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Tsai WH, Yeh WL, Chou CH, Wu CL, Lai CH, Yeh YT, Liao CA, Wu CC. Suppressive Effects of Lactobacillus on Depression through Regulating the Gut Microbiota and Metabolites in C57BL/6J Mice Induced by Ampicillin. Biomedicines 2023; 11:biomedicines11041068. [PMID: 37189686 DOI: 10.3390/biomedicines11041068] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Depression is a medical and social problem. Multiple metabolites and neuroinflammation regulate it. Modifying the gut microbiota with probiotics to reduce depression through the gut-brain axis is a potential treatment strategy. In this study, three anti-depressive potentials of Lactobacillus spp. (LAB), including L. rhamnosus GMNL-74, L. acidophilus GMNL-185 and L. plantarum GMNL-141, which combined to produce low dosage LAB (1.6 × 108 CFU/mouse, LABL) and high dosage LAB (4.8 × 108 CFU/mouse, LABH), were administered to C57BL/6 mice induced depression by ampicillin (Amp). A behavioral test of depression, 16S ribosomal RNA gene amplicon sequencing, bioinformatic analysis, and short-chain fatty acid (SCFA) content measurement were executed to investigate the gut microbiota composition, activation of nutrient metabolism pathways, levels of inflammatory factors, gut-derived 5-HT biosynthesis genes, and SCFA levels in C57BL/6 mice. Results showed that after mice were induced by Amp, both LAB groups recovered from depressive behaviors, decreased the abundance of Firmicutes, and increased the abundance of Actinobacteria and Bacteroidetes in the mouse ileum. The prediction of metabolism pathways of microbes revealed the activation of arginine and proline metabolism, cyanoamino acid metabolism, and nicotinate and nicotinamide metabolism were increased, and fatty acid synthesis was decreased in both LAB groups. The LABH groups showed increased levels of acetic acid, propanoic acid, and iso-butyric acid and decreased butyric acid levels in the cecum. LABH treatment increased claudin-5 and reduced IL-6 mRNA expression. Both LAB groups also reduced monoamine oxidase, and the LABH group increased vascular endothelial growth factor mRNA expression. These results showed that the composite of three LAB exerts antidepressant effects by regulating the gut microbiota and modifying the levels of depression-related metabolites in C57BL/6J Amp-treated mice.
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Affiliation(s)
- Wan-Hua Tsai
- Research and Development Department, GenMont Biotech Incorporation, Tainan 74144, Taiwan
| | - Wen-Ling Yeh
- Research and Development Department, GenMont Biotech Incorporation, Tainan 74144, Taiwan
| | - Chia-Hsuan Chou
- Research and Development Department, GenMont Biotech Incorporation, Tainan 74144, Taiwan
| | - Chia-Lin Wu
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Chih-Ho Lai
- Department of Microbiology, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Graduate Institute of Biomed—Ical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Yao-Tsung Yeh
- Aging and Diseases Prevention Research Center, Fooyin University, Kaohsiung 83102, Taiwan
| | - Chorng-An Liao
- Aging and Diseases Prevention Research Center, Fooyin University, Kaohsiung 83102, Taiwan
| | - Chih-Chung Wu
- Department of Food and Nutrition, Providence University, Taichung 43301, Taiwan
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2
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Liu Z, Zhang T, Wu K, Li Z, Chen X, Jiang S, Du L, Lu S, Lin C, Wu J, Wang X. Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:260-273. [PMID: 34252627 PMCID: PMC9684085 DOI: 10.1016/j.gpb.2021.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 04/30/2021] [Accepted: 07/01/2021] [Indexed: 01/05/2023]
Abstract
Periodontitis is an inflammatory disease that is characterized by progressive destruction of the periodontium and causes tooth loss in adults. Periodontitis is known to be associated with dysbiosis of the oral microflora, which is often linked to various diseases. However, the complexity of plaque microbial communities of periodontitis, antibiotic resistance, and enhanced virulence make this disease difficult to treat. In this study, using metagenomic shotgun sequencing, we investigated the etiology, antibiotic resistance genes (ARGs), and virulence genes (VirGs) of periodontitis. We revealed a significant shift in the composition of oral microbiota as well as several functional pathways that were represented significantly more abundantly in periodontitis patients than in controls. In addition, we observed several positively selected ARGs and VirGs with the Ka/Ks ratio > 1 by analyzing our data and a previous periodontitis dataset, indicating that ARGs and VirGs in oral microbiota may be subjected to positive selection. Moreover, 5 of 12 positively selected ARGs and VirGs in periodontitis patients were found in the genomes of respiratory tract pathogens. Of note, 91.8% of the background VirGs with at least one non-synonymous single-nucleotide polymorphism for natural selection were also from respiratory tract pathogens. These observations suggest a potential association between periodontitis and respiratory infection at the gene level. Our study enriches the knowledge of pathogens and functional pathways as well as the positive selection of antibiotic resistance and pathogen virulence in periodontitis patients, and provides evidence at the gene level for an association between periodontitis and respiratory infection.
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Affiliation(s)
- Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Tao Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Keke Wu
- Wenzhou Center for Disease Control and Prevention, Wenzhou 325000, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Lifeng Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Saisai Lu
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 352000, China
| | - Chongxiang Lin
- Department of Stomatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China,Corresponding authors.
| | - Xiaobing Wang
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 352000, China,Corresponding authors.
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3
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Urban C, Blom AA, Pfrengle S, Walker-Meikle K, Stone AC, Inskip SA, Schuenemann VJ. One Health Approaches to Trace Mycobacterium leprae's Zoonotic Potential Through Time. Front Microbiol 2021; 12:762263. [PMID: 34745073 PMCID: PMC8566891 DOI: 10.3389/fmicb.2021.762263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Hansen's disease (leprosy), mainly caused by infection with Mycobacterium leprae, has accompanied humanity for thousands of years. Although currently rare in Europe, there are over 200,000 new infections annually in South East Asia, Africa, and South America. Over the years many disciplines - palaeopathology, ancient DNA and other ancient biomolecules, and history - have contributed to a better understanding of leprosy's past, in particular its history in medieval Europe. We discuss their contributions and potential, especially in relation to the role of inter-species transmission, an unexplored phenomenon in the disease's history. Here, we explore the potential of interdisciplinary approaches that understand disease as a biosocial phenomenon, which is a product of both infection with M. leprae and social behaviours that facilitate transmission and spread. Genetic evidence of M. leprae isolated from archaeological remains combined with systematic zooarchaeological and historical analysis would not only identify when and in what direction transmission occurred, but also key social behaviours and motivations that brought species together. In our opinion, this combination is crucial to understand the disease's zoonotic past and current potential.
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Affiliation(s)
- Christian Urban
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Alette A. Blom
- Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | | | - Anne C. Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, United States
| | - Sarah A. Inskip
- School of Archaeology and Ancient History, University of Leicester, Leicester, United Kingdom
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4
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Guo H, Zhang W, Ni C, Cai Z, Chen S, Huang X. Heat map visualization for electrocardiogram data analysis. BMC Cardiovasc Disord 2020; 20:277. [PMID: 32513239 PMCID: PMC7281952 DOI: 10.1186/s12872-020-01560-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 05/28/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Most electrocardiogram (ECG) studies still take advantage of traditional statistical functions, and the results are mostly presented in tables, histograms, and curves. Few papers display ECG data by visual means. The aim of this study was to analyze and show data for electrocardiographic left ventricular hypertrophy (LVH) with ST-segment elevation (STE) by a heat map in order to explore the feasibility and clinical value of heat mapping for ECG data visualization. METHODS We sequentially collected the electrocardiograms of inpatients in the First Affiliated Hospital of Shantou University Medical College from July 2015 to December 2015 in order to screen cases of LVH with STE. HemI 1.0 software was used to draw heat maps to display the STE of each lead of each collected ECG. Cluster analysis was carried out based on the heat map and the results were drawn as tree maps (pedigree maps) in the heat map. RESULTS In total, 60 cases of electrocardiographic LVH with STE were screened and analyzed. STE leads were mainly in the V1, V2 and V3 leads. The ST-segment shifts of each lead of each collected ECG could be conveniently visualized in the heat map. According to cluster analysis in the heat map, STE leads were clustered into two categories, comprising of the right precordial leads (V1, V2, V3) and others (V4, V5, V6, I, II, III, aVF, aVL, aVR). Moreover, the STE amplitude in 40% (24 out of 60) of cases reached the threshold specified in the STEMI guideline. These cases also could be fully displayed and visualized in the heat map. Cluster analysis in the heat map showed that the III, aVF and aVR leads could be clustered together, the V1, V2, V3 and V4 leads could be clustered together, and the V5, V6, I and aVL leads could be clustered together. CONCLUSION Heat maps and cluster analysis can be used to fully display every lead of each electrocardiogram and provide relatively comprehensive information.
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Affiliation(s)
- Haisen Guo
- Department of Cardiology, Shantou Central Hospital, Shantou, 515000, Guangdong, China
| | - Weidai Zhang
- Department of Cardiology, Shantou Central Hospital, Shantou, 515000, Guangdong, China
| | - Chumin Ni
- Department of Cardiology, Shantou Central Hospital, Shantou, 515000, Guangdong, China
| | - Zhixiong Cai
- Department of Cardiology, Shantou Central Hospital, Shantou, 515000, Guangdong, China
| | - Songming Chen
- Department of Cardiology, the First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Shantou, 515000, Guangdong, China
| | - Xiansheng Huang
- Department of Cardiology, the First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Shantou, 515000, Guangdong, China.
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5
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Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen MF, Nielsen HB, Bork P, Wang J, Vilsbøll T, Hansen T, Knop FK, Arumugam M, Pedersen O. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol 2018; 3:1255-1265. [PMID: 30349083 DOI: 10.1038/s41564-018-0257-9] [Citation(s) in RCA: 402] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/28/2018] [Indexed: 12/18/2022]
Abstract
To minimize the impact of antibiotics, gut microorganisms harbour and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing-based metagenomics, we analysed the partial eradication and subsequent regrowth of the gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin. Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and the depletion of Bifidobacterium species and butyrate producers. The gut microbiota of the subjects recovered to near-baseline composition within 1.5 months, although 9 common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days. Species that harbour β-lactam resistance genes were positively selected for during and after the intervention. Harbouring glycopeptide or aminoglycoside resistance genes increased the odds of de novo colonization, however, the former also decreased the odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention and their antibiotics resistance gene carriage modulates their recovery processes.
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Affiliation(s)
- Albert Palleja
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Kristian H Mikkelsen
- Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Sofia K Forslund
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany.,Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité-Universitätsmedizin Berlin , Freie Universität Berlin Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alireza Kashani
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Danish Diabetes Academy, Odense, Denmark
| | - Kristine H Allin
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Epidemiology, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Trine Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Suisha Liang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Qiang Feng
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Chenchen Zhang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Paul Theodor Pyl
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Luis Pedro Coelho
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Athanasios Typas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Morten F Nielsen
- Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | | | - Peer Bork
- Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jun Wang
- iCarbonX, Shenzhen, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa Macau, China
| | - Tina Vilsbøll
- Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Filip K Knop
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark. .,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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6
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Crisan A, McKee G, Munzner T, Gardy JL. Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory. PeerJ 2018; 6:e4218. [PMID: 29340235 PMCID: PMC5767084 DOI: 10.7717/peerj.4218] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/12/2017] [Indexed: 11/23/2022] Open
Abstract
Background Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics—including clinicians, laboratorians, epidemiologists, and researchers—is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB) genomic test results. Methods We used Design Study Methodology—a human centered approach drawn from the information visualization domain—to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders’ needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report. Results We recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type). When we compared our four prototype reports against the existing design, we found that for the majority (86.7%) of design comparisons, participants preferred the alternative prototype designs over the existing version, and that both clinicians and non-clinicians expressed similar design preferences. Participants showed clearer design preferences when asked to compare individual design elements versus entire reports. Both the quantitative and qualitative data informed the design of a revised report, available online as a LaTeX template. Conclusions We show how a human-centered design approach integrating quantitative and qualitative feedback can be used to design an alternative report for representing complex microbial genomic data. We suggest experimental and design guidelines to inform future design studies in the bioinformatics and microbial genomics domains, and suggest that this type of mixed-methods study is important to facilitate the successful translation of pathogen genomics in the clinic, not only for clinical reports but also more complex bioinformatics data visualization software.
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Affiliation(s)
- Anamaria Crisan
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Geoffrey McKee
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tamara Munzner
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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7
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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8
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Carroll LN, Au AP, Detwiler LT, Fu TC, Painter IS, Abernethy NF. Visualization and analytics tools for infectious disease epidemiology: a systematic review. J Biomed Inform 2014; 51:287-98. [PMID: 24747356 PMCID: PMC5734643 DOI: 10.1016/j.jbi.2014.04.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 03/13/2014] [Accepted: 04/03/2014] [Indexed: 12/31/2022]
Abstract
BACKGROUND A myriad of new tools and algorithms have been developed to help public health professionals analyze and visualize the complex data used in infectious disease control. To better understand approaches to meet these users' information needs, we conducted a systematic literature review focused on the landscape of infectious disease visualization tools for public health professionals, with a special emphasis on geographic information systems (GIS), molecular epidemiology, and social network analysis. The objectives of this review are to: (1) identify public health user needs and preferences for infectious disease information visualization tools; (2) identify existing infectious disease information visualization tools and characterize their architecture and features; (3) identify commonalities among approaches applied to different data types; and (4) describe tool usability evaluation efforts and barriers to the adoption of such tools. METHODS We identified articles published in English from January 1, 1980 to June 30, 2013 from five bibliographic databases. Articles with a primary focus on infectious disease visualization tools, needs of public health users, or usability of information visualizations were included in the review. RESULTS A total of 88 articles met our inclusion criteria. Users were found to have diverse needs, preferences and uses for infectious disease visualization tools, and the existing tools are correspondingly diverse. The architecture of the tools was inconsistently described, and few tools in the review discussed the incorporation of usability studies or plans for dissemination. Many studies identified concerns regarding data sharing, confidentiality and quality. Existing tools offer a range of features and functions that allow users to explore, analyze, and visualize their data, but the tools are often for siloed applications. Commonly cited barriers to widespread adoption included lack of organizational support, access issues, and misconceptions about tool use. DISCUSSION AND CONCLUSION As the volume and complexity of infectious disease data increases, public health professionals must synthesize highly disparate data to facilitate communication with the public and inform decisions regarding measures to protect the public's health. Our review identified several themes: consideration of users' needs, preferences, and computer literacy; integration of tools into routine workflow; complications associated with understanding and use of visualizations; and the role of user trust and organizational support in the adoption of these tools. Interoperability also emerged as a prominent theme, highlighting challenges associated with the increasingly collaborative and interdisciplinary nature of infectious disease control and prevention. Future work should address methods for representing uncertainty and missing data to avoid misleading users as well as strategies to minimize cognitive overload.
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Affiliation(s)
- Lauren N Carroll
- Department of Biomedical Informatics and Medical Education, University of Washington, 850 Republican St., Box 358047, Seattle, WA 98109, United States.
| | - Alan P Au
- Department of Biomedical Informatics and Medical Education, University of Washington, 850 Republican St., Box 358047, Seattle, WA 98109, United States.
| | - Landon Todd Detwiler
- Department of Biological Structure, University of Washington, 1959 NE Pacific St., Box 357420, United States.
| | - Tsung-Chieh Fu
- Department of Epidemiology, University of Washington, 1959 NE Pacific St., Box 357236, Seattle, WA 98195, United States.
| | - Ian S Painter
- Department of Health Services, University of Washington, 1959 NE Pacific St., Box 359442, Seattle, WA 98195, United States.
| | - Neil F Abernethy
- Department of Biomedical Informatics and Medical Education, University of Washington, 850 Republican St., Box 358047, Seattle, WA 98109, United States; Department of Health Services, University of Washington, 1959 NE Pacific St., Box 359442, Seattle, WA 98195, United States.
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9
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Mao C, Abraham D, Wattam AR, Wilson MJC, Shukla M, Yoo HS, Sobral BW. Curation, integration and visualization of bacterial virulence factors in PATRIC. ACTA ACUST UNITED AC 2014; 31:252-8. [PMID: 25273106 PMCID: PMC4287947 DOI: 10.1093/bioinformatics/btu631] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Motivation: We’ve developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, www.patricbrc.org) to support infectious disease research. Although several VF databases are available, there is still a need to incorporate new knowledge found in published experimental evidence and integrate these data with other information known for these specific VF genes, including genomic and other omics data. This integration supports the identification of VFs, comparative studies and hypothesis generation, which facilitates the understanding of virulence and pathogenicity. Results: We have manually curated VFs from six prioritized NIAID (National Institute of Allergy and Infectious Diseases) category A–C bacterial pathogen genera, Mycobacterium, Salmonella, Escherichia, Shigella, Listeria and Bartonella, using published literature. This curated information on virulence has been integrated with data from genomic functional annotations, trancriptomic experiments, protein–protein interactions and disease information already present in PATRIC. Such integration gives researchers access to a broad array of information about these individual genes, and also to a suite of tools to perform comparative genomic and transcriptomics analysis that are available at PATRIC. Availability and implementation: All tools and data are freely available at PATRIC (http://patricbrc.org). Contact:cmao@vbi.vt.edu. Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chunhong Mao
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - David Abraham
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Alice R Wattam
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Maulik Shukla
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Hyun Seung Yoo
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Bruno W Sobral
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
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Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJC, Yoo HS, Zhang C, Zhang Y, Sobral BW. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 2013; 42:D581-91. [PMID: 24225323 PMCID: PMC3965095 DOI: 10.1093/nar/gkt1099] [Citation(s) in RCA: 880] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.
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Affiliation(s)
- Alice R Wattam
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60637, USA, Grado Department of Industrial & Systems Engineering, Virginia Tech, Blacksburg, VA 24060, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, IL 60637, USA and Nestlé Institute of Health Sciences SA, Campus EPFL, Quartier de L'innovation, Lausanne, Switzerland
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Protein arrays as tool for studies at the host-pathogen interface. J Proteomics 2013; 94:387-400. [PMID: 24140974 DOI: 10.1016/j.jprot.2013.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 09/06/2013] [Accepted: 10/08/2013] [Indexed: 01/10/2023]
Abstract
Pathogens and parasites encode a wide spectrum of multifunctional proteins interacting to and modifying proteins in host cells. However, the current lack of a reliable method to unveil the protein-protein interactions (PPI) at the host-pathogen interface is retarding our understanding of many important pathogenic processes. Thus, the identification of proteins involved in host-pathogen interactions is important for the elucidation of virulence determinants, mechanisms of infection, host susceptibility and/or disease resistance. In this sense, proteomic technologies have experienced major improvements in recent years and protein arrays are a powerful and modern method for studying PPI in a high-throughput format. This review focuses on these techniques analyzing the state-of-the-art of proteomic technologies and their possibilities to diagnose and explore host-pathogen interactions. Major technical advancements, applications and protocol concerns are presented, so readers can appreciate the immense progress achieved and the current technical options available for studying the host-pathogen interface. Finally, future uses of this kind of array-based proteomic tools in the fight against infectious and parasitic diseases are discussed.
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Lew JM, Mao C, Shukla M, Warren A, Will R, Kuznetsov D, Xenarios I, Robertson BD, Gordon SV, Schnappinger D, Cole ST, Sobral B. Database resources for the tuberculosis community. Tuberculosis (Edinb) 2013; 93:12-7. [PMID: 23332401 DOI: 10.1016/j.tube.2012.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 11/27/2012] [Indexed: 12/29/2022]
Abstract
Access to online repositories for genomic and associated "-omics" datasets is now an essential part of everyday research activity. It is important therefore that the Tuberculosis community is aware of the databases and tools available to them online, as well as for the database hosts to know what the needs of the research community are. One of the goals of the Tuberculosis Annotation Jamboree, held in Washington DC on March 7th-8th 2012, was therefore to provide an overview of the current status of three key Tuberculosis resources, TubercuList (tuberculist.epfl.ch), TB Database (www.tbdb.org), and Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org). Here we summarize some key updates and upcoming features in TubercuList, and provide an overview of the PATRIC site and its online tools for pathogen RNA-Seq analysis.
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Affiliation(s)
- Jocelyne M Lew
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
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Phylogeography of swine influenza H3N2 in the United States: translational public health for zoonotic disease surveillance. INFECTION GENETICS AND EVOLUTION 2012; 13:224-9. [PMID: 23137647 DOI: 10.1016/j.meegid.2012.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 12/31/2022]
Abstract
The field of phylogeography has received a lot of attention for its application to molecular evolution and geographic migration of species. More recent work has included infectious diseases especially zoonotic RNA viruses like influenza and rabies. Phylogeography of viruses has the potential to advance surveillance at agencies such as public health departments, agriculture departments, and wildlife agencies. However, little is known about how these agencies could use phylogeography for applied surveillance and the integration of animal and human sequence data. Here, we highlight its potential to support 'translational public health' that could bring sequence data to the forefront of surveillance. We focus on swine influenza H3N2 because of the recent link to a variant form that has also infected humans. We discuss the implications to applied surveillance and the need for an integrated biomedical informatics approach for adoption at agencies of animal and public health.
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Zhou H, Jin J, Wong L. Progress in computational studies of host-pathogen interactions. J Bioinform Comput Biol 2012; 11:1230001. [PMID: 23600809 DOI: 10.1142/s0219720012300018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Host-pathogen interactions are important for understanding infection mechanism and developing better treatment and prevention of infectious diseases. Many computational studies on host-pathogen interactions have been published. Here, we review recent progress and results in this field and provide a systematic summary, comparison and discussion of computational studies on host-pathogen interactions, including prediction and analysis of host-pathogen protein-protein interactions; basic principles revealed from host-pathogen interactions; and database and software tools for host-pathogen interaction data collection, integration and analysis.
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Affiliation(s)
- Hufeng Zhou
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore 117456, Singapore.
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