Journal of Microbiology

Volume 52(5); May 2014

Research Support, Non-U.S. Gov't

Variations in 16S rRNA-based Microbiome Profiling between Pyrosequencing Runs and between Pyrosequencing Facilities: Minseok Kim , Zhongtang Yu; J. Microbiol. 2014;52(5):355-365. Published online April 11, 2014; DOI: https://doi.org/10.1007/s12275-014-3443-3

41 View
0 Download
32 Crossref

Pyrosequencing of 16S rRNA gene amplicons on the 454 FLX Titanium platform has been widely used to analyze microbiomes in various environments. However, different results may stem from variations among sequencing runs or among sequencing facilities. This study aimed to evaluate these variations between different pyrosequencing runs by sequencing 16S rRNA gene amplicon libraries generated from three sets of rumen samples twice each on the 454 FLX Titanium system at two independent sequencing facilities. Similar relative abundances were found for predominant taxa represented by large numbers of sequence reads but not for minor taxa represented by small numbers of sequence reads. The two sequencing facilities revealed different bac-terial profiles with respect to both predominant taxa and minor taxa, including the most predominant genus Prevo-tella, the family Lachnospiraceae, and the phylum Proteo-bacteria. Differences in primers used to generate amplicon libraries may be a major source of variations in microbiome profiling. Because different primers and regions of 16S rRNA genes are often used by different researchers, significant variations likely exist among studies. Quantitative interpre-tation for relative abundance of taxa, especially minor taxa, from prevalence of sequence reads and comparisons of re-sults from different studies should be done with caution.

Citations

Citations to this article as recorded by

Analysis of Alterations in Intestinal Flora in Chinese Elderly with Cardiovascular Disease and Its Association with Trimethylamine
Yannan He, Song Chen, Yuling Xue, Han Lu, Ziteng Li, Xianxian Jia, Yibing Ning, Qingbin Yuan, Shijie Wang
Nutrients.2024; 16(12): 1864. CrossRef
The association between the respiratory tract microbiome and clinical outcomes in patients with COPD
Suyun Yu, Huiping Zhang, Liping Wan, Min Xue, Yunfeng Zhang, Xiwen Gao
Microbiological Research.2023; 266: 127244. CrossRef
SVep1, a temperate phage of human oral commensal Streptococcus vestibularis
Miaomiao Wu, Yanpeng Zhu, Yuhui Yang, Yali Gong, Zongyue Chen, Binyou Liao, Yu Xiong, Xia Zhou, Yan Li
Frontiers in Microbiology.2023;[Epub] CrossRef
Influence of dietary organic trace minerals on enteric methane emissions and rumen microbiota of heat-stressed dairy steers
A-Rang Son, Mahfuzul Islam, Seon-Ho Kim, Sung-Sill Lee, Sang-Suk Lee
Journal of Animal Science and Technology.2023; 65(1): 132. CrossRef
Gut microbiota is a potential goalkeeper of dyslipidemia
Lirong Lei, Ning Zhao, Lei Zhang, Jiamei Chen, Xiaomin Liu, Shenghua Piao
Frontiers in Endocrinology.2022;[Epub] CrossRef
Analyzing the Complicated Connection Between Intestinal Microbiota and Cardiovascular Diseases
Tanishq Kumar, Rajoshee R Dutta, Vivek R Velagala, Benumadhab Ghosh, Abhay Mudey
Cureus.2022;[Epub] CrossRef
Seasonal Influence on Rumen Microbiota, Rumen Fermentation, and Enteric Methane Emissions of Holstein and Jersey Steers under the Same Total Mixed Ration
Mahfuzul Islam, Seon-Ho Kim, A-Rang Son, Sonny C. Ramos, Chang-Dae Jeong, Zhongtang Yu, Seung Ha Kang, Yong-Il Cho, Sung-Sill Lee, Kwang-Keun Cho, Sang-Suk Lee
Animals.2021; 11(4): 1184. CrossRef
Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages
Lucia Bailoni, Lisa Carraro, Marco Cardin, Barbara Cardazzo
Microorganisms.2021; 9(4): 754. CrossRef
Holstein and Jersey Steers Differ in Rumen Microbiota and Enteric Methane Emissions Even Fed the Same Total Mixed Ration
Mahfuzul Islam, Seon-Ho Kim, Sonny C. Ramos, Lovelia L. Mamuad, A-Rang Son, Zhongtang Yu, Sung-Sil Lee, Yong-Il Cho, Sang-Suk Lee
Frontiers in Microbiology.2021;[Epub] CrossRef
Ruminal resistome of dairy cattle is individualized and the resistotypes are associated with milking traits
Ming-Yuan Xue, Yun-Yi Xie, Yi-Fan Zhong, Jian-Xin Liu, Le Luo Guan, Hui-Zeng Sun
Animal Microbiome.2021;[Epub] CrossRef
Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle
Fuyong Li, Changxi Li, Yanhong Chen, Junhong Liu, Chunyan Zhang, Barry Irving, Carolyn Fitzsimmons, Graham Plastow, Le Luo Guan
Microbiome.2019;[Epub] CrossRef
Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants
R.J. Gruninger, G.O. Ribeiro, A. Cameron, T.A. McAllister
Animal.2019; 13(9): 1843. CrossRef
Testing culture purity in prokaryotes: criteria and challenges
Alexander V. Pinevich, Eugeny E. Andronov, Elizaveta V. Pershina, Agnia A. Pinevich, Helena Y. Dmitrieva
Antonie van Leeuwenhoek.2018; 111(9): 1509. CrossRef
Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile
Filippo Biscarini, Fiorentina Palazzo, Federica Castellani, Giulia Masetti, Lisa Grotta, Angelo Cichelli, Giuseppe Martino, Juan J Loor
PLOS ONE.2018; 13(11): e0205670. CrossRef
Ruminal methane emissions, metabolic, and microbial profile of Holstein steers fed forage and concentrate, separately or as a total mixed ration
Rajaraman Bharanidharan, Selvaraj Arokiyaraj, Eun Bae Kim, Chang Hyun Lee, Yang Won Woo, Youngjun Na, Danil Kim, Kyoung Hoon Kim, Alex V. Chaves
PLOS ONE.2018; 13(8): e0202446. CrossRef
Investigation of the core microbiome in main soil types from the East European plain
Elizaveta V. Pershina, Ekaterina A. Ivanova, Ilia O. Korvigo, Evgeny L. Chirak, Nurlan H. Sergaliev, Evgeny V. Abakumov, Nikolai A. Provorov, Evgeny E. Andronov
Science of The Total Environment.2018; 631-632: 1421. CrossRef
Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation
Thomas Hartinger, Nina Gresner, Karl-Heinz Südekum
Journal of Animal Science and Biotechnology.2018;[Epub] CrossRef
Assessment of Rumen Microbiota from a Large Dairy Cattle Cohort Reveals the Pan and Core Bacteriomes Contributing to Varied Phenotypes
Mingyuan Xue, Huizeng Sun, Xuehui Wu, Le Luo Guan, Jianxin Liu, Hideaki Nojiri
Applied and Environmental Microbiology.2018;[Epub] CrossRef
Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle
Fuyong Li, Le Luo Guan, Andrew J. McBain
Applied and Environmental Microbiology.2017;[Epub] CrossRef
Impact of micro‐environmental changes on respiratory tract infections with intracellular bacteria
Kensuke Shima, Jonas Coopmeiners, Simon Graspeuntner, Klaus Dalhoff, Jan Rupp
FEBS Letters.2016; 590(21): 3887. CrossRef
Diversity at low abundance: The phenomenon of the rare bacterial biosphere
M. Yu. Skopina, A. A. Vasileva, E. V. Pershina, A. V. Pinevich
Microbiology.2016; 85(3): 272. CrossRef
Intestinal Microbiota of Broiler Chickens As Affected by Litter Management Regimens
Lingling Wang, Mike Lilburn, Zhongtang Yu
Frontiers in Microbiology.2016;[Epub] CrossRef
Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches
Fuyong Li, Gemma Henderson, Xu Sun, Faith Cox, Peter H. Janssen, Le Luo Guan
Frontiers in Microbiology.2016;[Epub] CrossRef
The Bacteriomes of Ileal Mucosa and Cecal Content of Broiler Chickens and Turkeys as Revealed by Metagenomic Analysis
Shan Wei, Michael Lilburn, Zhongtang Yu
International Journal of Microbiology.2016; 2016: 1. CrossRef
Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy
Ting Luo, Usha Srinivasan, Kirtana Ramadugu, Kerby A. Shedden, Katherine Neiswanger, Erika Trumble, Jiean J. Li, Daniel W. McNeil, Richard J. Crout, Robert J. Weyant, Mary L. Marazita, Betsy Foxman, S.-J. Liu
Applied and Environmental Microbiology.2016; 82(18): 5519. CrossRef
The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline
Jérôme Lluch, Florence Servant, Sandrine Païssé, Carine Valle, Sophie Valière, Claire Kuchly, Gaëlle Vilchez, Cécile Donnadieu, Michael Courtney, Rémy Burcelin, Jacques Amar, Olivier Bouchez, Benjamin Lelouvier, Markus M. Heimesaat
PLOS ONE.2015; 10(11): e0142334. CrossRef
RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis1,2,3
T. A. McAllister, S. J. Meale, E. Valle, L. L. Guan, M. Zhou, W. J. Kelly, G. Henderson, G. T. Attwood, P. H. Janssen
Journal of Animal Science.2015; 93(4): 1431. CrossRef
Library preparation methodology can influence genomic and functional predictions in human microbiome research
Marcus B. Jones, Sarah K. Highlander, Ericka L. Anderson, Weizhong Li, Mark Dayrit, Niels Klitgord, Martin M. Fabani, Victor Seguritan, Jessica Green, David T. Pride, Shibu Yooseph, William Biggs, Karen E. Nelson, J. Craig Venter
Proceedings of the National Academy of Sciences.2015; 112(45): 14024. CrossRef
Role of the normal gut microbiota
Sai Manasa Jandhyala
World Journal of Gastroenterology.2015; 21(29): 8787. CrossRef
RUMINANT NUTRITION SYMPOSIUM: How to use data on the rumen microbiome to improve our understanding of ruminant nutrition1,2
J. L. Firkins, Z. Yu
Journal of Animal Science.2015; 93(4): 1450. CrossRef
Effect of Haylage and Monensin Supplementation on Ruminal Bacterial Communities of Feedlot Cattle
Minseok Kim, Tara L. Felix, Steve C. Loerch, Zhongtang Yu
Current Microbiology.2014; 69(2): 169. CrossRef
Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities
M. Kim, L. Wang, M. Morrison, Z. Yu
Journal of Applied Microbiology.2014; 117(4): 949. CrossRef

Journal Article

Comparative Analysis of Superantigen Genes in Staphylococcus xylosus and Staphylococcus aureus Isolates Collected from a Single Mammary Quarter of Cows with Mastitis: Karol Fijałkowski , Magdalena Struk , Jolanta Karakulska , Aleksandra Paszkowska , Stefania Giedrys-Kalemba , Helena Masiuk , Danuta Czernomysy-Furowicz , Paweł Nawrotek; J. Microbiol. 2014;52(5):366-372. Published online April 11, 2014; DOI: https://doi.org/10.1007/s12275-014-3436-2

51 View
0 Download
15 Crossref

Abstract

The purpose of this study was to analyze and compare genes encoding superantigens (SAgs) in Staphylococcus xylosus and Staphylococcus aureus isolates collected simultaneously from milk of the same cows with clinical mastitis. Genes encoding staphylococcal enterotoxins and enterotoxin-like proteins (sea-selu), toxic shock syndrome toxin 1 (tst-1) and exfolia-tive toxins (eta and etd) were investigated. It was found that among 30 isolates of S. xylosus, 16 (53.3%) harbored from 1 to 10 SAg genes. In total, in 16 SAg positive S. xylosus, 11 different enterotoxin genes were detected: sec, sed, seg, seh, sei, selm, seln, selo, selp, ser, selu and one etd gene encoding exfoliative toxin D. The most prevalent genes were ser, selu, and selo. Among all the positive isolates of S. xylosus, a total of 14 different SAg gene combinations were detected. One combination was repeated in 3 isolates, whereas the rest were detected only once. However, in the case of S. aureus all the 30 isolates harbored the same combination of SAg genes: seg, sei, selm, seln, selo and on the basis of PFGE analysis all belonged to the same clonal type. Also noteworthy was the observation that SAg genes detected in S. aureus have also been found in S. xylosus. The findings of this study further extend previous observations that SAg genes are present not only in S. aureus but also in coagulase-negative staphy-lococci, including S. xylosus. Therefore, taking into account that the SAg genes are encoded on mobile genetic elements it is possible that these genes can be transferred between different species of coexisting staphylococci.

Citations

Citations to this article as recorded by

Whole genome sequence and comparative genomics analysis of multidrug-resistant Staphylococcus xylosus NM36 isolated from a cow with mastitis in Basrah city
Hassan M. Al-Tameemi, Husam Al-Hraishawi, Murtakab Y. Al-Hejjaj, Noor S. Abdulah, Haider R. Alrafas, Yessar A. Dawood
Journal of Genetic Engineering and Biotechnology.2023; 21(1): 163. CrossRef
Staphylococcus xylosus and Staphylococcus aureus as commensals and pathogens on murine skin
Michael Battaglia, Lee Ann Garrett-Sinha
Laboratory Animal Research.2023;[Epub] CrossRef
Identification of the Enterotoxigenic Potential of Staphylococcus spp. from Raw Milk and Raw Milk Cheeses
Patryk Wiśniewski, Joanna Gajewska, Anna Zadernowska, Wioleta Chajęcka-Wierzchowska
Toxins.2023; 16(1): 17. CrossRef
Identification, Superantigen Toxin Gene Profile and Antimicrobial Resistance of Staphylococci Isolated from Polish Primitive Sheep Breeds
Jolanta Karakulska, Marta Woroszyło, Małgorzata Szewczuk, Karol Fijałkowski
Animals.2022; 12(16): 2139. CrossRef
Relationship between L-lactate dehydrogenase and multidrug resistance in Staphylococcus xylosus
Zhongwei Yuan, Jinpeng Wang, Ruixiang Che, Bello-Onaghise God’spower, Yonghui Zhou, Chunliu Dong, Lu Li, Mingri Chen, Nsabimana Eliphaz, Xin Liu, Yanhua Li
Archives of Microbiology.2022;[Epub] CrossRef
Prevalence and distribution of multilocus sequence types of Staphylococcus aureus isolated from bulk tank milk and cows with mastitis in Pennsylvania
Asha Thomas, Shubhada Chothe, Maurice Byukusenge, Tammy Mathews, Traci Pierre, Subhashinie Kariyawasam, Erin Luley, Suresh Kuchipudi, Bhushan Jayarao, Yung-Fu Chang
PLOS ONE.2021; 16(3): e0248528. CrossRef
Short communication: Enterotoxigenic potential of coagulase-negative staphylococci isolated from bovine milk in Poland
I. Helak, E.G. Daczkowska-Kozon, A.A. Dłubała
Journal of Dairy Science.2020; 103(4): 3076. CrossRef
Comprehensive Virulence Gene Profiling of Bovine Non- aureus Staphylococci Based on Whole-Genome Sequencing Data
Sohail Naushad, S. Ali Naqvi, Diego Nobrega, Christopher Luby, John P. Kastelic, Herman W. Barkema, Jeroen De Buck, Angela D. Kent
mSystems.2019;[Epub] CrossRef
Short communication: Search for superantigen genes in coagulase-negative staphylococci isolated from bovine milk in Canada
A. Corbeil, J. Labrie, C. Goetz, S. Dufour, I. Doghri, L. Rivière, M. Jacques
Journal of Dairy Science.2019; 102(3): 2008. CrossRef
Influence of milk, milk fractions and milk proteins on the growth and viability of mastitis-causingStaphylococcus aureusstrain
Karol Fijałkowski, Dorota Peitler, Anna Żywicka, Jolanta Karakulska, Ewa Czerniawska-Piątkowska
Italian Journal of Animal Science.2017; 16(2): 321. CrossRef
Staphylococcus enterotoxin profile of China isolates and the superantigenicity of some novel enterotoxins
Menglu Shen, Yi Li, Linlin Zhang, Songbao Dai, Jiashun Wang, Yongqing Li, Lei Zhang, Jinhai Huang
Archives of Microbiology.2017; 199(5): 723. CrossRef
Relationships among superantigen toxin gene profiles, genotypes, and pathogenic characteristics of Staphylococcus aureus isolates from bovine mastitis
Dong Wang, Limei Zhang, Changfu Yong, Mingliang Shen, Tariq Ali, Muhammad Shahid, Kun Han, Xuezhang Zhou, Bo Han
Journal of Dairy Science.2017; 100(6): 4276. CrossRef
Staphylococci isolated from ready-to-eat meat – Identification, antibiotic resistance and toxin gene profile
Karol Fijałkowski, Dorota Peitler, Jolanta Karakulska
International Journal of Food Microbiology.2016; 238: 113. CrossRef
Antimicrobial susceptibility, virulence genes, and randomly amplified polymorphic DNA analysis of Staphylococcus aureus recovered from bovine mastitis in Ningxia, China
Dong Wang, Limei Zhang, Xuezhang Zhou, Yulong He, Changfu Yong, Mingliang Shen, Otto Szenci, Bo Han
Journal of Dairy Science.2016; 99(12): 9560. CrossRef
First Complete Genome Sequence of Staphylococcus xylosus, a Meat Starter Culture and a Host to Propagate Staphylococcus aureus Phages
Simon J. Labrie, Lynn El Haddad, Denise M. Tremblay, Pier-Luc Plante, Jessica Wasserscheid, Jeannot Dumaresq, Ken Dewar, Jacques Corbeil, Sylvain Moineau
Genome Announcements.2014;[Epub] CrossRef

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

Dyella jejuensis sp. nov., Isolated from Soil of Hallasan Mountain in Jeju Island: Min-Soo Kim , Dong-Wook Hyun , Joon Yong Kim , Soyeon Kim , Jin-Woo Bae , Eun-Jin Park; J. Microbiol. 2014;52(5):373-377. Published online May 9, 2014; DOI: https://doi.org/10.1007/s12275-014-3670-7

47 View
0 Download
19 Crossref

Abstract

A novel bacterium, designated JP1T, was isolated from soil of Hallasan Mountain in Jeju Island. The isolate was a Gram- negative, aerobic, motile and rod-shaped (0.2–0.4 × 1.2–2.0 μm) bacterium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain JP1T was closely related to Dyella koreensis with 97.6% similarity. Growth of strain JP1T occurred at 10–37°C, pH 5–7 and 0–1% (w/v) NaCl. The genomic DNA G+C content of strain JP1T was 62.1 mol%. The major fatty acids were iso-C16:0, iso-C17:1 ω9c, and iso- C15:0. The predominant quinone was ubiquinone-8. The major polar lipids of strain JP1T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, uniden-tified aminolipids and unidentified aminophospholipids. The DNA-DNA relatedness values between strain JP1T and pre-viously reported Dyella species were <10%. Based on pheno-typic, genotypic, and phylogenetic distinctness, strain JP1T represents a novel species in the genus Dyella, for which the name Dyella jejuensis sp. nov. is proposed. The type strain is JP1T (=KACC 17701T =JCM 19615T).

Citations

Citations to this article as recorded by

Effects of different cultivation media on root bacterial community characteristics of greenhouse tomatoes
Xinjian Zhang, Qiang Li, Fangyuan Zhou, Susu Fan, Xiaoyan Zhao, Chi Zhang, Kun Yan, Xiaoqing Wu
Frontiers in Microbiology.2023;[Epub] CrossRef
Soil pH and aridity influence distributions of branched tetraether lipids in grassland soils along an aridity transect
Jingjing Guo, Tian Ma, Nana Liu, Xinying Zhang, Huifeng Hu, Wenhong Ma, Zhiheng Wang, Xiaojuan Feng, Francien Peterse
Organic Geochemistry.2022; 164: 104347. CrossRef
Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(6): 576. CrossRef
Actinoplanes solisilvae sp. nov., Isolated from Birch Forest Soil
Qingyun Ma, Qi Zhang, Xu Jiang, Delong Kong, Xiaoyan Han, Huiying Xue, Yiqing Zhou, Yuqin Zhang, Wei Zhang, Zhiyong Ruan
Current Microbiology.2020; 77(11): 3799. CrossRef
Aerosticca soli gen. nov., sp. nov., an aerobic gammaproteobacterium isolated from crude oil-contaminated soil
Miho Watanabe, Hisaya Kojima, Manabu Fukui
Archives of Microbiology.2020; 202(5): 1069. CrossRef
The complex interactions between novel DEHP-metabolising bacteria and the microbes in agricultural soils
Mengke Song, Yujie Wang, Longfei Jiang, Ke Peng, Zikai Wei, Dayi Zhang, Yongtao Li, Gan Zhang, Chunling Luo
Science of The Total Environment.2019; 660: 733. CrossRef
Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China
Xiang-yue Zhou, Zeng-hong Gao, Mei-hong Chen, Mei-qi Jian, Li-hong Qiu
International Journal of Systematic and Evolutionary Microbiology .2019; 69(4): 1016. CrossRef
Dyella dinghuensis sp. nov. and Dyella choica sp. nov., isolated from forest soil
Fang-hong Ou, Zeng-hong Gao, Mei-hong Chen, Jie-yi Bi, Li-hong Qiu
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1496. CrossRef
Dyella halodurans sp. nov., isolated from lower subtropical forest soil
Yu-min Cai, Zeng-hong Gao, Mei-hong Chen, Yi-xian Huang, Li-hong Qiu
International Journal of Systematic and Evolutionary Microbiology.2018; 68(10): 3237. CrossRef
Dyella acidisoli sp. nov., D. flagellata sp. nov. and D. nitratireducens sp. nov., isolated from forest soil
Mei-hong Chen, Fan Xia, Ying-ying Lv, Xiang-yue Zhou, Li-hong Qiu
International Journal of Systematic and Evolutionary Microbiology.2017; 67(3): 736. CrossRef
Dyella lipolytica sp. nov., a lipolytic bacterium isolated from lower subtropical forest soil
Liang Tang, Mei-hong Chen, Xi-chen Nie, Meng-ran Ma, Li-hong Qiu
International Journal of Systematic and Evolutionary Microbiology .2017; 67(5): 1235. CrossRef
First case of neonatal bacteremia due to Dyella genus
Nesrine Hakima, Philippe Bidet, Maureen Lopez, Stéphane Rioualen, Agnès Carol, Stéphane Bonacorsi
Diagnostic Microbiology and Infectious Disease.2017; 87(2): 199. CrossRef
Dyella caseinilytica sp. nov., Dyella flava sp. nov. and Dyella mobilis sp. nov., isolated from forest soil
Fan Xia, Mei-hong Chen, Ying-ying Lv, Han-yun Zhang, Li-hong Qiu
International Journal of Systematic and Evolutionary Microbiology.2017; 67(9): 3237. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2016; 66(1): 1. CrossRef
Dyella humi sp. nov., isolated from forest soil
Mei-Hong Chen, Ying-Ying Lv, Jia Wang, Liang Tang, Li-Hong Qiu
International Journal of Systematic and Evolutionary Microbiology.2016; 66(11): 4372. CrossRef
Effect of lactic acid bacteria isolated from fermented mustard on immunopotentiating activity
Chen-Kai Chang, Shu-Chen Wang, Chih-Kwang Chiu, Shih-Ying Chen, Zong-Tsi Chen, Pin-Der Duh
Asian Pacific Journal of Tropical Biomedicine.2015; 5(4): 281. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2015; 65(Pt_11): 3763. CrossRef
In vitro study of the effect of a probiotic bacterium Lactobacillus rhamnosus against herpes simplex virus type 1
Soghra Khani, Mohammad Motamedifar, Hossein Golmoghaddam, Hamideh Mahmoodzadeh Hosseini, Zahra Hashemizadeh
The Brazilian Journal of Infectious Diseases.2012; 16(2): 129. CrossRef
Probiotics and Lung Diseases
Paul Forsythe
Chest.2011; 139(4): 901. CrossRef

Massilia kyonggiensis sp. nov., Isolated from Forest Soil in Korea: Jaisoo Kim; J. Microbiol. 2014;52(5):378-383. Published online May 9, 2014; DOI: https://doi.org/10.1007/s12275-014-4010-7

56 View
0 Download
17 Crossref

Abstract

A Gram-negative, short, rod-shaped bacterium, TSA1T, was isolated from forest soil collected at Kyonggi University, South Korea. Assessment of 16S rRNA gene sequence sim-ilarity indicated that the strain is related to Massilia niastensis 5516S-1T (98.3%), M. haematophila CCUG 38318T (97.9%), M. aerilata 5516S-11T (97.9%), M. tieshanensis TS3T (97.6%), and M. varians CCUG 3529T (97.1%). Colonies grown on Reasoner’s 2A agar at 30°C for 2 days were transparent, white, round, smooth, and glossy. The cells grew at 10–42°C (optimum: 25–37°C) and pH 5–9 (optimum: 5–9) and in 0–2% NaCl (optimum: 0–1%). TSA1T was able to grow on trypticase soy and nutrient agar, but not on Luria-Bertani or MacConkey agar. The strain was catalase- and oxidase- positive and able to degrade starch and casein, but not car-boxymethyl cellulose. The predominant quinone of TSA1T was Q-8, the major fatty acids were summed feature 3 and C16:0, and the DNA G+C content was 66.7 mol%. Given these findings, we propose that this strain is a novel species of the genus Massilia. We suggest the name Massilia kyonggiensis sp. nov. (type strain, KACC 17471T =KEMB 9005-031T =JCM 19189T).

Citations

Citations to this article as recorded by

Massilia luteola sp. nov., a novel indole-producing and cellulose-degrading bacterium isolated from soil
Xinbing Huang, Shengtao Qi, Wenshuai Song, Xiaoxin Yu, Haifeng Zhang, Wensheng Xiang, Junwei Zhao, Xiangjing Wang
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.
John P. Bowman
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Cold-shock gene cspC in the genome of Massilia polaris sp. nov. revealed cold-adaptation
Ram Hari Dahal, Dhiraj Kumar Chaudhary, Dong-Uk Kim, Jaisoo Kim
Antonie van Leeuwenhoek.2021; 114(8): 1275. CrossRef
Genome insight and description of antibiotic producing Massilia antibiotica sp. nov., isolated from oil-contaminated soil
Ram Hari Dahal, Dhiraj Kumar Chaudhary, Jaisoo Kim
Scientific Reports.2021;[Epub] CrossRef
Massilia rhizosphaerae sp. nov., a rice-associated rhizobacterium with antibacterial activity against Ralstonia solanacearum
Chenxu Li, Peng Cao, Chuanjiao Du, Xue Zhang, Hui Bing, Lei Li, Peng Sun, Wensheng Xiang, Junwei Zhao, Xiangjing Wang
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Large Blooms of Bacillales ( Firmicutes ) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity
Ulas Karaoz, Estelle Couradeau, Ulisses Nunes da Rocha, Hsiao-Chien Lim, Trent Northen, Ferran Garcia-Pichel, Eoin L. Brodie, Mark J. Bailey
mBio.2018;[Epub] CrossRef
Massilia variansIsolated from a Clinical Specimen
Jooyoung Cho, Keon-Han Kim, Jung Ok Kim, Jun Sung Hong, Seok Hoon Jeong, Kyungwon Lee
Infection & Chemotherapy.2017; 49(3): 219. CrossRef
Massilia phosphatilytica sp. nov., a phosphate solubilizing bacteria isolated from a long-term fertilized soil
Bang-Xiao Zheng, Qing-Fang Bi, Xiu-Li Hao, Guo-Wei Zhou, Xiao-Ru Yang
International Journal of Systematic and Evolutionary Microbiology.2017; 67(8): 2514. CrossRef
Massilia neuiana sp. nov., isolated from wet soil
Xin Zhao, Xuejie Li, Nan Qi, Meijun Gan, Yujin Pan, Tianfang Han, Xiaomin Hu
International Journal of Systematic and Evolutionary Microbiology.2017; 67(12): 4943. CrossRef
Massilia agri sp. nov., isolated from reclaimed grassland soil
Dhiraj Kumar Chaudhary, Jaisoo Kim
International Journal of Systematic and Evolutionary Microbiology.2017; 67(8): 2696. CrossRef
Massilia psychrophila sp. nov., isolated from an ice core
Bixi Guo, Yongqin Liu, Zhengquan Gu, Liang Shen, Keshao Liu, Ningliang Wang, Tingting Xing, Hongcan Liu, Yuguang Zhou, Jiule Li
International Journal of Systematic and Evolutionary Microbiology.2016; 66(10): 4088. CrossRef
Massilia pinisoli sp. nov., isolated from forest soil
Khulan Altankhuu, Jaisoo Kim
International Journal of Systematic and Evolutionary Microbiology.2016; 66(9): 3669. CrossRef
Massilia putida sp. nov., a dimethyl disulfide-producing bacterium isolated from wolfram mine tailing
Guang-Da Feng, Song-Zhen Yang, Hua-Ping Li, Hong-Hui Zhu
International Journal of Systematic and Evolutionary Microbiology.2016; 66(1): 50. CrossRef
Efficient biodegradation of phenanthrene by a novel strain Massilia sp. WF1 isolated from a PAH-contaminated soil
Haizhen Wang, Jun Lou, Haiping Gu, Xiaoyan Luo, Li Yang, Laosheng Wu, Yong Liu, Jianjun Wu, Jianming Xu
Environmental Science and Pollution Research.2016; 23(13): 13378. CrossRef
Massilia arvi sp. nov., isolated from fallow-land soil previously cultivated with Brassica oleracea, and emended description of the genus Massilia
Hina Singh, Juan Du, KyungHwa Won, Jung-Eun Yang, ChangShik Yin, MooChang Kook, Tae-Hoo Yi
International Journal of Systematic and Evolutionary Microbiology .2015; 65(Pt_10): 3690. CrossRef
Characterizing microbial communities dedicated for conversion of coal to methane in situ and ex situ
Ji Zhang, Yanna Liang, Rohit Pandey, Satya Harpalani
International Journal of Coal Geology.2015; 146: 145. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2014; 64(Pt_9): 2927. CrossRef

Isolation and Characterization of Novel Lipase Gene LipHim1 from the DNA Isolated from Soil Samples: Pavan Kumar Pindi , Raja Srinath Rebba , Theetha L. Pavankumar; J. Microbiol. 2014;52(5):384-388. Published online April 11, 2014; DOI: https://doi.org/10.1007/s12275-014-3302-2

46 View
0 Download
3 Crossref

Abstract

Metagenomics is a magnificent tool to isolate genes from unknown/uncharacterized species and also from organisms that cannot be cultured. In this study, we constructed a meta-genomic library from isolated DNA of soil samples collected from Palamuru University campus premises, in Mahabub-nagar district of Andhra Pradesh, India. We isolated a novel lipase gene LipHim1, which has an open reading frame of 591 base pairs and encodes ~23 kDa protein consisting of 196 amino acids. The Lipase LipHim1 showed maximum 32% homology at the protein level with the extracellular Aeromonas hydrophila lipase (Class II, GDSL family) and was significantly different from all other known lipases. The isolated lipase catalyzed the hydrolysis of fatty acid esters of polyoxyethylene sorbitan such as Tween 60. Our results in-dicate that the isolated lipase gene is novel.

Citations

Citations to this article as recorded by

High-Throughput, Fluorescence-Based Esterase Activity Assay for Assessing Polysorbate Degradation Risk during Biopharmaceutical Development
Adithi C. Bhargava, Kathryn Mains, Albert Siu, Jie Gu, Jonathan Zarzar, Li Yi, Inn H. Yuk
Pharmaceutical Research.2021; 38(3): 397. CrossRef
Isolation and characterization of novel and efficient protease producing bacteria from drinking water resources
S. Jeevan Chandra, A. Shiva Shanker, Pavan Kumar Pindi
Water Supply.2020; 20(1): 157. CrossRef
Integrative computational approach for genome-based study of microbial lipid-degrading enzymes
Tayvich Vorapreeda, Chinae Thammarongtham, Kobkul Laoteng
World Journal of Microbiology and Biotechnology.2016;[Epub] CrossRef

Journal Article

Production of an Endoinulinase from Aspergillus niger AUMC 9375, by Solid State Fermentation of Agricultural Wastes, with Purification and Characterization of the Free and Immobilized Enzyme: Manal M. Housseiny; J. Microbiol. 2014;52(5):389-398. Published online May 9, 2014; DOI: https://doi.org/10.1007/s12275-014-3561-y

48 View
0 Download
15 Crossref

Abstract

Two different substrates, sunflower (Helianthus annuus L.) tubers and lettuce (Lactuca sativa) roots, were tested. Using a mixture of both wastes resulted in higher production of endoinulinase than either waste alone. Also, ten fungal spe-cies grown on these substrates as inexpensive, carbon sour-ces were screened for the best production of endoinulinase activities. Of these, Aspergillus niger AUMC 9375 was the most productive, when grown on the mixture using a 6:1 w/w ratio of sun flower: lettuce, and yielded the highest levels of inulinase at 50% moisture, 30°C, pH 5.0, with seven days of incubation, and with yeast extract as the best nitrogen source. Inulinase was purified to homogeneity by ion-exchange chro-matography and gel-filtration giving a 51.11 fold purification. The mixture of sunflower tubers and lettuce roots has poten-tial to be an effective and economical substrate for inulinase production. Inulinase was successfully immobilized with an immobilization yield of 71.28%. After incubation for 2 h at 60°C, the free enzyme activity decreased markedly to 10%, whereas that of the immobilized form decreased only to 87%. A reusability test demonstrated the durability of the immo-bilized inulinase for 10 cycles and in addition, that it could be stored for 32 days at 4°C. These results indicate that this inulinase, in the immobilized form, is a potential candidate for large-scale production of high purity fructose syrups.

Citations

Citations to this article as recorded by

Production of β-mannanase, inulinase, and oligosaccharides from coffee wastes and extracts
Selin Basmak, Irfan Turhan
International Journal of Biological Macromolecules.2024; 261: 129798. CrossRef
Sustainable inulinase enzyme production from novel strain Fusarium parceramosum with mixed biomass substrates of rice husk and banana shoot through solid-state fermentation
Shreya Hegde, Ramananda Bhat M, Subbalaxmi Selvaraj
Biomass Conversion and Biorefinery.2024;[Epub] CrossRef
Bio-utilization of agricultural residue banana plant shoot through solid state fermentation for production of inulinase using newly isolated Nothophoma anigozanthi JAM
Nisarga Tippanavar, Divya Bhat, Orline Rebello, Girisa Prabhu, Subbalaxmi Selvaraj, Ramananda M. Bhat
Biomass Conversion and Biorefinery.2024; 14(13): 14755. CrossRef
Aspergillus welwitschiae inulinase enzyme cocktails obtained on agro-material inducers for the purpose of fructooligosaccharides production
Sanja Stojanović, Marina Ristović, Jelena Stepanović, Aleksandra Margetić, Bojan Duduk, Zoran Vujčić, Biljana Dojnov
Food Research International.2022; 160: 111755. CrossRef
Solid-state fermentation enhances inulinase and invertase production by Aspergillus brasiliensis
C. Guerrero-Urrutia, T. Volke-Sepulveda, F. Figueroa-Martinez, E. Favela-Torres
Process Biochemistry.2021; 108: 169. CrossRef
Statistical optimization of solid-state fermentation for the production of fungal inulinase from apple pomace
Ram Sarup Singh, Kanika Chauhan, Karminder Kaur, Ashok Pandey
Bioresource Technology Reports.2020; 9: 100364. CrossRef
Optimization of inulinase production by a newly isolated strain Aspergillus flavus var. flavus by solid state fermentation of Saccharum arundinaceum
Deblina Das, Raja Selvaraj, M. Ramananda Bhat
Biocatalysis and Agricultural Biotechnology.2019; 22: 101363. CrossRef
Review of inulinase production using solid-state fermentation
Deblina Das, Ramananda Bhat M, Raja Selvaraj
Annals of Microbiology.2019; 69(3): 201. CrossRef
Immobilized inulinase: a new horizon of paramount importance driving the production of sweetener and prebiotics
Gerard Neeraj, Shobana Ravi, Ravindran Somdutt, ShriAishvarya Kaliyur Ravi, Vaidyanathan Vinoth Kumar
Critical Reviews in Biotechnology.2018; 38(3): 409. CrossRef
The cell wall anchored β-fructosidases of Lactobacillus paracasei : Overproduction, purification, and gene expression control
Petya Velikova, Kaloyan Petrov, Penka Petrova
Process Biochemistry.2017; 52: 53. CrossRef
Continuous generation of fructose from Taraxacum officinale tap root extract and inulin by immobilized inulinase in a packed-bed reactor
Hemant Kumar Rawat, Hemant Soni, Naveen Kango, C. Ganesh Kumar
Biocatalysis and Agricultural Biotechnology.2017; 9: 134. CrossRef
Biotechnological potential of microbial inulinases: Recent perspective
Hemant Kumar Rawat, Hemant Soni, Helen Treichel, Naveen Kango
Critical Reviews in Food Science and Nutrition.2017; 57(18): 3818. CrossRef
Development of heterogeneous preparation with inulinase for tubular reactor systems
M.G. Holyavka, M.P. Evstigneev, V.G. Artyukhov, V.V. Savin
Journal of Molecular Catalysis B: Enzymatic.2016; 129: 1. CrossRef
Recent insights in enzymatic synthesis of fructooligosaccharides from inulin
Ram Sarup Singh, Rupinder Pal Singh, John F. Kennedy
International Journal of Biological Macromolecules.2016; 85: 565. CrossRef
Production of inulinase, fructosyltransferase and sucrase from fungi on low-value inulin-rich substrates and their use in generation of fructose and fructo-oligosaccharides
Hemant Kumar Rawat, Mohd Anis Ganaie, Naveen Kango
Antonie van Leeuwenhoek.2015; 107(3): 799. CrossRef

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

Characterization of Recombinant β-Glucosidase from Arthrobacter chlorophenolicus and Biotransformation of Ginsenosides Rb1, Rb2, Rc, and Rd: Myung Keun Park , Chang-Hao Cui , Sung Chul Park , Seul-Ki Park , Jin-Kwang Kim , Mi-Sun Jung , Suk-Chae Jung , Mi-Sun Jung , Suk-Chae Jung , Sun-Chang Kim , Wan-Taek Im; J. Microbiol. 2014;52(5):399-406. Published online May 9, 2014; DOI: https://doi.org/10.1007/s12275-014-3601-7

46 View
0 Download
10 Crossref

Abstract

The focus of this study was the cloning, expression, and characterization of recombinant ginsenoside hydrolyzing β-glucosidase from Arthrobacter chlorophenolicus with an ultimate objective to more efficiently bio-transform ginse-nosides. The gene bglAch, consisting of 1,260 bp (419 amino acid residues) was cloned and the recombinant enzyme, over-expressed in Escherichia coli BL21 (DE3), was characterized. The GST-fused BglAch was purified using GST·Bind agarose resin and characterized. Under optimal conditions (pH 6.0 and 37°C) BglAch hydrolyzed the outer glucose and arabino-pyranose moieties of ginsenosides Rb1 and Rb2 at the C20 position of the aglycone into ginsenoside Rd. This was fol-lowed by hydrolysis into F2 of the outer glucose moiety of ginsenoside Rd at the C3 position of the aglycone. Additio-nally, BglAch more slowly transformed Rc to F2 via C-Mc1 (compared to hydrolysis of Rb1 or Rb2). These results in-dicate that the recombinant BglAch could be useful for the production of ginsenoside F2 for use in the pharmaceutical and cosmetic industries.

Citations

Citations to this article as recorded by

Production and pharmaceutical research of minor saponins in Panax notoginseng (Sanqi): Current status and future prospects
Hui Zhang, Jianxiu Li, Mengxue Diao, Jianbin Li, Nengzhong Xie
Phytochemistry.2024; 223: 114099. CrossRef
Microbial production and applications of β-glucosidase-A review
Wenqi Yang, Yaowu Su, Rubing Wang, Huanyu Zhang, Hongyan Jing, Jie Meng, Guoqi Zhang, Luqi Huang, Lanping Guo, Juan Wang, Wenyuan Gao
International Journal of Biological Macromolecules.2024; 256: 127915. CrossRef
Progress in the Conversion of Ginsenoside Rb1 into Minor Ginsenosides Using β-Glucosidases
Hongrong Zhu, Rui Zhang, Zunxi Huang, Junpei Zhou
Foods.2023; 12(2): 397. CrossRef
Enzymatic biotransformation of ginsenoside Rb1 by recombinant β-glucosidase of bacterial isolates from Indonesia
Almando Geraldi, Ni'matuzahroh, Fatimah, Chang-Hao Cui, Thi Thuy Nguyen, Sun Chang Kim
Biocatalysis and Agricultural Biotechnology.2020; 23: 101449. CrossRef
Characterization of a Novel Ginsenoside MT1 Produced by an Enzymatic Transrhamnosylation of Protopanaxatriol-Type Ginsenosides Re
Byeong-Min Jeon, Jong-In Baek, Min-Sung Kim, Sun-Chang Kim, Chang-hao Cui
Biomolecules.2020; 10(4): 525. CrossRef
In silico Approach to Elucidate Factors Associated with GH1 β-Glucosidase Thermostability
Amer Ahmed, Ayesha Sumreen, Aasia Bibi, Faiz ul Hassan Nasim, Kashfa Batool
Journal of Pure and Applied Microbiology.2019; 13(4): 1953. CrossRef
A literature update elucidating production of Panax ginsenosides with a special focus on strategies enriching the anti-neoplastic minor ginsenosides in ginseng preparations
Tanya Biswas, A. K. Mathur, Archana Mathur
Applied Microbiology and Biotechnology.2017; 101(10): 4009. CrossRef
Classification of glycosidases that hydrolyze the specific positions and types of sugar moieties in ginsenosides
Kyung-Chul Shin, Deok-Kun Oh
Critical Reviews in Biotechnology.2016; 36(6): 1036. CrossRef
Insight into a novel β-1,4-glucosidase from Streptomyces griseorubens JSD-1
H.-W. Feng, Y.-E. Zhi, Y.-J. Sun, L.-R. Xu, L.-M. Wang, X.-J. Zhan, P. Zhou
Applied Biochemistry and Microbiology.2016; 52(4): 371. CrossRef
Overexpression and characterization of a glycoside hydrolase family 1 enzyme from Cellulosimicrobium cellulans sp. 21 and its application for minor ginsenosides production
Ye Yuan, Yanbo Hu, Chenxing Hu, Jiayi Leng, Honglei Chen, Xuesong Zhao, Juan Gao, Yifa Zhou
Journal of Molecular Catalysis B: Enzymatic.2015; 120: 60. CrossRef

Biodegradation of C5-C8 Fatty Acids and Production of Aroma Volatiles by Myroides sp. ZB35 Isolated from Activated Sludge: Zijun Xiao , Xiankun Zhu , Lijun Xi , Xiaoyuan Hou , Li Fang , Jian R. Lu; J. Microbiol. 2014;52(5):407-412. Published online May 9, 2014; DOI: https://doi.org/10.1007/s12275-014-4109-x

46 View
0 Download
10 Crossref

Abstract

In the effluents of a biologically treated wastewater from a heavy oil-refining plant, C5-C8 fatty acids including penta-noic acid, hexanoic acid, heptanoic acid, octanoic acid, and 2-methylbutanoic acid are often detected. As these residual fatty acids can cause further air and water pollution, a new Myroides isolate ZB35 from activated sludge was explored to degrade these C5-C8 fatty acids in this study. It was found that the biodegradation process involved a lag phase that became prolonged with increasing acyl chain length when the fatty acids were individually fed to this strain. However, when fed as a mixture, the ones with longer acyl chains were found to become more quickly assimilated. The branched 2- methylbutanoic acid was always the last one to be depleted among the five fatty acids under both conditions. Metabolite analysis revealed one possible origin of short chain fatty acids in the biologically treated wastewater. Aroma volatiles inclu-ding 2-methylbutyl isovalerate, isoamyl 2-methylbutanoate, isoamyl isovalerate, and 2-methylbutyl 2-methylbutanoate were subsequently identified from ZB35 extracts, linking the source of the fruity odor to these esters excreted by Myroides species. To our best knowledge, this is the first finding of these aroma esters in bacteria. From a biotechnological viewpoint, this study has revealed the potential of Myroides species as a promising source of aroma esters attractive for food and fragrance industries.

Citations

Citations to this article as recorded by

Biotreatment of crude oil waste sludge using a novel bacterial formula
Onyedikachi Ubani, Harrison Ifeanyichukwu Atagana
Environmental Challenges.2024; 15: 100943. CrossRef
Unravelling the correlations among the microbial community, physicochemical properties, and volatile compounds of traditional mung bean sour liquid
Xuan Li, Ying Wu, Linyan Shu, Lina Zhao, Li Cao, Xin Li, Shanshan Tie, Pingping Tian, Shaobin Gu
LWT.2024; 198: 115971. CrossRef
Analysis of changes in volatile compounds and evolution in free fatty acids, free amino acids, nucleotides, and microbial diversity in tilapia (Oreochromis mossambicus) fillets during cold storage
Hao Cheng, Jun Mei, Jing Xie
Journal of the Science of Food and Agriculture.2024; 104(5): 2959. CrossRef
Ex-situ biological treatment of industrial saline seafood wastewater by salt-tolerant mixed cultures and phytotoxicity evaluation
Argyro Tsipa, Maria Papalli, Andreas Christou, Panayiota Pissaridou, Marlen I. Vasquez
Journal of Environmental Chemical Engineering.2023; 11(1): 109195. CrossRef
Analysis of Bacterial Diversity in Different Types of Daqu and Fermented Grains From Danquan Distillery
Changhua Shang, Yujia Li, Jin Zhang, Shanling Gan
Frontiers in Microbiology.2022;[Epub] CrossRef
Distinct bacterial community of a solid-state fermented Chinese traditional food huase sufu revealed by high-throughput sequencing
Zhang Zhen-dong, Wang Yu-rong, Xiang Fan-shu, Hou Qiang-chuan, Guo Zhuang
Food Science and Biotechnology.2021; 30(9): 1233. CrossRef
Abundance and diversity of microbial arsenic biotransformation genes in the sludge of full-scale anaerobic digesters from a municipal wastewater treatment plant
Weiwei Zhai, Tianyue Qin, Liguan Li, Ting Guo, Xiaole Yin, Muhammad Imran Khan, Muhammad Zaffar Hashmi, Xingmei Liu, Xianjin Tang, Jianming Xu
Environment International.2020; 138: 105535. CrossRef
How the bacterial community of a tannery effluent responds to bioaugmentation with the consortium SFC 500-1. Impact of environmental variables
Marilina Fernandez, Paola P. Pereira, Elizabeth Agostini, Paola S. González
Journal of Environmental Management.2019; 247: 46. CrossRef
Revelation of mechanism for aqueous saponins content decrease during storage of Dioscorea zingiberensis C. H. Wright tubers: An essential prerequisite to ensure clean production of diosgenin
Liwei Zhang, Hailiang Qiu, Shu Yuan, Mengzhen Guo, Zaiyang Guo, Longjiang Yu
Industrial Crops and Products.2018; 125: 178. CrossRef
Solid-state fermentative production of aroma esters by Myroides sp. ZB35 and its complete genome sequence
Zijun Xiao, Wenlong Liang, Xiankun Zhu, Jing-yi Zhao
Journal of Biotechnology.2017; 245: 28. CrossRef

Low Cell Density Regulator AphA Upregulates the Expression of Vibrio vulnificus iscR Gene Encoding the Fe-S Cluster Regulator IscR: Jong Gyu Lim , Jin Hwan Park , Sang Ho Choi; J. Microbiol. 2014;52(5):413-421. Published online February 17, 2014; DOI: https://doi.org/10.1007/s12275-014-3592-4

53 View
0 Download
11 Crossref

Abstract

IscR is a global transcriptional regulator that contributes to the pathogenesis of Vibrio vulnificus, a food-borne pathogen. In the present study, the regulatory mechanism for the iscR expression of V. vulnificus was evaluated. The expression of iscR was found to be upregulated by a transcriptional regu-lator AphA, a homologue of the low cell density regulator AphA of the Vibrio species, in the exponential phase of growth. The promoter activity of iscR appeared to be acti-vated and repressed by AphA and IscR, respectively. EMSA and DNase I protection assay showed that both AphA and IscR bind to the iscR regulatory region and the binding site for AphA overlapped with part of the binding site for IscR. Further mutational analysis suggested that AphA upregu-lates the iscR expression only in the presence of functional IscR. An examination of the roles of AphA and the binding sites revealed that the binding of AphA would hinder the IscR-mediated repression of the iscR transcription. The com-bined results show that V. vulnificus AphA upregulates iscR expression by antagonizing its negative autoregulation.

Citations

Citations to this article as recorded by

Environmental magnesium ion affects global gene expression, motility, biofilm formation and virulence of Vibrio parahaemolyticus
Xue Li, Xiaobai Zhang, Miaomiao Zhang, Xi Luo, Tingting Zhang, Xianjin Liu, Renfei Lu, Yiquan Zhang
Biofilm.2024; 7: 100194. CrossRef
Fe-S cluster homeostasis and beyond: The multifaceted roles of IscR
Erin L. Mettert, Patricia J. Kiley
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research.2024; 1871(6): 119749. CrossRef
Complex regulatory networks of virulence factors in Vibrio vulnificus
Garam Choi, Sang Ho Choi
Trends in Microbiology.2022; 30(12): 1205. CrossRef
A Nitric Oxide-Responsive Transcriptional Regulator NsrR Cooperates With Lrp and CRP to Tightly Control the hmpA Gene in Vibrio vulnificus
Garam Choi, Dukyun Kim, Hanhyeok Im, Sang Ho Choi
Frontiers in Microbiology.2021;[Epub] CrossRef
A MARTX Toxin rtxA Gene Is Controlled by Host Environmental Signals through a CRP-Coordinated Regulatory Network in Vibrio vulnificus
Zee-Won Lee, Seung-Ho Hwang, Garam Choi, Kyung Ku Jang, Tae Hee Lee, Kyung Min Chung, Byoung Sik Kim, Sang Ho Choi, Caroline S. Harwood
mBio.2020;[Epub] CrossRef
The transcriptional regulator IscR integrates host-derived nitrosative stress and iron starvation in activation of the vvhBA operon in Vibrio vulnificus
Garam Choi, Kyung Ku Jang, Jong Gyu Lim, Zee-Won Lee, Hanhyeok Im, Sang Ho Choi
Journal of Biological Chemistry.2020; 295(16): 5350. CrossRef
Role and Regulation of the Orphan Apha Protein of Quorum Sensing in Pathogenic Vibrios
Renfei Lu, George Osei-Adjei, Xinxiang Huang, Yiquan Zhang
Future Microbiology.2018; 13(3): 383. CrossRef
Crystal Structure of the Regulatory Domain of AphB from Vibrio vulnificus, a Virulence Gene Regulator
Nohra Park, Saemee Song, Garam Choi, Kyung Ku Jang, Inseong Jo, Sang Ho Choi, Nam-Chul Ha
Molecules and Cells.2017; 40(4): 299. CrossRef
Iron- and Quorum-sensing Signals Converge on Small Quorum-regulatory RNAs for Coordinated Regulation of Virulence Factors in Vibrio vulnificus
Yancheng Wen, In Hwang Kim, Kun-Soo Kim
Journal of Biological Chemistry.2016; 291(27): 14213. CrossRef
What a difference a cluster makes: The multifaceted roles of IscR in gene regulation and DNA recognition
Joana A. Santos, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics.2015; 1854(9): 1101. CrossRef
Characterization of the Vibrio vulnificus 1-Cys Peroxiredoxin Prx3 and Regulation of Its Expression by the Fe-S Cluster Regulator IscR in Response to Oxidative Stress and Iron Starvation
Jong Gyu Lim, Ye-Ji Bang, Sang Ho Choi
Journal of Biological Chemistry.2014; 289(52): 36263. CrossRef

The Role as Inoculum Sources of Xanthomonas citri pv. citri Surviving on the Infected Satsuma mandarin Fruits: So Young Kang , Ki Deok Kim , Jeum Kyu Hong , He Nam Hyun , Yong Chull Jeun; J. Microbiol. 2014;52(5):422-426. Published online April 11, 2014; DOI: https://doi.org/10.1007/s12275-014-3366-z

44 View
0 Download
2 Crossref

Abstract

Importing citrus fruits infected by Asiatic citrus canker caused by Xanthomonas citri pv. citri (Xcc) can act as an inoculum source for the disease epidemic in citrus canker-free countries. In this study, the pathogenicity of the causal agent of Asiatic citrus canker surviving on infected Satsuma mandarin fruits was evaluated. The washing solution of infected Satsuma mandarin fruits did not cause lesion formation on the citrus leaves. However, a typical citrus canker lesion was formed on the leaves after inoculation with higher concentrations of the inoculum from the washing solution (washing solu-tion II). It indicated that the pathogenicity of the citrus can-ker surviving on the symptomatic Satsuma mandarin fruits was not changed. Scanning electron microscopic observation showed that the numbers of bacterial cells on the leaves of Satsuma mandarin which inoculated with the washing solu-tion directly (washing solution I) was less compared to those of leaves inoculated with the washing solution II. This result supports that the pathogenicity of Xcc surviving on Satsuma mandarin fruits may not be changed but that the sucessful infection of citrus caker may depend on the concentration of the inoculum.

Citations

Citations to this article as recorded by

Seasonal and post-harvest population dynamics of the Asiatic citrus canker pathogen Xanthomonas citri subsp. citri on grapefruit in Florida
Weiqi Luo, Drew Posny, Alissa B. Kriss, Jim H. Graham, Gavin H. Poole, Earl L. Taylor, Greg McCollum, Tim R. Gottwald, Clive H. Bock
Crop Protection.2020; 137: 105227. CrossRef
Effects of Nonionic Surfactants on Xanthan Gum Production: a Survey on Cellular Interactions
Tahereh Ghashghaei, Mohammad Reza Soudi, Saman Hoseinkhani, Morteza Shiri
Iranian Journal of Biotechnology.2018; 16(1): 60. CrossRef

Genetic Analysis of the Capsid Region of Norovirus GII.4 Variants Isolated in South Korea: Ju-Eun Kim , Sung-Geun Lee , Han-Gil Cho , Sang-Ha Han , Lae-Hyung Kang , Youn-Mi Lee , Chul-Jong Park , Soon-Young Paik; J. Microbiol. 2014;52(5):427-434. Published online April 11, 2014; DOI: https://doi.org/10.1007/s12275-014-3538-x

49 View
0 Download
5 Crossref

Abstract

Norovirus is one of the major causes of non-bacterial gas-troenteritis in humans. The aim of this study was to analyze the amino acid variation of open reading frame 2 of GII.4 variants in South Korea during the period from November 2006 to December 2012. Sixty-nine complete nucleotide se-quences of open reading frame 2 were obtained from 113 GII.4 strains. The GII.4 2006b variants were detected pre-dominantly between 2006 and 2009; however, new GII.4 variants, which were termed the 2010 variant and the 2012 variant, emerged in 2010 and 2012, respectively. The num-ber of GII.4 2006b variants steadily decreased until 2012, whereas the number of gastroenteritis cases caused by the new variants increased between 2010 and 2012. The amino acid sequence in the ORF2 region obtained in this study was compared with other GII.4 variants isolated in various countries. Amino acid variations were observed primarily at epitope sites and the surrounding regions. Amino acids 294, 359, 393, and 413 of the P2 subdomain were the most variable sites among the GII.4 variants. The information in this study can be useful in basic research to predict the emergence and determine the genetic functions of new GII.4 variants.

Citations

Citations to this article as recorded by

Determining the efficacy of 27 commercially available disinfectants against human noroviruses
Jae-Woong Lee, Lae-Hyung Kang, Min-Kyeong Kim, Jeong-Soon Kim, Myung L. Kim, Sung-Geun Lee, In-Hye Choi, Chul-Jong Park, Soon-Young Paik
Journal of Infection and Public Health.2021; 14(2): 244. CrossRef
Evolutionary changes in the capsid P2 region of Australian strains of the norovirus GII.Pe_GII.4
Leesa D. Bruggink, Jean M. Moselen, Jason A. Roberts, John A. Marshall
Journal of Medical Microbiology.2017; 66(7): 1014. CrossRef
A norovirus intervariant GII.4 recombinant in Victoria, Australia, June 2016: the next epidemic variant?
Leesa Bruggink, Michael Catton, John Marshall
Eurosurveillance.2016;[Epub] CrossRef
Complete Nucleotide Sequence Analysis of the Norovirus GII.4 Sydney Variant in South Korea
Ji-Sun Park, Sung-Geun Lee, Ji-Young Jin, Han-Gil Cho, Weon-Hwa Jheong, Soon-Young Paik
BioMed Research International.2015; 2015: 1. CrossRef
Molecular epidemiology of norovirus GII.4 variants in children under 5 years with sporadic acute gastroenteritis in South Korea during 2006–2013
Han-Gil Cho, Sung-Geun Lee, Ju-Eun Kim, Kyeong-Sin Yu, Deog-Yong Lee, Po-Hyun Park, Mi-hye Yoon, Eek-Hoon Jho, Jaehong Kim, Soon-Young Paik
Journal of Clinical Virology.2014; 61(3): 340. CrossRef

Validation Study

Comparison of JEV Neutralization Assay Using Pseudotyped JEV with the Conventional Plaque-Reduction Neutralization Test: Hee-Jung Lee , Kyung-Il Min , Ki Hoon Park , Hyo Jung Choi , Min-Kyoung Kim , Chi-Young Ahn , Young-Jin Hong , Young Bong Kim; J. Microbiol. 2014;52(5):435-440. Published online March 7, 2014; DOI: https://doi.org/10.1007/s12275-014-3529-y

47 View
0 Download
12 Crossref

Abstract

We previously reported the development of a neutralization assay system for evaluating Japanese Encephalitis Virus (JEV) neutralizing antibody (NAb) using pseudotyped-JEV (JEV- PV). JEV-PV-based neutralization assay offers several advan-tages compared with the current standard plaque-reduc-tion neutralization test (PRNT), including simplicity, safety, and speed. To evaluate the suitability of the JEV-PV assay as new replacement neutralization assay, we compared its repeatability, reproducibility, specificity, and correlated its results with those obtained using the PRNT. These analyses showed a close correlation between the results obtained with the JEV-PV assay and the PRNT, using the 50% plaque re-duction method as a standard for measuring NAb titers to JEV. The validation results met all analytical acceptance criteria. These results suggest that the JEV-PV assay could serve as a safe and simple method for measuring NAb titer against JEV and could be used as an alternative approach for assaying the potency of JEV neutralization.

Citations

Citations to this article as recorded by

Role of pseudotyped viruses in understanding epidemiology, pathogenesis and immunity of viral diseases affecting both horses and humans
Rebecca L. Sedgwick, Ola ElBohy, Janet M. Daly
Virology.2024; 597: 110164. CrossRef
Correlation between pseudotyped virus and authentic virus neutralisation assays, a systematic review and meta-analysis of the literature
Diego Cantoni, Craig Wilkie, Emma M. Bentley, Martin Mayora-Neto, Edward Wright, Simon Scott, Surajit Ray, Javier Castillo-Olivares, Jonathan Luke Heeney, Giada Mattiuzzo, Nigel James Temperton
Frontiers in Immunology.2023;[Epub] CrossRef
Changes in age-specific seroprevalence of Japanese encephalitis virus and impact of Japanese encephalitis vaccine in Korea
Byung Ok Kwak, Young Jin Hong, Dong Hyun Kim
Clinical and Experimental Pediatrics.2022; 65(3): 108. CrossRef
Prevalence of Malaria and Chikungunya Co-Infection in Febrile Patients: A Systematic Review and Meta-Analysis
Wanida Mala, Polrat Wilairatana, Kwuntida Uthaisar Kotepui, Manas Kotepui
Tropical Medicine and Infectious Disease.2021; 6(3): 119. CrossRef
Development of a neutralization assay based on the pseudotyped chikungunya virus of a Korean isolate
Woo-Chang Chung, Kwang Yeon Hwang, Suk-Jo Kang, Jae-Ouk Kim, Moon Jung Song
Journal of Microbiology.2020; 58(1): 46. CrossRef
Retention of neutralizing antibodies to Japanese encephalitis vaccine in age groups above fifteen years in Korea
Hee-Jung Lee, Hanul Choi, Ki Hoon Park, Yuyeon Jang, Young-jin Hong, Young Bong Kim
International Journal of Infectious Diseases.2020; 100: 53. CrossRef
Graphene functionalized field-effect transistors for ultrasensitive detection of Japanese encephalitis and Avian influenza virus
Akanksha Roberts, Neha Chauhan, Saurav Islam, Subhasis Mahari, Bhaskar Ghawri, Ravi Kumar Gandham, S. S. Majumdar, Arindam Ghosh, Sonu Gandhi
Scientific Reports.2020;[Epub] CrossRef
Seroprevalence of Neutralizing Antibodies against Japanese Encephalitis Virus among Adolescents and Adults in Korea: A Prospective Multicenter Study
Byung Ok Kwak, Young Se Kwon, Young Jin Hong, Chung Hyun Nahm, Woori Jang, Young Uh, Yong Gon Cho, Jimyung Kim, Myungshin Kim, Dong Hyun Kim
Vaccines.2020; 8(2): 328. CrossRef
The Functions and Mechanism of a New Oligopeptide BP9 from Avian Bursa on Antibody Responses, Immature B Cell, and Autophagy
Xiu Li Feng, Man Man Zong, Guang Fang Zhou, Yang Zheng, Yuan Nan Yu, Rui Bing Cao, Pu Yan Chen, Mei Yang
Journal of Immunology Research.2019; 2019: 1. CrossRef
MLKL Mediated Necroptosis Accelerates JEV-Induced Neuroinflammation in Mice
Peiyu Bian, Xuyang Zheng, Li Wei, Chuantao Ye, Hong Fan, Yanhui Cai, Ying Zhang, Fanglin Zhang, Zhansheng Jia, Yingfeng Lei
Frontiers in Microbiology.2017;[Epub] CrossRef
Carbon nanoparticle modified screen printed carbon electrode as a disposable electrochemical immunosensor strip for the detection of Japanese encephalitis virus
Suk Fun Chin, Lih Shan Lim, Suh Cem Pang, Magdline Sia Henry Sum, David Perera
Microchimica Acta.2017; 184(2): 491. CrossRef
Mesenchymal stem cells alleviate Japanese encephalitis virus-induced neuroinflammation and mortality
Peiyu Bian, Chuantao Ye, Xuyang Zheng, Jing Yang, Wei Ye, Yuan Wang, Yun Zhou, Hongwei Ma, Peijun Han, Hai Zhang, Ying Zhang, Fanglin Zhang, Yingfeng Lei, Zhansheng Jia
Stem Cell Research & Therapy.2017;[Epub] CrossRef

Journal Article

Note] Antifungal Chitinase against Human Pathogenic Yeasts from Coprinellus congregatus: Yeeun Yoo Hyoung T. Choi; J. Microbiol. 2014;52(5):441-443. Published online February 17, 2014; DOI: https://doi.org/10.1007/s12275-014-3257-3

49 View
0 Download
2 Crossref

Abstract

The inky cap, Coprinellus congregatus, produces mushrooms which become autolyzed rapidly to generate black liquid droplets, in which no cell wall is detected by microscopy. A chitinase (Chi2) which is synthesized during the autolytic phase of C. congregatus inhibits the growths of Candida al-bicans and Cryptococcus neoformans up to 10% at the con-centration of 10 μg/ml, about 50% at concentration of 20 μg/ml, and up to 95% at the concentration of 70 μg/ml. Upon treatment these yeast cells are observed to be severely de-formed, with the formation of large holes in the cell wall. The two yeast species show no growth inhibition at the concen-tration of 5 μg/ml, which means the minimum inhibitory concentrations for both yeast species are 10 μg/ml under these experimental conditions.

Citations

Citations to this article as recorded by

Analysis of the Antifungal Potential of Macrocybe Titans Extract Against Candida Albicans
Fernanda CBN Pereira, Gabrielle C Peiter, Vivian EMS Justo, Gabrieli M Huff, Pollyanna CV Conrado, Mauro AP da Silva, Patrícia S Bonfim-Mendonça, Terezinha IE Svidzinski, Fabio R Rosado, Adriana Fiorini
Future Microbiology.2023; 18(6): 357. CrossRef
Disarming Fungal Pathogens: Bacillus safensis Inhibits Virulence Factor Production and Biofilm Formation by Cryptococcus neoformans and Candida albicans
François L. Mayer, James W. Kronstad, Yong-Sun Bahn, J. Andrew Alspaugh, Deborah Hogan
mBio.2017;[Epub] CrossRef

First
Prev
Page of 1
Next
Last

Previous issues