells
Krzysztof Łopata, Emilia Wojdas, Roman Nowak, Paweł Łopata, Urszula Mazurek
Frontiers in Microbiology.2018;[Epub] CrossRef

Growth Phase-dependent Roles of Sir2 in Oxidative Stress Resistance and Chronological Lifespan in Yeast: Woo Kyu Kang , Yeong Hyeock Kim , Byoung-Soo Kim , Jeong-Yoon Kim; J. Microbiol. 2014;52(8):652-658. Published online July 5, 2014; DOI: https://doi.org/10.1007/s12275-014-4173-2

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Abstract

Silent Information Regulator 2 (Sir2), a conserved NAD+- dependent histone deacetylase, has been implicated as one of the key factors in regulating stress response and longevity. Here, we report that the role of Sir2 in oxidative stress resistance and chronological lifespan is dependent on growth phase in yeast. In exponential phase, sir2Δ cells were more resistant to H2O2 stress and had a longer chronological lifespan than wild type. By contrast, in post-diauxic phase, sir2Δ cells were less resistant to H2O2 stress and had a shorter chronological lifespan than wild type cells. Similarly, the expression of antioxidant genes, which are essential to cope with oxidative stress, was regulated by Sir2 in a growth phasedependent manner. Collectively, our findings highlight the importance of the metabolic state of the cell in determining whether Sir2 can protect against or accelerate cellular aging of yeast.

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Sirt1: Role Under the Condition of Ischemia/Hypoxia
Xiaofei Meng, Jin Tan, Mengmeng Li, Shuling Song, Yuyang Miao, Qiang Zhang
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A haploproficient interaction of the transaldolase paralogue NQM1 with the transcription factor VHR1 affects stationary phase survival and oxidative stress resistance
Steve Michel, Markus A Keller, Mirjam MC Wamelink, Markus Ralser
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Sir2 phosphorylation through cAMP-PKA and CK2 signaling inhibits the lifespan extension activity of Sir2 in yeast
Woo Kyu Kang, Yeong Hyeock Kim, Hyun Ah Kang, Ki-Sun Kwon, Jeong-Yoon Kim
eLife.2015;[Epub] CrossRef

Review

REVIEW] Mechanisms of Synergy in Polymicrobial Infections: Justine L. Murray , Jodi L. Connell , Apollo Stacy , Keith H. Turner , Marvin Whiteley; J. Microbiol. 2014;52(3):188-199. Published online March 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4067-3

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Abstract

Communities of microbes can live almost anywhere and contain many different species. Interactions between members of these communities often determine the state of the habitat in which they live. When these habitats include sites on the human body, these interactions can affect health and disease. Polymicrobial synergy can occur during infection, in which the combined effect of two or more microbes on disease is worse than seen with any of the individuals alone. Powerful genomic methods are increasingly used to study microbial communities, including metagenomics to reveal the members and genetic content of a community and metatranscriptomics to describe the activities of community members. Recent efforts focused toward a mechanistic understanding of these interactions have led to a better appreciation of the precise bases of polymicrobial synergy in communities containing bacteria, eukaryotic microbes, and/or viruses. These studies have benefited from advances in the development of in vivo models of polymicrobial infection and modern techniques to profile the spatial and chemical bases of intermicrobial communication. This review describes the breadth of mechanisms microbes use to interact in ways that impact pathogenesis and techniques to study polymicrobial communities.

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Journal of Clinical Periodontology.2020; 47(9): 1064. CrossRef
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Paula Jorge, Andreia Patrícia Magalhães, Tânia Grainha, Diana Alves, Ana Margarida Sousa, Susana Patrícia Lopes, Maria Olívia Pereira
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Infection and Immunity.2019;[Epub] CrossRef
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Mutations in bacterial genes induce unanticipated changes in the relationship between bacterial pathogens in experimental otitis media
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Research Support, Non-U.S. Gov't

Isolation and Characterization of the Smallest Bacteriophage P4 Derivatives Packaged into P4-Size Head in Bacteriophage P2-P4 System: Kyoung-Jin Kim , Jaeho Song; J. Microbiol. 2006;44(5):530-536.; DOI: https://doi.org/2444 [pii]

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Abstract: Bacteriophage P4, a satellite phage of coliphage P2, is a very useful experimental tool for the study of viral capsid assembly and cos-cleavage. For an in vitro cos-cleavage reaction study of the P2-P4 system, new shortened and selectable markers containing P4 derivative plasmids were designed as a substrate molecules. They were constructed by swapping the non-essential segment of P4 DNA for either the kanamycin resistance (kmr) gene or the ampicillin resistance (apr) gene. The size of the genomes of the resulting markers were 82% (P4 ash8 delRI:: kmr) and 79% (P4 ash8 delRI:: apr) of the wild type P4 genome. To determine the lower limit of genome size that could be packaged into the small P4-size head, these shortened P4 plasmids were converted to phage particles with infection of the helper phage P2. The conversion of plasmid P4 derivatives to bacteriophage particles was verified by the heat stability test and the burst size determination experiment. CsCl buoyant equilibrium density gradient experiments confirmed not only the genome size of the viable phage form of shortened P4 derivatives, but also their packaging into the small P4-size head. P4 ash8 delRI:: apr turned out to be the smallest P4 genome that can be packaged into P4-sized head.

Characterization and Identification of the Bacteriophage P4 Mutant Suppressin sir Mutations of Bacteriophage P2: Kim, Kyoung Jin , Sunshine, Melvin G. , Six, Erich W.; J. Microbiol. 1998;36(4):262-265.

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Abstract: Bacteriophage P4 ost1 was isolated as a suppressor mutant of P2 sir3 and identified by restriction enzyme site analysis. The mutant DNA turned out to be an imperfect P4 trimer containing deletions. It was suggested that the deletion resulted from int-mediated site-specific recombination. CsCl equilibrium density gradient experiment confirmed the genome size of P4 ostl.

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