Journal of Microbiology

Journal Article

Heterologous Production and Structure Determination of a New Lanthipeptide Sinosporapeptin Using a Cryptic Gene Cluster in an Actinobacterium Sinosporangium siamense: Keita Saito , Keiichiro Mukai , Issara Kaweewan , Hiroyuki Nakagawa , Takeshi Hosaka , Shinya Kodani; J. Microbiol. 2023;61(6):641-648. Published online June 12, 2023; DOI: https://doi.org/10.1007/s12275-023-00059-z

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Lipolanthine is a subclass of lanthipeptide that has the modification of lipid moiety at the N-terminus. A cryptic biosynthetic gene cluster comprising four genes (sinA, sinKC, sinD, and sinE) involved in the biosynthesis of lipolanthine was identified in the genome of an actinobacterium Sinosporangium siamense. Heterologous coexpression of a precursor peptide coding gene sinA and lanthipeptide synthetase coding gene sinKC in the host Escherichia coli strain BL21(DE3) resulted in the synthesis of a new lanthipeptide, sinosporapeptin. It contained unusual amino acids, including one labionin and two dehydrobutyrine residues, as determined using NMR and MS analyses. Another coexpression experiment with two additional genes of decarboxylase (sinD) and N-acetyl transferase (sinE) resulted in the production of a lipolanthine-like modified sinosporapeptin.

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Heterologous biosynthesis of myxobacterial lanthipeptides melittapeptins
Issara Kaweewan, Keiichiro Mukai, Pratchaya Rukthanapitak, Hiroyuki Nakagawa, Takeshi Hosaka, Shinya Kodani
Applied Microbiology and Biotechnology.2024;[Epub] CrossRef
Facile Method for Determining Lanthipeptide Stereochemistry
Youran Luo, Shuyun Xu, Autumn M. Frerk, Wilfred A. van der Donk
Analytical Chemistry.2024; 96(4): 1767. CrossRef
Antimicrobial Peptides Derived from Bacteria: Classification, Sources, and Mechanism of Action against Multidrug-Resistant Bacteria
Raynichka Mihaylova-Garnizova, Slavena Davidova, Yordan Hodzhev, Galina Satchanska
International Journal of Molecular Sciences.2024; 25(19): 10788. CrossRef

Review

A comprehensive review of SARS-CoV-2 genetic mutations and lessons from animal coronavirus recombination in one health perspective: Woonsung Na , Hyoungjoon Moon , Daesub Song; J. Microbiol. 2021;59(3):332-340. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0660-4

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Abstract

SARS-CoV-2 was originated from zoonotic coronaviruses and confirmed as a novel beta-coronavirus, which causes serious respiratory illness such as pneumonia and lung failure, COVID-19. In this review, we describe the genetic characteristics of SARS-CoV-2, including types of mutation, and molecular epidemiology, highlighting its key difference from animal coronaviruses. We further summarized the current knowledge on clinical, genetic, and pathological features of several animal coronaviruses and compared them with SARSCoV- 2, as well as recent evidences of interspecies transmission and recombination of animal coronaviruses to provide a better understanding of SARS-CoV-2 infection in One Health perspectives. We also discuss the potential wildlife hosts and zoonotic origin of this emerging virus in detail, that may help mitigate the spread and damages caused by the disease.

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IN SILICO COMPARATIVE ANALYSIS OF SARS-COV-2 MUTATIONS IN BRAZIL
Gabriel Ferrari de Oliveira, Sarah De Oliveira Rodrigues, Kolawole Banwo, Isabela Bacelar de Assis, Celso Iwata Frison, Jorge Pamplona Pagnossa
Multidisciplinary Sciences Reports.2023; 3(3): 1. CrossRef
A New Polymorphic Comprehensive Model for COVID-19 Transition Cycle Dynamics with Extended Feed Streams to Symptomatic and Asymptomatic Infections
Yas Al-Hadeethi, Intesar F. El Ramley, Hiba Mohammed, Abeer Z. Barasheed
Mathematics.2023; 11(5): 1119. CrossRef
Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
COVID-19 Recovery Patterns Across Alpha (B.1.1.7) and Delta (B.1.617.2) Variants of SARS-CoV-2
Nitya Kumar, Suha Quadri, Abdulla Ismaeel AlAwadhi, Manaf AlQahtani
Frontiers in Immunology.2022;[Epub] CrossRef
BCG-Based Vaccines Elicit Antigen-Specific Adaptive and Trained Immunity against SARS-CoV-2 and Andes orthohantavirus
Jorge A. Soto, Fabián E. Díaz, Angello Retamal-Díaz, Nicolás M. S. Gálvez, Felipe Melo-González, Alejandro Piña-Iturbe, Mario A. Ramírez, Karen Bohmwald, Pablo A. González, Susan M. Bueno, Alexis M. Kalergis
Vaccines.2022; 10(5): 721. CrossRef
Detection and molecular characteristics of canine coronavirus in Chengdu city, Southwest China from 2020 to 2021
Xue Sha, Yan Li, Jian Huang, Qun Zhou, Xin Song, Bin Zhang
Microbial Pathogenesis.2022; 166: 105548. CrossRef
Appraisal of SARS-CoV-2 mutations and their impact on vaccination efficacy: an overview
Nastaran Hadizadeh, Mousa Naderi, Jafar Khezri, Meysam Yazdani, Mehdi Shamsara, Ehsan Hashemi
Journal of Diabetes & Metabolic Disorders.2022; 21(2): 1763. CrossRef
Impact of X-radiation in the management of COVID-19 disease
Divya K Mohan, K Nandhini, Venkateswarlu Raavi, Venkatachalam Perumal
World Journal of Radiology.2022; 14(7): 219. CrossRef
An integrative pan-cancer analysis reveals the carcinogenic effects of NCAPH in human cancer
Ying Liu, Xiao Ma, Linyuan Feng, Zhenhua Lin, Xianchun Zhou
Mathematical Biosciences and Engineering.2022; 20(1): 76. CrossRef
Profiles in conspiracism: Associations with two psychiatric syndromes, religiosity and pandemic-related health behaviors
Michael J. Minzenberg, Jong H. Yoon
Frontiers in Psychiatry.2022;[Epub] CrossRef
Prevalence and Molecular Characteristics of Canine Coronavirus in Southwest China from 2020 to 2021
Xue Sha, Bin Zhang, Xin Song, Yan Li, Jian Huang, Qun Zhou
SSRN Electronic Journal .2022;[Epub] CrossRef
Prevalence and molecular characteristics of feline coronavirus in southwest China from 2017 to 2020
Qun Zhou, Yan Li, Jian Huang, Nengsheng Fu, Xin Song, Xue Sha, Bin Zhang
Journal of General Virology .2021;[Epub] CrossRef
Preparedness and activities of the anti-SARS-CoV-2 convalescent plasma bank in the Veneto region (Italy): An organizational model for future emergencies
Giustina De Silvestro, Giorgio Gandini, Francesco Fiorin, Piero Marson, Ersilia Barbone, Andrea Frigato, Gianluca Gessoni, Arianna Veronesi, Monia Pacenti, Monica Castelli, Marianna Rinaldi, Monica Rizzi, Francesca Stefani, Giovanni Roveroni
Transfusion and Apheresis Science.2021; 60(4): 103154. CrossRef
The oral vaccine based on self-replicating RNA lipid nanoparticles can simultaneously neutralize both SARS-CoV-2 variants alpha and delta
Golamabbas Mohammadi, Zahra Sotoudehnia Koranni, Ali Jebali
International Immunopharmacology.2021; 101: 108231. CrossRef
SARS-CoV2 spike protein gene variants with N501T and G142D mutation–dominated infections in mink in the United States
Hugh Y. Cai, Allison Cai
Journal of Veterinary Diagnostic Investigation.2021; 33(5): 939. CrossRef
Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef
COVID-19 infections in pets such as cats and dogs
Mehmet DEMİRCİ, Akin YIĞIN, Bekir KOCAZEYBEK, Oktay KESKİN
Veterinary Journal of Mehmet Akif Ersoy University.2021; 6(3): 158. CrossRef
Nanotechnology‐Assisted RNA Delivery: From Nucleic Acid Therapeutics to COVID‐19 Vaccines
Chiara Rinoldi, Seyed Shahrooz Zargarian, Pawel Nakielski, Xiaoran Li, Anna Liguori, Francesca Petronella, Dario Presutti, Qiusheng Wang, Marco Costantini, Luciano De Sio, Chiara Gualandi, Bin Ding, Filippo Pierini
Small Methods.2021;[Epub] CrossRef

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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Abstract

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

Evidence of the genetic diversity and clonal population structure of Oenococcus oeni strains isolated from different wine-making regions of China: Dongliang Yu , Kan Shi , Xiangyuan Wen , Fangshu Xie , Tao Wang , Shuwen Liu , Ling He; J. Microbiol. 2018;56(8):556-564. Published online July 25, 2018; DOI: https://doi.org/10.1007/s12275-018-7568-7

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Abstract

Studies of the genetic diversity and population structure of Oenococcus oeni (O. oeni) strains from China are lacking compared to other countries and regions. In this study, amplified fragment length polymorphism (AFLP) and multilocus sequence typing (MLST) methods were used to investigate the genetic diversity and regional evolutionary patterns of 38 O. oeni strains isolated from different wine-making regions in China. The results indicated that AFLP was markedly more efficient than MLST for typing O. oeni strains. AFLP distinguished 37 DNA patterns compared to 7 sequence types identified using MLST, corresponding to discriminatory indices of 0.999 and 0.602, respectively. The AFLP results revealed a high level of genetic diversity among the O. oeni strains from different regions of China, since two subpopulations and an intraspecific homology higher than 60% were observed. Phylogenetic analysis of the O. oeni strains using the MLST method also identified two major phylogroups, which were differentiated into two distinct clonal complexes by minimum spanning tree analysis. Neither intragenic nor intergenic recombination verified the existence of the clonal population structure of the O. oeni strains.

Citations

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Impact of indigenous Oenococcus oeni and Lactiplantibacillus plantarum species co-culture on Cabernet Sauvignon wine malolactic fermentation: Kinetic parameters, color and aroma
Biying Zhang, Doudou Liu, Hui Liu, Jiaxin Shen, Jiaxuan Zhang, Ling He, Jin Li, Penghui Zhou, Xueqiang Guan, Shuwen Liu, Kan Shi
Food Chemistry: X.2024; 22: 101369. CrossRef
Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects
Haitam Lahmamsi, Samir Ananou, Rachid Lahlali, Abdessalem Tahiri
Folia Microbiologica.2024; 69(3): 465. CrossRef
Molecular and Physiological Properties of Indigenous Strains of Oenococcus oeni Selected from Nero di Troia Wine (Apulia, Italy)
Maria Stella Cappello, Vittorio Falco, Rosita Curcio, Giovanni Mita, Giacomo Zapparoli
Microorganisms.2022; 10(4): 795. CrossRef
Molecular typing tools for identifying and characterizing lactic acid bacteria: a review
Anshul Sharma, Sulhee Lee, Young-Seo Park
Food Science and Biotechnology.2020; 29(10): 1301. CrossRef

Phenotypic and genotypic correlates of daptomycin-resistant methicillin-susceptible Staphylococcus aureus clinical isolates: Kyoung-Mi Kang , Nagendra N. Mishra , Kun Taek Park , Gi-Yong Lee , Yong Ho Park , Arnold S. Bayer , Soo-Jin Yang; J. Microbiol. 2017;55(2):153-159. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6509-1

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Abstract

Daptomycin (DAP) has potent activity in vitro and in vivo against both methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) strains. DAP-resistance (DAP-R) in S. aureus has been mainly observed in MRSA strains, and has been linked to single nucleotide polymorphisms (SNPs) within the mprF gene leading to altered cell membrane (CM) phospholipid (PL) profiles, enhanced positive surface charge, and changes in CM fluidity. The current study was designed to delineate whether these same genotypic and phenotypic perturbations are demonstrated in clinically-derived DAP-R MSSA strains. We used three isogenic DAP-susceptible (DAP-S)/DAP-R strainpairs and compared: (i) presence of mprF SNPs, (ii) temporal expression profiles of the two key determinants (mprF and dltABCD) of net positive surface charge, (iii) increased production of mprF-dependent lysinylated-phosphatidylglycerol (L-PG), (iv) positive surface charge assays, and (v) susceptibility to cationic host defense peptides (HDPs) of neutrophil and platelet origins. Similar to prior data in MRSA, DAP-R (vs DAP-S) MSSA strains exhibited hallmark hot-spot SNPs in mprF, enhanced and dysregulated expression of both mprF and dltA, L-PG overproduction, HDP resistance and enhanced positive surface charge profiles. However, in contrast to most DAP-R MRSA strains, there were no changes in CM fluidity seen. Thus, charge repulsion via mprF- and dlt-mediated enhancement of positive surface charge may be the main mechanism to explain DAP-R in MSSA strains.

Citations

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The Effect of Shock Gentamicin Concentrations on the Formation of Resistance and Small Colony Variants in Staphylococcus aureus
V. V. Gostev, O. S. Kalinogorskaya, O. S. Sulian, P. S. Chulkova, J. V. Sopova, M. E. Velizhanina, V. Yu. Pleshkov, V. A. Ageevets, S. V. Sidorenko
Antibiotics and Chemotherapy.2024; 68(9-10): 25. CrossRef
Investigating a possible link between antiseptic treatment and the increased occurrence of daptomycin-resistant Staphylococcus aureus
Andreas F. Wendel, Robin Otchwemah, Franziska Layer-Nicolaou, Frauke Mattner, Carlos J. Tellez-Castillo, Robert Skov, Henrik Oberländer, Guido Werner, Birgit Strommenger
Clinical Microbiology and Infection.2023; 29(10): 1334.e1. CrossRef
Acquisition of Daptomycin Resistance by Enterococcus faecium Confers Collateral Sensitivity to Glycopeptides
Weiliang Zeng, Luozhu Feng, Changrui Qian, Tao Chen, Sipei Wang, Ying Zhang, Xiangkuo Zheng, Lingbo Wang, Shixing Liu, Tieli Zhou, Yao Sun
Frontiers in Microbiology.2022;[Epub] CrossRef
A Decade of Research on Daptomycin
Scott D. Taylor
Synlett.2022; 33(17): 1695. CrossRef
Establishing the Structure–Activity Relationship between Phosphatidylglycerol and Daptomycin
Ryan Moreira, Scott D. Taylor
ACS Infectious Diseases.2022; 8(8): 1674. CrossRef
Polymyxin and lipopeptide antibiotics: membrane-targeting drugs of last resort
Elizabeth V. K. Ledger, Akshay Sabnis, Andrew M. Edwards
Microbiology .2022;[Epub] CrossRef
Evaluating the Rapid Emergence of Daptomycin Resistance in Corynebacterium : a Multicenter Study
Kaitlin F. Mitchell, Erin McElvania, Meghan A. Wallace, Lauren E. Droske, Amy E. Robertson, Lars F. Westblade, Carey-Ann D. Burnham, Patricia J. Simner
Journal of Clinical Microbiology.2021;[Epub] CrossRef
Novel Daptomycin Tolerance and Resistance Mutations in Methicillin-Resistant Staphylococcus aureus from Adaptive Laboratory Evolution
Jordy Evan Sulaiman, Henry Lam, Patricia A. Bradford
mSphere.2021;[Epub] CrossRef
A narrative review of single-nucleotide polymorphism detection methods and their application in studies of Staphylococcus aureus
Ying Jian, Min Li
Journal of Bio-X Research.2021; 04(01): 1. CrossRef
Prolonged Exposure to β-Lactam Antibiotics Reestablishes Susceptibility of Daptomycin-Nonsusceptible Staphylococcus aureus to Daptomycin
Rachel E. Jenson, Sarah L. Baines, Benjamin P. Howden, Nagendra N. Mishra, Sabrina Farah, Cassandra Lew, Andrew D. Berti, Sanjay K. Shukla, Arnold S. Bayer, Warren E. Rose
Antimicrobial Agents and Chemotherapy.2020;[Epub] CrossRef
Selection of Resistance to Daptomycin in Methicillin-Resistant Staphylococcus aureus: Role of Homo- and Hetero-Mutations
V. V. Gostev, Yu. V. Sopova, O. S. Kalinogorskaya, I. A. Tsvetkova, S. V. Sidorenko
Russian Journal of Genetics.2020; 56(3): 289. CrossRef
Association of mprF mutations with cross-resistance to daptomycin and vancomycin in methicillin-resistant Staphylococcus aureus (MRSA)
Kanate Thitiananpakorn, Yoshifumi Aiba, Xin-Ee Tan, Shinya Watanabe, Kotaro Kiga, Yusuke Sato’o, Tanit Boonsiri, Feng-Yu Li, Teppei Sasahara, Yusuke Taki, Aa Haeruman Azam, Yuancheng Zhang, Longzhu Cui
Scientific Reports.2020;[Epub] CrossRef
Multidrug-Resistant Bacteria and Alternative Methods to Control Them: An Overview
Roberto Vivas, Ana Andréa Teixeira Barbosa, Silvio Santana Dolabela, Sona Jain
Microbial Drug Resistance.2019; 25(6): 890. CrossRef
Insights Into the Evolution of Staphylococcus aureus Daptomycin Resistance From an in vitro Bioreactor Model
Erica Lasek-Nesselquist, Jackson Lu, Ryan Schneider, Zhuo Ma, Vincenzo Russo, Smruti Mishra, Manjunath P. Pai, Janice D. Pata, Kathleen A. McDonough, Meenakshi Malik
Frontiers in Microbiology.2019;[Epub] CrossRef
Antibiotic Resistance and the MRSA Problem
Martin Vestergaard, Dorte Frees, Hanne Ingmer, Vincent A. Fischetti, Richard P. Novick, Joseph J. Ferretti, Daniel A. Portnoy, Miriam Braunstein, Julian I. Rood
Microbiology Spectrum.2019;[Epub] CrossRef
An entirely fmoc solid phase approach to the synthesis of daptomycin analogs
Ghufran Barnawi, Michael Noden, Robert Taylor, Chuda Lohani, David Beriashvili, Michael Palmer, Scott D. Taylor
Peptide Science.2019;[Epub] CrossRef
One Drug Multiple Targets: An Approach To Predict Drug Efficacies on Bacterial Strains Differing in Membrane Composition
Ayan Majumder, Malay Ranjan Biswal, Meher K. Prakash
ACS Omega.2019; 4(3): 4977. CrossRef
Daptomycin resistance in methicillin-resistant Staphylococcus aureus is conferred by IS256 insertion in the promoter of mprF along with mutations in mprF and walK
Yuyao Yin, Hongbin Chen, Shuguang Li, Hua Gao, Shijun Sun, Henan Li, Ruobing Wang, Longyang Jin, Yudong Liu, Hui Wang
International Journal of Antimicrobial Agents.2019; 54(6): 673. CrossRef
IS256-Mediated Overexpression of the WalKR Two-Component System Regulon Contributes to Reduced Vancomycin Susceptibility in a Staphylococcus aureus Clinical Isolate
Makoto Kuroda, Tsuyoshi Sekizuka, Hidehito Matsui, Jun Ohsuga, Toshio Ohshima, Hideaki Hanaki
Frontiers in Microbiology.2019;[Epub] CrossRef
A partial reconstitution implicates DltD in catalyzing lipoteichoic acid d-alanylation
B. McKay Wood, John P. Santa Maria, Leigh M. Matano, Christopher R. Vickery, Suzanne Walker
Journal of Biological Chemistry.2018; 293(46): 17985. CrossRef
Daptomycin Resistant Staphylococcus aureus Clinical Strain With Novel Non-synonymous Mutations in the mprF and vraS Genes: A New Insight Into Daptomycin Resistance
Artur J. Sabat, Marco Tinelli, Hajo Grundmann, Viktoria Akkerboom, Monica Monaco, Maria Del Grosso, Giulia Errico, Annalisa Pantosti, Alexander W. Friedrich
Frontiers in Microbiology.2018;[Epub] CrossRef
Daptomycin: New Insights into an Antibiotic of Last Resort
Vera Pader, Andrew M Edwards
Future Microbiology.2017; 12(6): 461. CrossRef

Genetic diversity of Clavispora lusitaniae isolated from Agave fourcroydes Lem, as revealed by DNA fingerprinting: Daisy Pérez-Brito , Anuar Magaña-Alvarez , Patricia Lappe-Oliveras , Alberto Cortes-Velazquez , Claudia Torres-Calzada , Teófilo Herrera-Suarez , Alfonso Larqué-Saavedra , Raul Tapia-Tussell; J. Microbiol. 2015;53(1):14-20. Published online January 4, 2015; DOI: https://doi.org/10.1007/s12275-015-4373-4

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Abstract

This study characterized Clavispora lusitaniae strains isolated from different stages of the processing and early fermentation of a henequen (Agave fourcroydes) spirit produced in Yucatan, Mexico using a molecular technique. Sixteen strains identified based on morphological features, obtained from different substrates, were typed molecularly. Nine different versions of the divergent D1/D2 domain of the large-subunit ribosomal DNA sequence were identified among the C. lusitaniae strains. The greatest degree of polymorphism was found in the 90-bp structural motif of the D2 domain. The MSP-PCR technique was able to differentiate 100% of the isolates. This study provides significant insight into the genetic diversity of the mycobiota present during the henequen fermentation process, especially that of C. lusitaniae, for which only a few studies in plants have been published. The applied MSP-PCR markers were very efficient in revealing polymorphisms between isolates of this species.

Citations

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Clavispora lusitaniae: From a saprophytic yeast to an emergent pathogen
Olga C. Rojas, Alexandra M. Montoya, Rogelio de J. Treviño-Rangel
Fungal Biology.2024; 128(5): 1933. CrossRef
Effect of precursors and stress factors on yeast isolated from fermented maesil extract and their biogenic amine formation
So Hee Yoon, Sanghyeon Lee, Sun-Young Lee, BoKyung Moon
Food Science and Biotechnology.2024; 33(1): 211. CrossRef
Isolation of Clavispora lusitaniae from the Oral Cavity of Immunocompetent Young Adults from the North of Mexico
Olga C. Rojas, Cintia Amaral-Montesino, Soraya Mendoza-Olazaran, Diego Carrión-Alvarez, Rafael González-Álvarez, Alexandra M. Montoya
Indian Journal of Microbiology.2024; 64(2): 475. CrossRef
Influence of the Biotechnological Process of Mezcal Fermentation on Yeast Diversity in Four palenques of Oaxaca, Mexico
Victor Adrian Espinoza-Martinez, Peggy Elizabeth Alvarez-Gutierrez, Felipe de Jesus Palma-Cruz, Raul Enriquez-Valencia, Marcos Pedro Ramirez-Lopez, Claudia Lopez-Sanchez, Hector Gilberto Vazquez-Lopez
Beverages.2023; 9(4): 99. CrossRef
A novel strategy to construct multi-strain starter cultures: an insight to evolve from natural to directed fermentation
J. L. Navarrete-Bolaños, O. Serrato-Joya
Preparative Biochemistry & Biotechnology.2023; 53(10): 1199. CrossRef
Environmental reservoirs of the drug-resistant pathogenic yeast Candida auris
Ayorinde B. Akinbobola, Ryan Kean, Syed Manzoor Ahmed Hanifi, Richard S. Quilliam, N.Luisa Hiller
PLOS Pathogens.2023; 19(4): e1011268. CrossRef
Bioremediation potential and lead removal capacity of heavy metal-tolerant yeasts isolated from Dayet Oum Ghellaz Lake water (northwest of Algeria)
Chahrazed Aibeche, Nawel Selami, Fatima El-Houaria Zitouni-Haouar, Khadidja Oeunzar, Amira Addou, Meriem Kaid-Harche, Abderrezak Djabeur
International Microbiology.2022; 25(1): 61. CrossRef
Phylogeny, evolution, and potential ecological relationship of cytochrome CYP52 enzymes in Saccharomycetales yeasts
Jossue Ortiz-Álvarez, Arturo Becerra-Bracho, Alfonso Méndez-Tenorio, Jazmin Murcia-Garzón, Lourdes Villa-Tanaca, César Hernández-Rodríguez
Scientific Reports.2020;[Epub] CrossRef
Yeast Microbiota during Sauerkraut Fermentation and Its Characteristics
Paweł Satora, Magdalena Skotniczny, Szymon Strnad, Katarína Ženišová
International Journal of Molecular Sciences.2020; 21(24): 9699. CrossRef
Potential production of 2-phenylethanol and 2-phenylethylacetate by non-Saccharomyces yeasts from Agave durangensis
Pablo Jaciel Adame-Soto, Elva Teresa Aréchiga-Carvajal, Mercedes G López, Silvia Marina González-Herrera, Martha Rocio Moreno-Jiménez, Norma Urtiz-Estrada, Olga Miriam Rutiaga-Quiñones
Annals of Microbiology.2019; 69(9): 989. CrossRef
Genetic variation of Colletotrichum magnum isolated from Carica papaya as revealed by DNA fingerprinting
Daisy Pérez-Brito, Alberto Cortes-Velázquez, Teresita Valencia-Yah, Anuar Magaña-Álvarez, Cuauhtémoc Navarro, Blanca Moreno, Steven Quiroga, Raúl Tapia-Tussell
Journal of Microbiology.2018; 56(11): 813. CrossRef

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

Allelic MHC Class I Chain Related B (MICB) Molecules Affect the Binding to the Human Cytomegalovirus (HCMV) Unique Long 16 (UL16) Protein: Implications for Immune Surveillance: Kanya Klumkrathok , Amonrat Jumnainsong , Chanvit Leelayuwat; J. Microbiol. 2013;51(2):241-246. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2514-1

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Abstract: Unique long 16 (UL16) is a viral glycoprotein produced in a host cell infected with human cytomegalovirus (HCMV). It down regulates surface expression of MICB, one of the NKG2D ligands, by forming stable intracellular complexes and retained in the endoplasmic reticulum. Down expression of MICB renders cells less susceptible to NK cell lysis via the NKG2D receptor. Diverse UL16 sequences were identified from different strains of HCMV. MICB is known to be polymorphic. It is not known whether these polymorphisms affect the interactions between these molecules leading to alteration of the immune surveillance of HCMV. The soluble Fc fusion variant UL16 proteins from four laboratory and clinical isolates (AD169, Toledo, PH, and TR) were produced. Four allelic MICB alleles (008, 003, 004, and 00502) were cloned and stable cell lines expressing these MICB alleles were produced. The binding activities of variant UL16 to allelic MICB proteins were determined by flow cytometry. The variants of UL16 proteins did not affect the binding activities to allelic MICB proteins. However, diverse MICB alleles differentially bound UL16. We found that MICB*008 which contains methionine and asparagine at the amino acid positions 98 and 113, respectively, in the alpha 2 domain showed decreased binding activities to UL16 when compared to MICB*003, 004, and MICB*00502 containing isoleucine and aspartic acid, respectively. This finding may imply that MICB*008 is a protective allele and involved in the immune surveillance of HCMV infected patients.

Application of Terminal Restriction Fragment Length Polymorphism (T-RFLP) Analysis to Monitor Effect of Biocontrol Agents on Rhizosphere Microbial Community of Hot Pepper (Capsicum annuum L.): Young Tae Kim , Myoungho Cho , Je Yong Jeong , Hyang Burm Lee , Seung Bum Kim; J. Microbiol. 2010;48(5):566-572. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0126-6

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Abstract: Microbial communities in hot pepper (Capsicum annuum L.) cultivation fields under different cultivation methods were investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis. Rhizosphere soil and leaf samples were collected from control, conventional and nature-friendly cultivation fields between May and July, 2009. Two Bacillus subtilis strains were applied to nature-friendly cultivation fields as biocontrol agents during the sampling period. Relative abundances of bacteria and plant pathogenic fungi related T-RFs were also measured to monitor the effect of biocontrol agents on potential plant pathogenic fungi. In the principal component analysis (PCA) based on T-RFLP profiles, the microbial communities from rhizosphere soil samples in July, including bacteria and fungi, showed distinct difference between nature-friendly cultivation fields and other cultivation fields. However, there was no correlation between cultivation methods and leaf microbial communities at any sampling period. Changes in the abundance of bacteria related T-RF in the rhizosphere of nature-friendly cultivation fields were observed clearly two months after application of biocontrol agent, while the abundance of plant pathogenic fungi related T-RFs significantly decreased.

Molecular Characterization of Polychlorinated Biphenyl-Dechlorinating Populations in Contaminated Sediments: Kyoung-Hee Oh , Ellen B. Ostrofsky , Young-Cheol Cho; J. Microbiol. 2008;46(2):165-173. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0214-4

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11 Scopus

Abstract: Polychlorinated biphenyl (PCB)-dechlorinating microorganisms were characterized in PCB-contaminated sediments using amplified ribosomal DNA restriction analysis (ARDRA). The sediments were prepared by spiking Aroclor 1248 into PCB-free sediments, and were inoculated with microorganisms eluted from St. Lawrence River sediments. PCB-free sediments inoculated with the same inoculum served as the control. Four restriction fragment length polymorphism (RFLP) groups in the eubacterial and two in the archaeal domain were found exclusively in PCB-spiked sediment clone libraries. Sequence analysis of the four eubacterial clones showed homology to Escherichia coli, Lactosphaera pasteurii, Clostridium thermocellum, and Dehalobacter restrictus. The predominant archaeal sequence in the PCB-spiked sediment clone library was closely related to Methanosarcina barkeri, which appear to support earlier findings that methanogens are involved in PCB dechlorination. When the dot-blot hybridization was performed between the sediment DNA extract and the probes designed with eubacterial RFLP groups, the intensity of two of eubacterial RFLP groups, which showed high sequence homology to C. pascui and D. restrictus, was highly correlated with the number of dechlorinating microorganisms suggesting these two members intend to contribute to PCB dechlorination.

PCR-RFLP and Sequence Analysis of the rDNA ITS Region in the Fusarium spp.: Lee , Young-Mi , Yong-Keel Choi , Byung-Re Min; J. Microbiol. 2000;38(2):66-73.

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Abstract: To investigate the genetic relationship among 12 species belonging to the Fusarium section Martiella, Dlaminia, Gibbosum, Arthrosporiella, Liseola and Elegans, the internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA) were amplified with primer pITS1 and pITS4 using the polymerase chain reaction (PCR). After the amplified products were digested with 7 restriction enzymes, restriction fragment length polymorphism (RFLP) patterns were analyzed. The partial nucleotide sequences of the ITS region were determined and compared. Little variation was observed in the size of the amplified product having sizes of 550bp or 570bp. Based on the RFLP analysis, the 12 species studied were divided into 5 RFLP types. In particular, strains belonging to the section Martiella were separated into three RFLP types. Interestingly, the RFLP type of F. solani f. sp. piperis was identical with that of isolates belonging to the section Elegans. In the dendrogram derived from RFLP analysis of the ITS region, the Fusarium spp. examined were divided into two major groups. In general, section Martiella excluding F. solani f. sp. piperis showed relatively low similarity with the other section. The dendrogram based on the sequencing analysis of the ITS2 region also gave the same results as that of the RFLP analysis. As expected, 5.8S, a coding region, was highly conserved, whereas the ITS2 region was more variable and informative. The difference in the ITS2 region between the length of F. solani and its formae speciales excluding F. solani f. sp. piperis and that of other species was caused by the insertion/deletion of nucleotides in positions 143-148 and 179-192.

High Prevalence of the China 1 Strain of Epstein-Barr Virus in Korea as Determined by Sequence Polymorphisms in the Carboxy-Terminal Tail of LMP1: Sung-Gyu Cho , Won-Keun Lee; J. Microbiol. 2003;41(2):129-136.

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Abstract: The Epstein-Barr virus (EBV)-encoded latent membrane protein 1 (LMP1) exhibits considerable sequence heterogeneity among EBV isolates. Seven distinct EBV strains have been defined based on sequence polymorphisms in the LMP1 gene, which are designated China 1, China 2, China 3, Alaskan, Mediterranean, NC, and the B95-8 strains. In this study, we analyzed a 30-bp deletion and sequence variations in the carboxy-terminal region of the LMP1 gene in 12 EBV isolates from spontaneous lymphoblastoid cell lines derived from individuals with non-EBV associated cancers in Korea. Eleven of the 12 isolates showed a 30-bp deletion spanning LMP1 amino acids 342 to 353, suggesting a high prevalence of the LMP1 30-bp deletion variant among EBV isolates in Korea. In addition, all 12 isolates had a 15-bp common deletion in the 33-bp repeat region and multiple base-pair changes relative to the prototype B95-8 EBV strain along with variations in the number of the 33-bp repeats. The bp changes at positions 168746, 168694, 168687, 168395, 168357, 168355, 168631, 168320, 168308, 168295, and 168225 were highly conserved among the isolates. Comparative analysis of sequence change patterns in the LMP1 carboxy-terminal coding region identified nine 30-bp deletion variants as China 1, two deletion variants as a possible interstrain between the Alaskan and China 1 strains, and a single undeleted variant as a possible variant of the Alaskan strain. These results suggest the predominance of the China 1 EBV strain in the Korean population.

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