Journal Articles
- Quantitative Analysis of RNA Polymerase Slippages for Production of P3N‑PIPO Trans‑frame Fusion Proteins in Potyvirids
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Dongjin Choi , Yoonsoo Hahn
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J. Microbiol. 2023;61(10):917-927. Published online October 16, 2023
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DOI: https://doi.org/10.1007/s12275-023-00083-z
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Abstract
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Potyvirids, members of the family Potyviridae, produce the P3N-PIPO protein, which is crucial for the cell-to-cell transport
of viral genomic RNAs. The production of P3N-PIPO requires an adenine (A) insertion caused by RNA polymerase slippage
at a conserved GAA AAA A (
GA6) sequence preceding the PIPO open reading frame. Presently, the slippage rate of
RNA polymerase has been estimated in only a few potyvirids, ranging from 0.8 to 2.1%. In this study, we analyzed publicly
available plant RNA-seq data and identified 19 genome contigs from 13 distinct potyvirids. We further investigated the RNA
polymerase slippage rates at the GA6
motif. Our analysis revealed that the frequency of the A insertion variant ranges from
0.53 to 4.07% in 11 potyviruses (genus Potyvirus). For the two macluraviruses (genus Macluravirus), the frequency of the
A insertion variant was found to be 0.72% and 10.96% respectively. Notably, the estimated RNA polymerase slippage rates
for 12 out of the 13 investigated potyvirids were reported for the first time in this study. Our findings underscore the value of
plant RNA-seq data for quantitative analysis of potyvirid genome variants, specifically at the GA6
slippage site, and contribute
to a more comprehensive understanding of the RNA polymerase slippage phenomenon in potyvirids.
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Citations
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- Discovery of novel tepovirus genomes with a nucleic acid-binding protein homolog by systematic analysis of plant transcriptome data
Dongjin Choi, Hyerin Park, Seungwoo Baek, Myeung Seok Choi, Sylvain Legay, Gea Guerriero, Jean-François Hausman, Yoonsoo Hahn
Acta Virologica.2025;[Epub] CrossRef - Potyviral Helper-Component Protease: Multifaced Functions and Interactions with Host Proteins
Veronika Hýsková, Kateřina Bělonožníková, Josef Chmelík, Hana Hoffmeisterová, Noemi Čeřovská, Tomáš Moravec, Helena Ryšlavá
Plants.2024; 13(9): 1236. CrossRef - Reconceptualizing transcriptional slippage in plant RNA viruses
Adrian A. Valli, María Luisa Domingo-Calap, Alfonso González de Prádena, Juan Antonio García, Hongguang Cui, Cécile Desbiez, Juan José López-Moya, Shou-Wei Ding, Andrew Firth
mBio.2024;[Epub] CrossRef
- Comparative genomics analysis of Pediococcus acidilactici species
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Zhenzhen Li , Qi Song , Mingming Wang , Junli Ren , Songling Liu , Shancen Zhao
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J. Microbiol. 2021;59(6):573-583. Published online May 15, 2021
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DOI: https://doi.org/10.1007/s12275-021-0618-6
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54
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18
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Abstract
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Pediococcus acidilactici is a reliable bacteriocin producer and
a promising probiotic species with wide application in the
food and health industry. However, the underlying genetic
features of this species have not been analyzed. In this study,
we performed a comprehensive comparative genomic analysis
of 41 P. acidilactici strains from various ecological niches.
The bacteriocin production of 41 strains were predicted and
three kinds of bacteriocin encoding genes were identified in
11 P. acidilactici strains, namely pediocin PA-1, enterolysin
A, and colicin-B. Moreover, whole-genome analysis showed
a high genetic diversity within the population, mainly related
to a large proportion of variable genomes, mobile elements,
and hypothetical genes obtained through horizontal gene
transfer. In addition, comparative genomics also facilitated
the genetic explanation of the adaptation for host environment,
which specify the protection mechanism against the
invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as
carbohydrate fermentation. The 41 strains of P. acidilactici
can metabolize a variety of carbon sources, which enhances
the adaptability of this species and survival in different environments.
This study evaluated the antibacterial ability, genome
evolution, and ecological flexibility of P. acidilactici
from the perspective of genetics and provides strong supporting
evidence for its industrial development and application.
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Citations
Citations to this article as recorded by

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Pediococcus acidilactici Y01 reduces HFD-induced obesity via altering gut microbiota and metabolomic profiles and modulating adipose tissue macrophage M1/M2 polarization
Yujing Wang, Yu Xue, Huan Xu, Qian Zhu, Kaili Qin, Zhonglei He, Aixiang Huang, Min Mu, Xinrong Tao
Food & Function.2025;[Epub] CrossRef -
Draft genome sequence of
Pediococcus acidilactici
3G3 isolated from Philippine fermented pork
Zachary B. Lara, Mia Beatriz C. Amoranto, Francisco B. Elegado, Leslie Michelle M. Dalmacio, Marilen Parungao Balolong, Catherine Putonti
Microbiology Resource Announcements.2024;[Epub] CrossRef - The Potential of Pediococcus acidilactici Cell-Free Supernatant as a Preservative in Food Packaging Materials
Katherine Kho, Adinda Darwanti Kadar, Mario Donald Bani, Ihsan Tria Pramanda, Leon Martin, Matthew Chrisdianto, Ferren Pratama, Putu Virgina Partha Devanthi
Foods.2024; 13(5): 644. CrossRef - The complete genome sequences of the two novel probiotics were isolated from the human gut microbiota: Pediococcus acidilactici WNYM01 and Pediococcus acidilactici WNYM02, vitamin B9, and B2-producers
Wagiha S. Elkalla, Yasser M. Ragab, Mohamed A. Ramadan, Nahla M. Mansour
Egyptian Pharmaceutical Journal.2024; 23(4): 702. CrossRef - Effects of Pediococcus acidilactici and Rhizopus Oryzae on protein degradation and flavor formation in fermented mutton sausages
Zihan Li, Wei Su, Yingchun Mu, Qi Qi, Li Jiang
LWT.2024; 213: 117075. CrossRef - Putative Probiotic Ligilactobacillus salivarius Strains Isolated from the Intestines of Meat-Type Pigeon Squabs
Shaoqi Tian, Yinhong Jiang, Qiannan Han, Chuang Meng, Feng Ji, Bin Zhou, Manhong Ye
Probiotics and Antimicrobial Proteins.2024;[Epub] CrossRef - Effect of ginsenoside fermented by Pediococcus acidilactici XM-06 on preventing diarrhea in mice via regulating intestinal barrier function and gut microbiota
Wen-Man Xu, Qi Liu, Si-Yao Fan, Zi-Xin Wang, Shi-Rui Lu, Jie Liu, Hong-Jie Piao, Wenxiu Ji, Wei-Wei Dong
Journal of Functional Foods.2024; 123: 106594. CrossRef - Population and functional genomics of lactic acid bacteria, an important group of food microorganism: Current knowledge, challenges, and perspectives
Weicheng Li, Qiong Wu, Lai‐yu Kwok, Heping Zhang, Renyou Gan, Zhihong Sun
Food Frontiers.2024; 5(1): 3. CrossRef - CRISPR-Cas systems of lactic acid bacteria and applications in food science
Yanhua Cui, Xiaojun Qu
Biotechnology Advances.2024; 71: 108323. CrossRef - Analyzing the genetic diversity and biotechnological potential of Leuconostoc pseudomesenteroides by comparative genomics
Ismail Gumustop, Fatih Ortakci
Frontiers in Microbiology.2023;[Epub] CrossRef - Recent developments in horizontal gene transfer with the adaptive innovation of fermented foods
Ruhong Wang, Junrui Wu, Nan Jiang, Hao Lin, Feiyu An, Chen Wu, Xiqing Yue, Haisu Shi, Rina Wu
Critical Reviews in Food Science and Nutrition.2023; 63(5): 569. CrossRef - Changes in Lacto-Fermented Agaricus bisporus (White and Brown Varieties) Mushroom Characteristics, including Biogenic Amine and Volatile Compound Formation
Elena Bartkiene, Paulina Zarovaite, Vytaute Starkute, Ernestas Mockus, Egle Zokaityte, Gintare Zokaityte, João Miguel Rocha, Romas Ruibys, Dovile Klupsaite
Foods.2023; 12(13): 2441. CrossRef - Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6, Two Bacteriocinogenic Isolated Strains from Andalusian Spontaneous Fermented Sausages
José García-López, Claudia Teso-Pérez, Antonio Martín-Platero, Juan Peralta-Sánchez, Juristo Fonollá-Joya, Manuel Martínez-Bueno, Alberto Baños
Foods.2023; 12(13): 2445. CrossRef - Exploring the impact of initial moisture content on microbial community and flavor generation in Xiaoqu baijiu fermentation
Huan Wang, Chunhong Sun, Shengzhi Yang, Yulei Ruan, Linjie Lyu, Xuewu Guo, Xiaole Wu, Yefu Chen
Food Chemistry: X.2023; 20: 100981. CrossRef - Screening and Constructing a Library of Promoter-5′-UTR Complexes with Gradient Strength in Pediococcus acidilactici
Yize Jia, Chao Huang, Yin Mao, Shenghu Zhou, Yu Deng
ACS Synthetic Biology.2023; 12(6): 1794. CrossRef - Novel pathways in bacteriocin synthesis by lactic acid bacteria with special reference to ethnic fermented foods
Basista Rabina Sharma, Prakash M. Halami, Jyoti Prakash Tamang
Food Science and Biotechnology.2022; 31(1): 1. CrossRef - Genomic analysis and in vivo efficacy of Pediococcus acidilactici as a potential probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections
Hassan M. Al-Emran, Jannatul Ferdouse Moon, Md. Liton Miah, Nigar Sultana Meghla, Rine Christopher Reuben, Mohammad Jashim Uddin, Habiba Ibnat, Shovon Lal Sarkar, Pravas Chandra Roy, M. Shaminur Rahman, A. S. M. Rubayet Ul Alam, Ovinu Kibria Islam, Iqbal
Scientific Reports.2022;[Epub] CrossRef - Production of Antibacterial Agents and Genomic Characteristics of
Probiotics Strains for the Foodborne Pathogen Control
Su Jin Kim, Jin Song Shin, Han Sol Park, Ji Seop Song, Ki Won Lee, Woo-Suk Bang, Tae Jin Cho
Current Topic in Lactic Acid Bacteria and Probiotics.2022; 8(1): 1. CrossRef
- The effects of cigarettes and alcohol on intestinal microbiota in healthy men
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Renbin Lin , Yawen Zhang , Luyi Chen , Yadong Qi , Jiamin He , Mengjia Hu , Ying Zhang , Lina Fan , Tao Yang , Lan Wang , Misi Si , Shujie Chen
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J. Microbiol. 2020;58(11):926-937. Published online October 30, 2020
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DOI: https://doi.org/10.1007/s12275-020-0006-7
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51
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Abstract
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Human intestinal microbiota is affected by the exogenous
microenvironment. This study aimed to determine the effects
of cigarettes and alcohol on the gut microbiota of healthy
men. In total, 116 healthy male subjects were enrolled and
divided into four groups: non-smoking and non-drinking
(Group A), smoking only (Group B), drinking only (Group
C), and smoking and drinking combined (Group D). Fecal
samples were collected and sequenced using 16S rRNA to
analyze the microbial composition. Short-chain fatty acid
(SCFAs) levels in feces were determined by gas chromatography.
We found that cigarette and alcohol consumptions
can alter overall composition of gut microbiota in healthy
men. The relative abundances of phylum Bacteroidetes and
Firmicutes and more than 40 genera were changed with cigarette
and alcohol consumptions. SCFAs decreased with smoking
and alcohol consumption. Multivariate analysis indicated
that when compared with group A, group B/C/D had higher
Bacteroides, and lower Phascolarctobacterium, Ruminococcaceae_
UCG-002, Ruminococcaceae_UCG-003, and Ruminiclostridium_
9 regardless of BMI and age. Additionally, the
abundance of Bacteroides was positively correlated with the
smoking pack-year (r = 0.207, p < 0.05), the abundance of predicted
pathway of bacterial toxins (r = 0.3672, p < 0.001) and
the level of carcinoembryonic antigen in host (r = 0.318, p
< 0.01). Group D shared similar microbial construction with
group B, but exerted differences far from group C with lower
abundance of Haemophilus. These results demonstrated that
cigarette and alcohol consumption separately affected the
intestinal microbiota and function in healthy men; furthermore,
the co-occurrence of cigarette and alcohol didn’t exacerbate
the dysbiosis and cigarette played the predominated
role on the alteration.
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Citations
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- Potential roles of cigarette smoking on gut microbiota profile among Chinese men
Jiayao Fan, Fangfang Zeng, Haili Zhong, Jun Cai, Wentao Shen, Chunxiao Cheng, Chunfeng He, Yuanjiao Liu, Yuan Zhou, Shujie Chen, Yimin Zhu, Tao Liu, Ju-Sheng Zheng, Lan Wang, Yu-Ming Chen, Wenjun Ma, Dan Zhou
BMC Medicine.2025;[Epub] CrossRef - Gut Microbiota at the Crossroad of Hepatic Oxidative Stress and MASLD
Fabrizio Termite, Sebastiano Archilei, Francesca D’Ambrosio, Lucrezia Petrucci, Nicholas Viceconti, Roberta Iaccarino, Antonio Liguori, Antonio Gasbarrini, Luca Miele
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Sun-Young Kim, So-Youn Woo, Hyung-Lae Kim, Yoosoo Chang, Seungho Ryu, Han-Na Kim
Journal of Affective Disorders.2025; 376: 26. CrossRef - An Investigation into the Relationship of Circulating Gut Microbiome Molecules and Inflammatory Markers with the Risk of Incident Dementia in Later Life
Kolade Oluwagbemigun, Andrea Anesi, Urska Vrhovsek, Fulvio Mattivi, Pamela Martino Adami, Michael Pentzek, Martin Scherer, Steffi G. Riedel-Heller, Siegfried Weyerer, Horst Bickel, Birgitt Wiese, Matthias Schmid, John F. Cryan, Alfredo Ramirez, Michael Wa
Molecular Neurobiology.2024; 61(12): 9776. CrossRef - Effect of chronic alcohol consumption on oral microbiota in rats with periodontitis
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Zhouhai Zhu, Meng Wang, Ying Guan, Meng Li, Qiyuan Peng, Ning Zheng, Wenbin Ma
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Neil Daniel, Flavia Genua, Mazda Jenab, Ana-Lucia Mayén, Anastasia Chrysovalantou Chatziioannou, Pekka Keski-Rahkonen, David J. Hughes
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Translational Psychiatry.2021;[Epub] CrossRef - Microbiology of the American Smokeless Tobacco
A. J. Rivera, R. E. Tyx
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Research Support, Non-U.S. Gov'ts
- Microbial Community on Healthy and Diseased Leaves of an Invasive Plant Eupatorium adenophorum in Southwest China
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Zhen-Xin Zhou , Huan Jiang , Chen Yang , Ming-Zhi Yang , Han-Bo Zhang
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J. Microbiol. 2010;48(2):139-145. Published online May 1, 2010
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DOI: https://doi.org/10.1007/s12275-010-9185-y
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Abstract
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Invasive plants have caused great economic losses and environmental problems worldwide. Eupatorium adenophorum is one of the most invasive weeds in China. To better understand its invasive mechanisms, in the present paper, the microbial communities of healthy and diseased leaves of E. adenophorum were obtained using both culture-independent and -dependent methods and their diversities were compared. The bacteria obtained from culture-independent method belong to Proteobacteria (95.8%), Actinobacteria (2.1%), and Firmicutes (2.1%) and fungi belong to Ascomycota (65.2%) and Basidiomycota (34.8%). Very few overlapped microbial species were found by culture-dependent and -independent methods. Healthy leaves display higher bacterial diversity than diseased leaves. Phylogenetic structures are very different between healthy and diseased phyllosphere microbial communities. Bacteria close to Acinetobacter and Pseudomonas were dominant on healthy leaves, whereas those close to Shigella were dominant on diseased leaves. 52.9% of fungal clones from healthy leaves were Ustilaginomycetes, close to Rhodotorula phylloplana and uncultured basidomycete; by contrast, 60% of clones from diseased leaves were Lecanoromycetes, close to Umbilicaria muehlenbergii. No bacteria but four fungal strains phylogenetically close to Myrothecium sp. and Alternaria alternate were pathogenic to seedlings and detached leaves of the invasive plant. Therefore, this plant may be resistant to pathogens from bacteria but not fungi in its introduced range.
- Bacterial, Archaeal, and Eukaryal Diversity in the Intestines of Korean People
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Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Seong Woon Roh , Min-Soo Kim , Mi-Ja Jung , Si-Woo Lee , Jong-Yeol Kim , Jung-Hoon Yoon , Jin-Woo Bae
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J. Microbiol. 2008;46(5):491-501. Published online October 31, 2008
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DOI: https://doi.org/10.1007/s12275-008-0199-7
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Abstract
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The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).
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