Article
Multidisciplinary Sciences
Avik Mukherjee, Jade Ealy, Yanqing Huang, Nina Catherine Benites, Mark Polk, Markus Basan
Summary: Utilizing a combination of experiments and computer simulations, researchers have found that the emergence and persistence of coexistence of multiple ecotypes in Escherichia coli long-term evolution experiment can be explained by two interacting trade-offs rooted in biochemical constraints. Faster growth enabled by higher fermentation and obligate acetate excretion results in longer lag times when utilizing acetate after glucose is depleted, creating an ecological niche for a slower-growing ecotype specialized in switching to acetate. These findings highlight the importance of trade-offs in the evolution of complex microbial communities.
NATURE COMMUNICATIONS
(2023)
Article
Infectious Diseases
Rasha El-Mahdy, Rasha Mahmoud, Raghdaa Shrief
Summary: The study aimed to characterize different uropathogenic E. coli (UPEC) phylogroups from catheter-associated UTI (CAUTI) and community UTI (Com-UTI) in terms of antibiotic resistance, biofilm formation, and pathogenicity islands (PAIs). UPEC strains from CAUTI and Com-UTI showed similar high antibiotic resistance, with higher biofilm formation in CAUTI strains. Phylogroup A was the most common, and PAI IV536 was the prevalent marker in all phylogroups from both types of UTI.
INFECTION AND DRUG RESISTANCE
(2021)
Article
Physics, Multidisciplinary
Kento Nakamura, Tetsuya J. Kobayashi
Summary: The study revealed the optimality of E. coli's chemotactic network in inferring information, demonstrating the equivalence between biochemical network and information-theoretically optimal dynamics, and reproducing experimentally observed non-linear response relation.
PHYSICAL REVIEW LETTERS
(2021)
Article
Microbiology
Rie Ikeda, Keiji Nakamura, Marc Saulmont, Audrey Habets, Jean-Noel Duprez, Nicolas Korsak, Tetsuya Hayashi, Damien Thiry, Jacques G. Mainil
Summary: The aim of this study was to identify E. coli O80 in healthy cattle and determine its potential role in human and calf infections. 16 E. coli O80 strains were isolated from bulls and cows, but they were not identified as the melibiose non-fermenting E. coli O80:H2 strain. These isolates belonged to serotypes and sequence types O80:H6/ST8619 and O80:H45/ST4175, which were phylogenetically related to E. coli O80:H6 and O80:H45 from different animal species. Therefore, healthy adult cattle were not found to be a source of contamination by STEC or EPEC O80:H2 in humans and calves.
Article
Immunology
Ligang Xue, Xia Luo, Jun-Hong Xing, Dan Wang, Dong-Xing Zhang
Summary: In this study, a pathogenic bacterium named X21, identified as Escherichia coli O157:H7, was isolated from infected carp through genetic sequencing, phylogenetic analysis, and physiological and biochemical tests. The pathogenicity of isolate X21 was studied using crucian carp as a model, and severe pathological damage in fish tissues was observed. The expression of IgT+ B cells and various cytokines in the tissues also showed significant changes. The survivability of crucian carp infected with isolate X21 was only 14.27%. This is the first report of E. coli O157:H7 infecting the freshwater fish C. carpio, indicating its potential threat to public health and freshwater fish aquaculture.
MICROBIAL PATHOGENESIS
(2023)
Article
Multidisciplinary Sciences
Jyot D. Antani, Rachit Gupta, Annie H. Lee, Kathy Y. Rhee, Michael D. Manson, Pushkar P. Lele
Summary: The bacterial flagellar motor is able to adapt its switching between clockwise and counterclockwise rotation in response to changes in mechanical load by controlling the binding affinity of the chemotaxis response regulator, CheY-P. This allows the motor to maintain optimal function in environments of varying viscosities. The interplay between mechanical forces and CheY-P binding tunes the chemotactic function to match the load, resembling proprioceptive feedback in neuromuscular systems.
NATURE COMMUNICATIONS
(2021)
Article
Veterinary Sciences
Gongmei Li, Maohui Li, Dan Yu, Wuwen Sun
Summary: This study evaluated the pathogenic effect of TGF-beta 1/Smad3 pathway in a mouse model infected with HPI+ and HPI- strains of Escherichia coli isolated from diarrhea in calves. The results showed significant injuries in the liver and kidney tissues of mice in the HPI+ and HPI- infection groups, increased apoptotic cells, and up-regulated expression of TGF-beta 1, Collagen I, and Smad3.
RESEARCH IN VETERINARY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Dandan Fu, Jianmei Wu, Yi Gu, Qianwen Li, Ying Shao, Hanshuang Feng, Xiangjun Song, Jian Tu, Kezong Qi
Summary: This study constructed ompR gene mutant and complement strains using the CRISPR-Cas9 system. It was found that inactivation of ompR gene attenuated the pathogenicity of APEC and affected bacterial motility, biofilm formation, and curli production.
Article
Microbiology
Hongxia Niu, Tuodi Li, Yunjie Du, Zhuoxuan Lv, Qianqian Cao, Ying Zhang
Summary: The roles of gltS, gltP, and gltI genes in E. coli tolerance and pathogenicity were investigated. The transcripts of these genes were found to be higher in stationary phase E. coli. Deletion of these genes resulted in decreased tolerance to antibiotics and stressors, as well as reduced adhesion, invasion, and survival ability in human bladder cells and mice. These findings enhance our understanding of bacterial tolerance and pathogenicity mechanisms.
Article
Microbiology
Kien Trung Le, Lam Thanh Nguyen, Loc Tan Huynh, Duc-Huy Chu, Long Van Nguyen, Tien Ngoc Nguyen, Tien Ngoc Tien, Keita Matsuno, Masatoshi Okamatsu, Takahiro Hiono, Norikazu Isoda, Yoshihiro Sakoda
Summary: The H9 and H6 subtypes of low pathogenicity avian influenza viruses (LPAIVs) cause significant economic losses in poultry, including Vietnam. Analysis of Vietnamese H9 and H6 LPAIVs revealed their genetic characteristics and antigenicity, indicating their circulation and potential impact on the poultry industry. The systemic replication of a representative H9 LPAIV in chickens was enhanced by coinfection with avian pathogenic Escherichia coli O2.
Review
Microbiology
Remy Colin, Bin Ni, Leanid Laganenka, Victor Sourjik
Summary: Swimming bacteria can follow gradients of nutrients and signaling molecules for optimal growth, with chemotaxis enhancing efficiency in environmental colonization. The balance between individual and collective behaviors is crucial, with multiple roles of motility and chemotaxis in bacterial swarming, biofilm formation, and interactions with hosts.
FEMS MICROBIOLOGY REVIEWS
(2021)
Review
Biology
Katherine M. Lagerstrom, Elizabeth A. Hadly
Summary: There is a lack of information on Escherichia coli in wild animals, despite evidence of pathogenic and antimicrobial-resistant strains in their gut microbiomes. As human populations expand into wild areas, the potential for harmful microorganisms to transfer between humans and wildlife increases, highlighting the need for greater research efforts to understand the implications for global public health.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Microbiology
Arya Suresh, Sabiha Shaik, Ramani Baddam, Amit Ranjan, Shamsul Qumar, Savita Jadhav, Torsten Semmler, Irfan A. Ghazi, Lothar H. Wieler, Niyaz Ahmed
Summary: The genotoxin colibactin produced by pathogenic E. coli strains is increasingly recognized for its critical implications in human health. This study analyzed the distribution, horizontal transmission, and evolution patterns of the island in different E. coli subtypes, shedding light on how pathogenic islands contribute to the clinical implications of infections.
Article
Immunology
Jin Hu, Dongfang Wang, Xingfa Huang, Yang Yang, Xin Lian, Wenjun Wang, Xiao Xu, Yulan Liu
Summary: This study explores the role of TolC in the pathogenesis of ExPEC strain PPECC42 and finds that TolC is closely associated with the virulence of ExPEC.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Safoura Derakhshan, Sanaz Ahmadi, Erfan Ahmadi, Sherko Nasseri, Abbas Aghaei
Summary: This study investigated the effect of antibiotics on the virulence of Escherichia coli in urinary tract infections. The results showed that sub-inhibitory concentrations of ciprofloxacin and ceftriaxone can reduce the expression levels of virulence factors and hemolysis.
Article
Biochemistry & Molecular Biology
Ting Liu, Kui Lin
MOLECULAR BIOSYSTEMS
(2015)
Article
Genetics & Heredity
Yan-Cong Zhang, Yan Zhang, Bi-Ru Zhu, Bo-Wen Zhang, Chuan Ni, Da-Yong Zhang, Ying Huang, Erli Pang, Kui Lin
STANDARDS IN GENOMIC SCIENCES
(2015)
Article
Evolutionary Biology
Wenpan Dong, Chao Xu, Tao Cheng, Kui Lin, Shiliang Zhou
GENOME BIOLOGY AND EVOLUTION
(2013)
Article
Plant Sciences
Da-Yong Zhang, Bo-Yu Zhang, Kui Lin, Xinhua Jiang, Yi Tao, Stephen Hubbell, Fangliang He, Annette Ostling
JOURNAL OF PLANT ECOLOGY
(2012)
Article
Plant Sciences
Fangliang He, Da-Yong Zhang, Kui Lin
JOURNAL OF PLANT ECOLOGY
(2012)
Article
Genetics & Heredity
Shaogui Guo, Jianguo Zhang, Honghe Sun, Jerome Salse, William J. Lucas, Haiying Zhang, Yi Zheng, Linyong Mao, Yi Ren, Zhiwen Wang, Jiumeng Min, Xiaosen Guo, Florent Murat, Byung-Kook Ham, Zhaoliang Zhang, Shan Gao, Mingyun Huang, Yimin Xu, Silin Zhong, Aureliano Bombarely, Lukas A. Mueller, Hong Zhao, Hongju He, Yan Zhang, Zhonghua Zhang, Sanwen Huang, Tao Tan, Erli Pang, Kui Lin, Qun Hu, Hanhui Kuang, Peixiang Ni, Bo Wang, Jingan Liu, Qinghe Kou, Wenju Hou, Xiaohua Zou, Jiao Jiang, Guoyi Gong, Kathrin Klee, Heiko Schoof, Ying Huang, Xuesong Hu, Shanshan Dong, Dequan Liang, Juan Wang, Kui Wu, Yang Xia, Xiang Zhao, Zequn Zheng, Miao Xing, Xinming Liang, Bangqing Huang, Tian Lv, Junyi Wang, Ye Yin, Hongping Yi, Ruiqiang Li, Mingzhu Wu, Amnon Levi, Xingping Zhang, James J. Giovannoni, Jun Wang, Yunfu Li, Zhangjun Fei, Yong Xu
Article
Genetics & Heredity
Tao Lin, Guangtao Zhu, Junhong Zhang, Xiangyang Xu, Qinghui Yu, Zheng Zheng, Zhonghua Zhang, Yaoyao Lun, Shuai Li, Xiaoxuan Wang, Zejun Huang, Junming Li, Chunzhi Zhang, Taotao Wang, Yuyang Zhang, Aoxue Wang, Yancong Zhang, Kui Lin, Chuanyou Li, Guosheng Xiong, Yongbiao Xue, Andrea Mazzucato, Mathilde Causse, Zhangjun Fei, James J. Giovannoni, Roger T. Chetelat, Dani Zamir, Thomas Staedler, Jingfu Li, Zhibiao Ye, Yongchen Du, Sanwen Huang
Article
Multidisciplinary Sciences
Xiaomei Wu, Erli Pang, Kui Lin, Zhen-Ming Pei
Article
Multidisciplinary Sciences
Yingqin Luo, Fabia Battistuzzi, Kui Lin
Article
Genetics & Heredity
Kui Lin, Erik Limpens, Zhonghua Zhang, Sergey Ivanov, Diane G. O. Saunders, Desheng Mu, Erli Pang, Huifen Cao, Hwangho Cha, Tao Lin, Qian Zhou, Yi Shang, Ying Li, Trupti Sharma, Robin van Velzen, Norbert de Ruijter, Duur K. Aanen, Joe Win, Sophien Kamoun, Ton Bisseling, Rene Geurts, Sanwen Huang
Article
Biochemical Research Methods
Jindan Guo, Erli Pang, Hongtao Song, Kui Lin
Summary: The study presents a new method called colored superbubble (cSupB) for organizing and analyzing spatial structure of genome graphs, proposing a novel tri-tuple coordinate system. The method efficiently detects small indels and can adapt to complex cycle structures.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Xinrui Lin, Ning Zhang, Hongtao Song, Kui Lin, Erli Pang
Summary: This study identified population-specific recent positive selection in cultivated cucumber populations using genomic variation data. The selected sites were associated with reproduction, stress response, and developmental regulation processes. Genes related to fruit traits were also observed, and soft sweeps were common in certain populations. These findings provide valuable insights into the biological mechanisms of cucumber adaptation and domestication.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Mingzhu Sun, Erli Pang, Wei-Ning Bai, Da-Yong Zhang, Kui Lin
Summary: Polyploidy is common and its effects are complex and variable. Computational tools for ploidy estimation are urgently needed to avoid cumbersome experiments. We developed ploidyfrost, a method for estimating ploidy levels without a reference genome, and evaluated its performance using different samples.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemical Research Methods
Jia Song, Sisi Zheng, Nhung Nguyen, Youjun Wang, Yubin Zhou, Kui Lin
BMC BIOINFORMATICS
(2017)
Proceedings Paper
Engineering, Biomedical
Peifeng Liang, Yancong Zhang, Kui Lin, Jinglu Hu
2014 36TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC)
(2014)