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Chen CX, Sun LN, Hou XX, Du PC, Wang XL, Du XC, Yu YF, Cai RK, Yu L, Li TJ, Luo MN, Shen Y, Lu C, Li Q, Zhang C, Gao HF, Ma X, Lin H, Cao ZF. Prevention and Control of Pathogens Based on Big-Data Mining and Visualization Analysis. Front Mol Biosci 2021; 7:626595. [PMID: 33718431 PMCID: PMC7947816 DOI: 10.3389/fmolb.2020.626595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Morbidity and mortality caused by infectious diseases rank first among all human illnesses. Many pathogenic mechanisms remain unclear, while misuse of antibiotics has led to the emergence of drug-resistant strains. Infectious diseases spread rapidly and pathogens mutate quickly, posing new threats to human health. However, with the increasing use of high-throughput screening of pathogen genomes, research based on big data mining and visualization analysis has gradually become a hot topic for studies of infectious disease prevention and control. In this paper, the framework was performed on four infectious pathogens (Fusobacterium, Streptococcus, Neisseria, and Streptococcus salivarius) through five functions: 1) genome annotation, 2) phylogeny analysis based on core genome, 3) analysis of structure differences between genomes, 4) prediction of virulence genes/factors with their pathogenic mechanisms, and 5) prediction of resistance genes/factors with their signaling pathways. The experiments were carried out from three angles: phylogeny (macro perspective), structure differences of genomes (micro perspective), and virulence and drug-resistance characteristics (prediction perspective). Therefore, the framework can not only provide evidence to support the rapid identification of new or unknown pathogens and thus plays a role in the prevention and control of infectious diseases, but also help to recommend the most appropriate strains for clinical and scientific research. This paper presented a new genome information visualization analysis process framework based on big data mining technology with the accommodation of the depth and breadth of pathogens in molecular level research.
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Affiliation(s)
- Cui-Xia Chen
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Li-Na Sun
- National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xue-Xin Hou
- National Institute for Communicable Disease Control and Prevention, Beijing, China
| | | | - Xiao-Long Wang
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Chen Du
- Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu-Fei Yu
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Rui-Kun Cai
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Lei Yu
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Tian-Jun Li
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Min-Na Luo
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Yue Shen
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Chao Lu
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Qian Li
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Chuan Zhang
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Hua-Fang Gao
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zong-Fu Cao
- National Research Institute for Family Planning, Beijing, China.,National Center of Human Genetic Resources, Beijing, China
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Jacquemot L, Bettarel Y, Monjol J, Corre E, Halary S, Desnues C, Bouvier T, Ferrier-Pagès C, Baudoux AC. Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen. Front Microbiol 2018; 9:2501. [PMID: 30405564 PMCID: PMC6207643 DOI: 10.3389/fmicb.2018.02501] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 11/13/2022] Open
Abstract
Biological control using bacteriophages is a promising approach for mitigating the devastating effects of coral diseases. Several phages that infect Vibrio coralliilyticus, a widespread coral pathogen, have been isolated, suggesting that this bacterium is permissive to viral infection and is, therefore, a suitable candidate for treatment by phage therapy. In this study, we combined functional and genomic approaches to evaluate the therapeutic potential of BONAISHI, a novel V. coralliilyticus phage, which was isolated from the coral reef in Van Phong Bay (Vietnam). BONAISHI appears to be strictly lytic for several pathogenic strains of V. coralliilyticus and remains infectious over a broad range of environmental conditions. This candidate has an unusually large dsDNA genome (303 kb), with no genes that encode known toxins or implicated in lysogeny control. We identified several proteins involved in host lysis, which may offer an interesting alternative to the use of whole bacteriophages for controlling V. coralliilyticus. A preliminary therapy test showed that adding BONAISHI to an infected culture of Symbiodinium sp. cells reduced the impact of V. coralliilyticus on Symbiodinium sp. photosynthetic activity. This study showed that BONAISHI is able to mitigate V. coralliilyticus infections, making it a good candidate for phage therapy for coral disease.
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Affiliation(s)
- Loïc Jacquemot
- Sorbonne Universités UPMC Paris 06, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Yvan Bettarel
- MARBEC, Université Montpellier, IRD, CNRS, Ifremer, Montpellier, France
| | - Joanne Monjol
- Sorbonne Universités UPMC Paris 06, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Erwan Corre
- Sorbonne Universités UPMC Paris 06, CNRS, FR2424 Fédération de Recherche, Station Biologique de Roscoff, Roscoff, France
| | - Sébastien Halary
- Aix Marseille Université, Microbes, Evolution Phylogeny and infection (MEPHI), CNRS FRE2013, IRD 198, AP-HM, IHU - Méditerranée Infection, Marseille, France
| | - Christelle Desnues
- Aix Marseille Université, Microbes, Evolution Phylogeny and infection (MEPHI), CNRS FRE2013, IRD 198, AP-HM, IHU - Méditerranée Infection, Marseille, France
| | - Thierry Bouvier
- MARBEC, Université Montpellier, IRD, CNRS, Ifremer, Montpellier, France
| | | | - Anne-Claire Baudoux
- Sorbonne Universités UPMC Paris 06, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
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Abstract
Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.
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Darde TA, Sallou O, Becker E, Evrard B, Monjeaud C, Le Bras Y, Jégou B, Collin O, Rolland AD, Chalmel F. The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. Nucleic Acids Res 2015; 43:W109-16. [PMID: 25883147 PMCID: PMC4489245 DOI: 10.1093/nar/gkv345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/06/2015] [Indexed: 12/23/2022] Open
Abstract
We report the development of the ReproGenomics Viewer (RGV), a multi- and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org.
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Affiliation(s)
- Thomas A Darde
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Olivier Sallou
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | | | - Bertrand Evrard
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France
| | - Cyril Monjeaud
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Yvan Le Bras
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Bernard Jégou
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France Ecole des Hautes Études en Santé Publique, Avenue du Professeur Léon-Bernard, F-35043 Rennes, France
| | - Olivier Collin
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | | | - Frédéric Chalmel
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France
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