Article
Biochemistry & Molecular Biology
Brett Trost, Bhooma Thiruvahindrapuram, Ada J. S. Chan, Worrawat Engchuan, Edward J. Higginbotham, Jennifer L. Howe, Livia O. Loureiro, Miriam S. Reuter, Delnaz Roshandel, Joe Whitney, Mehdi Zarrei, Matthew Bookman, Cherith Somerville, Rulan Shaath, Mona Abdi, Elbay Aliyev, Rohan Patel, Thomas Nalpathamkalam, Giovanna Pellecchia, Omar Hamdan, Gaganjot Kaur, Zhuozhi Wang, Jeffrey R. MacDonald, John Wei, Wilson W. L. Sung, Sylvia Lamoureux, Ny Hoang, Thanuja Selvanayagam, Nicole Deflaux, Melissa Geng, Siavash Ghaffari, John Bates, Edwin J. Young, Qiliang Ding, Carole Shum, Lia D'Abate, Clarrisa A. Bradley, Annabel Rutherford, Vernie Aguda, Beverly Apresto, Nan Chen, Sachin Desai, Xiaoyan Du, Matthew L. Y. Fong, Sanjeev Pullenayegum, Kozue Samler, Ting Wang, Karen Ho, Tara Paton, Sergio L. Pereira, Jo-Anne Herbrick, Richard F. Wintle, Jonathan Fuerth, Juti Noppornpitak, Heather Ward, Patrick Magee, Ayman Al Baz, Usanthan Kajendirarajah, Sharvari Kapadia, Jim Vlasblom, Monica Valluri, Joseph Green, Vicki Seifer, Morgan Quirbach, Olivia Rennie, Elizabeth Kelley, Nina Masjedi, Catherine Lord, Michael J. Szego, Ma'n H. Zawati, Michael Lang, Lisa J. Strug, Christian R. Marshall, Gregory Costain, Kristina Calli, Alana Iaboni, Afiqah Yusuf, Patricia Ambrozewicz, Louise Gallagher, David G. Amaral, Jessica Brian, Mayada Elsabbagh, Stelios Georgiades, Daniel S. Messinger, Sally Ozonoff, Jonathan Sebat, Calvin Sjaarda, Isabel M. Smith, Peter Szatmari, Lonnie Zwaigenbaum, Azadeh Kushki, Thomas W. Frazier, Jacob A. S. Vorstman, Khalid A. Fakhro, Bridget A. Fernandez, M. E. Suzanne Lewis, Rosanna Weksberg, Marc Fiume, Ryan K. C. Yuen, Evdokia Anagnostou, Neal Sondheimer, David Glazer, Dean M. Hartley, Stephen W. Scherer
Summary: This study identifies rare variants associated with autism spectrum disorder (ASD) through whole-genome sequencing (WGS) and provides a research guide to explore genotype-phenotype correlations in families carrying these rare variants.
Article
Biotechnology & Applied Microbiology
Adepeju E. Onasanya, Charles El-Hage, Andres Diaz-Mendez, Paola K. Vaz, Alistair R. Legione, Glenn F. Browning, Joanne M. Devlin, Carol A. Hartley
Summary: This study analyzed the genome diversity and recombination mechanism of EHV2 virus. The results showed a high degree of genetic diversity and extensive recombination networks in EHV2 genomes. Recombination may be an important mechanism for EHV2 genome variation and evolution.
Article
Genetics & Heredity
Ulykbek Kairov, Askhat Molkenov, Aigul Sharip, Saule Rakhimova, Madina Seidualy, Arang Rhie, Ulan Kozhamkulov, Maxat Zhabagin, Jong-Il Kim, Joseph H. Lee, Joseph D. Terwilliger, Jeong-Sun Seo, Zhaxybay Zhumadilov, Ainur Akilzhanova
Summary: Kazakhstan, located along the Great Silk Road, has a rich history and a multiethnic population. By sequencing and analyzing the genomes of five ethnic Kazakhs, this study identified genetic variants associated with higher risks of diseases and demonstrated the importance of genotype-phenotype relations at the population level.
FRONTIERS IN GENETICS
(2022)
Article
Microbiology
Hongbo Jiang, Jie Bao, Yuenan Xing, Xiaodong Li, Qijun Chen
Summary: This study sequenced the whole genome of the pathogenic yeast M. bicuspidata LNES0119 and performed comparative genomic analysis, identifying several characteristics related to pathogenicity and virulence. The findings provide valuable insights into understanding the molecular basis of M. bicuspidata pathogenicity and potential therapeutic targets.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Jose R. Aguirre-Sanchez, Beatriz Quinones, Jose A. Ortiz-Munoz, Rogelio Prieto-Alvarado, Ines F. Vega-Lopez, Jaime Martinez-Urtaza, Bertram G. Lee, Cristobal Chaidez
Summary: Comparative genomic analysis of C. werkmanii strains revealed distinct clades with different virulence and antimicrobial resistance genes. Strains in clade V, mainly from clinical sources, showed high pathogenicity and multidrug resistance, including resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. This study highlights the virulence potential of C. werkmanii as an opportunistic human pathogen.
Article
Microbiology
Guangcun Zhang, Qiang Zhao, Kun Ye, Liyan Ye, Yanning Ma, Jiyong Yang
Summary: This study analyzed 164 clinical isolates of Citrobacter spp. using whole-genome sequencing and identified 14 different species. Some strains showed potential pathogenicity. Conventional identification methods have limitations in identifying Citrobacter spp.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Plant Sciences
Siyoung Lee, Girim Park, Yunseo Choi, Seoyeon Park, Hoytaek Kim, Oakjin Lee, Taebok Kim, Younghoon Park
Summary: In this study, the genetic basis of high trans-lycopene contents in red-fleshed watermelons was evaluated. The results showed that CIR6 on chromosome 6 is a major genomic region associated with the variation in trans-lycopene contents. Additionally, two CAPS markers (CIR6-M1 and CIR6-M4) were identified for marker-assisted selection.
Article
Microbiology
Daniel Castillo, Valentina L. Donati, Johanna Jorgensen, Krister Sundell, Inger Dalsgaard, Lone Madsen, Tom Wiklund, Mathias Middelboe
Summary: This study analyzed whole-genome sequences of 25 F. psychrophilum isolates from Baltic Sea countries and found a conserved population across these countries, with no clear association between genomic information and virulence traits. Analysis of four isolates at the whole-genome level revealed genetic variances in certain proteins and gene regions, providing insights into the genetic variation and potential role in modulating F. psychrophilum virulence.
Article
Microbiology
Zhoujie Ma, Yufei Huang, Zhaoran Zhang, Xiaodi Liu, Yuanhu Xuan, Bo Liu, Zenggui Gao
Summary: Setosphaeria turcica f. sp. zeae and S. turcica f. sp. sorghi, as two formae speciales, exhibit host specificity related to cellulase, with fewer pathogen numbers seen in corn compared to sorghum. The study provides a theoretical basis for future research on the pathogenicity of these two formae speciales.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Agronomy
Elsa Baltazar, Sara Rodrigues, Aitana Ares, Alexandra Camelo, Ines Brandao, Christophe Espirito Santo, Joao Trovao, Eva Garcia, Joana Costa
Summary: Cova da Beira region in Portugal is known for its peach production, however, recent surveys have shown symptoms of decline and the presence of the Brown rot disease caused by Monilinia fructicola. Symptomatic plant material from thirteen orchards was collected and used for fungal isolation and molecular detection. M. fructicola was confirmed in two orchards morphologically and molecularly, and detected in two others using duplex real-time PCR. This is the first detection of M. fructicola in P. persica in Portugal.
Article
Biotechnology & Applied Microbiology
David Longbottom, Morag Livingstone, Paolo Ribeca, Delphine Sylvie Anne Beeckman, Arie van der Ende, Yvonne Pannekoek, Daisy Vanrompay
Summary: The study classified a strain of Chlamydia psittaci as more closely related to Chlamydia abortus through various methods. It was also discovered that the strain carries an extrachromosomal plasmid, which has implications for gene function research and vaccine development.
Article
Microbiology
Menghan Li, Shaofei Yan, Seamus Fanning, Fengqin Li, Jin Xu
Summary: This study identified multi-drug resistant L. innocua isolated from food, revealing resistance islands on plasmids and chromosomes, and highlighting the potential gene transfer between L. monocytogenes and L. innocua. The findings emphasize the importance of including both L. monocytogenes and L. innocua in food surveillance programs to understand the origins of antimicrobial resistance and virulence markers.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung, Isheng Jason Tsai
Summary: This study investigates the genome diversity and transcriptome responses of the Fusarium solani species complex (FSSC), which includes fungal pathogens responsible for mortality in animals and plants. The study provides insights into the evolution of FSSC chromosomes and establishes an animal model for fungal pathogens.
Article
Agriculture, Dairy & Animal Science
Zhanwei Zhuang, Jie Wu, Yibin Qiu, Donglin Ruan, Rongrong Ding, Cineng Xu, Shenping Zhou, Yuling Zhang, Yiyi Liu, Fucai Ma, Jifei Yang, Ying Sun, Enqin Zheng, Ming Yang, Gengyuan Cai, Jie Yang, Zhenfang Wu
Summary: In this study, whole genome sequence (WGS) data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction (GBLUP) for meat quality in large-scale crossbred commercial pigs. The results showed that using WGS data for genomic prediction resulted in different accuracies for different meat quality traits, ranging from 0.08 to 0.47. The study also found that MultiBLUP outperformed GBLUP and yielded accuracy increases ranging from 17.39% to 75%. Furthermore, genotype imputation from 50K chip to WGS level showed a high concordance rate and correlation coefficient.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2023)
Article
Microbiology
Belen Gonzalez-Santamarina, Silvia Garcia-Soto, Helmut Hotzel, Diana Meemken, Reinhard Fries, Herbert Tomaso
Summary: S. Derby is a common cause of salmonellosis in humans and animals. Understanding its genetic diversity and resistance to antimicrobial treatment is crucial for epidemiological control. In this study, 15 S. Derby strains from Germany were analyzed, showing similar genetic diversity among strains from different sources, with most isolates carrying resistance genes and plasmids carrying antimicrobial resistance genes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Tianyuan Jia, Bin Liu, Huiqian Mu, Chengqian Qian, Lu Wang, Linxing Li, Gege Lu, Wenxuan Zhu, Xi Guo, Bin Yang, Di Huang, Lu Feng
Summary: The study introduces a novel sRNA, EsrF, in Enterohemorrhagic Escherichia coli O157:H7, which senses high ammonium concentrations in the colon and promotes pathogenicity by enhancing bacterial motility and adhesion to host cells. The findings demonstrate that EsrF interacts with the flagellar biosynthetic gene, flhB, mRNA and upregulates the expression of flagellar genes, leading to increased motility and virulence. Additionally, high ammonium concentrations in the colon induce EsrF expression, releasing the inhibition by NtrC and promoting bacterial colonization in the host colon.
Article
Microbiology
Chengqian Qian, Min Huang, Yuhui Du, Jingjie Song, Huiqian Mu, Yi Wei, Si Zhang, Zhiqiu Yin, Chao Yuan, Bin Liu
Summary: This study shows that the C. sakazakii G4023 strain has stronger desiccation tolerance than the ATCC 29544 strain. Transcriptome and proteome analysis reveal the genes and proteins involved in desiccation adaptation mechanisms. Understanding these mechanisms can guide the production and preservation of infant formula and other foods to reduce the survival odds of C. sakazakii and lower its exposure to infants.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Yuhui Du, Xinbei Liu, Xusheng Dong, Zhiqiu Yin
Summary: The pollution caused by plastic waste is a serious environmental crisis, with plastic being detected even in human tissues. In the ocean, plastic waste fragments into microplastics and forms a surface biofilm called plastisphere, inhabited by microbial communities. This review summarizes recent studies on microorganisms in the plastisphere, explores the interactions between microplastics and the plastisphere, discusses types of microplastic-degrading bacteria in the ocean, and speculates on their potential sources using the seed bank theory.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Yuhui Du, Yuan Jin, Beiping Li, Junjie Yue, Zhiqiu Yin
Summary: In this study, a comparative genomic analysis of Vibrio cincinnatiensis was conducted, revealing its genetic diversity and genomic plasticity. The evolution of the core genome was mainly driven by purifying selection, and horizontal gene transfer events from other Vibrio species contributed to its pathogenicity. This pan-genome study provides comprehensive insights into this poorly understood species from the genomic perspective.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Yuhui Du, Wei Song, Zhiqiu Yin, Shengbo Wu, Jiaheng Liu, Ning Wang, Hua Jin, Jianjun Qiao, Yi-Xin Huo
Summary: A high-quality chromosome-level genome assembly of Azadirachta indica was constructed, providing insights into its genome architecture and facilitating comparative genomic analysis. The estimated genome size is 281 Mb, with 115 Mb of repetitive elements and 25,767 protein-coding genes. Evolutionary analysis suggests no whole-genome duplication, but recent duplications of some genes and genomic segments. Specific clusters of secondary metabolites, TPS genes, and CYP genes were identified, with many located on chromosome 13, indicating its importance in terpene biosynthesis in A. indica.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Zhiqiu Yin, Xin Wang, Yujie Hu, Jikun Zhang, Hui Li, Yanru Cui, Dongying Zhao, Xusheng Dong, Xiaohang Zhang, Kai Liu, Binghai Du, Yanqin Ding, Chengqiang Wang
Summary: A novel PGPR strain BY2G20 was isolated from saline-alkaline soil in Dongying, China. It showed the ability to grow in a wide range of salt concentration and pH, and can inhibit the growth of Ralstonia solanacearum. Comparative genomic analysis revealed its evolutionary plasticity and adaptation to saline-alkaline environment. Maize inoculated with BY2G20 exhibited enhanced growth under salt stress.
Article
Microbiology
Zhiqiu Yin, Xinbei Liu, Chengqian Qian, Li Sun, Shiqi Pang, Jianing Liu, Wei Li, Weiwei Huang, Shiyu Cui, Chengkai Zhang, Weixing Song, Dandan Wang, Zhihong Xie
Summary: This study conducted a comprehensive pan-genome analysis of D. tsuruhatensis, revealing extensive genetic diversity and plasticity. Horizontal gene transfer and purifying selection are important forces in the genetic evolution of this bacterium. Diverse genetic elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance were found, indicating the pathogenic potential. The genetic traits related to secondary metabolism, carbohydrate active enzymes, and phosphate transporter suggest potential applications in agriculture and biological control.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Xinbei Liu, Dandan Wang, Zhiqiu Yin, Li Sun, Shiqi Pang, Jianing Liu, Wei Li, Shiyu Cui, Weiwei Huang, Yuhui Du, Zhihong Xie
Summary: Although PVA is biodegradable, its widespread use has caused serious environmental problems. Limited knowledge exists regarding effective PVA-degrading bacteria, highlighting the importance of discovering new PVA biodegraders. In this study, a novel bacterium AC3 was isolated and its complete genome was sequenced. The genomic characteristics and potential genetic basis of PVA degradation were comprehensively investigated, providing insights into C. nepalense and PVA bioremediation.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Bin Liu, Yutao Liu, Bin Yang, Qian Wang, Xingmei Liu, Jingliang Qin, Ke Zhao, Fan Li, Xiaohui Feng, Linxing Li, Pan Wu, Miaomiao Liu, Siwei Zhu, Lu Feng, Lei Wang
Summary: This study reveals that EHEC O157:H7 acquired a previously uncharacterized regulatory system rbfSR, which senses riboflavin produced by gut microbiota and activates the expression of virulence genes. This acquisition represents an essential step in the evolution of the highly pathogenic O157:H7. The introduction of rbfSR into other EHEC serotypes also increased their pathogenicity, indicating a potential public health issue.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Tianyuan Jia, Pan Wu, Bin Liu, Miaomiao Liu, Huiqian Mu, Dan Liu, Min Huang, Linxing Li, Yi Wei, Lu Wang, Qian Yang, Yutao Liu, Bin Yang, Di Huang, Liang Yang
Summary: Escherichia coli strains including enterohemorrhagic E. coli (EHEC) and enteropathogenic E. coli (EPEC) can cause severe gastroenteritis. An RNA called EsrL promotes the pathogenicity, adhesion, and biofilm formation of these strains. The expression of EsrL is repressed by PhoB under low-phosphate conditions, but relieved in a phosphate-rich environment. EsrL interacts with and stabilizes important transcripts, leading to increased adhesion and colonization in the host intestine.
Article
Gastroenterology & Hepatology
Jialin Wu, Yutao Liu, Wendi Li, Fan Li, Ruiying Liu, Hao Sun, Jingliang Qin, Xiaohui Feng, Di Huang, Bin Liu
Summary: This study systematically investigates the influence of MerR family regulators on intestinal colonization of V. cholerae. The researchers found that MlrA significantly promotes the colonization capacity of V. cholerae in the host intestine by directly enhancing the expression of the important virulence factor tcpA. Furthermore, they revealed that mlrA is activated by anaerobic signals in the small intestine of the host through Fnr during infection. These findings provide insights into a MlrA-mediated virulence regulation pathway in V. cholerae, allowing it to sense environmental signals and activate virulence gene expression.
Article
Microbiology
Dandan Wang, Li Sun, Zhiqiu Yin, Shiyu Cui, Weiwei Huang, Zhihong Xie
Summary: The accumulation of autotoxins in soil can impact crop growth, but the bioremediation of autotoxins by microorganisms offers a solution. In this study, strain ZH07 was found to utilize various autotoxins and promote plant growth, highlighting its potential as a plant growth stimulator.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Yanan Liu, Xiaolin Liu, Xiaoyan Dong, Zhiqiu Yin, Zhihong Xie, Yongming Luo
Summary: Protein acetylation can modify the physiology of bacteria to respond to changes in environmental or nutritional conditions. In this study, the lysine acetylome of Azorhizobium caulinodans strain ORS571 was identified, and it was found that acetylation plays a role in various physiological processes and is involved in chemotaxis.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Yuhui Du, Jinrong Zou, Zhiqiu Yin, Tingjian Chen
Summary: We evaluated the genetic diversity and evolutionary dynamics of Agrobacterium fabrum through comparative genomic analysis. The study revealed high genomic plasticity and the presence of mobile genetic elements and potentially horizontally transferred genes. The core genome underwent stronger purifying selection with some positively selected sites. Additionally, significant differences in functional features and evolutionary constraints were observed between chromosome 1 and the chromid.
MICROBIOLOGY SPECTRUM
(2023)
Article
Chemistry, Multidisciplinary
Jian Yuan, Xiaolong Jiang, Huijing Zhang, Jing Bai, Jing Zhang, Yuhui Wang, Gege Lu, Huimin Xu, Huanhuan Liu, Bin Liu, Di Huang
Summary: This study developed a green artificial biosynthesis pathway for catalyzing the poly-LacNAc glycosylation of protein in the cytoplasm of Escherichia coli, utilizing enzymes from Streptococcus parasanguinis, Neisseria meningitidis, and Helicobacter pylori. By rewiring the metabolic network of the strain, the researchers achieved the goal of poly-LacNAc glycoprotein biosynthesis and further improved the degree of polymerization. This approach opens up new avenues for efficient and green manufacturing of various glycoprotein structures with diverse biomedical applications, reducing or eliminating the use or generation of hazardous substances.