Integration of Host, Pathogen and Microbiome -omics Data for Studying Infectious Diseases

Integration of Host, Pathogen and Microbiome -omics Data for Studying Infectious Diseases
Author: Mohammadhassan Mirhakkak Esfahani
Publisher:
Total Pages: 0
Release: 2022*
Genre:
ISBN:

In an ever-growing worldwide population, human infectious diseases are an increasingly serious problem for public health. In particular, more than a million deaths and millions of infectious disease cases per year caused by fungal pathogens have been reported globally in recent years. Hence, more investments must be put into fungal research to overcome the problem. The opportunistic pathogen Candida albicans and the airborne Aspergillus fumigatus are the two most prevalent fungal pathogens causing serious issues in medical care units. Despite the recent advances in fungal research, there is little knowledge about the role of fungal metabolism in developing the infection when coexisting within the human body with microbial community members in different organs. This dissertation applied computational tools, and implemented systems biology approaches to uncover key factors in the colonization of the pathogens, especially C. albicans and A. fumigatus, from a systems biology perspective and unseen by wet-lab experiments alone. Next to multi-omics data analysis, a major effort was put into genome-scale metabolic models (GEMs) generation and analysis as a promising approach to shed light on the role of metabolism in developing the infection. In brief, this thesis sheds light on key factors leading to the inhibition or promotion of fungal growth. This especially includes the first available GEM reconstruction of C. albicans to theoretically study the intricate interaction of the fungus with the human host and the microbial community members. Lastly, a platform of 252 A. fumigatus GEMs at the strain resolution was generated. It revealed the phenotypic diversity of A. fumigatus strains isolated from different hospitals and farms in Germany and explained the contribution of the fungus to the shaping of the metabolic landscape of the lung microbiome in a favorable manner for fungal growth.

Integrated Omics Approaches to Infectious Diseases

Integrated Omics Approaches to Infectious Diseases
Author: Saif Hameed
Publisher: Springer Nature
Total Pages: 538
Release: 2021-07-18
Genre: Medical
ISBN: 9811606919

This book examines applications of multi-omics approaches for understanding disease etiology, pathogenesis, host-pathogen interactions. It also analyzes the genetics, immunological and metabolic mechanisms underlying the infections. The book also explores genomics, transcriptomics, translational-omics, and metabolomics approaches to understand the pathogenesis and identify potential drug targets. It reviews the role of epigenetic reprogramming in shaping the host-pathogen interactions and presents bioinformatics application in the identification of drug targets. Further, it examines the potential applications of RNA sequencing and non-coding RNA profiling to identify the pathogenesis. Lastly, it offers the current challenges, technological advances, and prospects of using multi-omics technologies in infectious biology.

Host - Pathogen Interaction

Host - Pathogen Interaction
Author: Gottfried Unden
Publisher: John Wiley & Sons
Total Pages: 236
Release: 2016-09-06
Genre: Science
ISBN: 3527337458

In light of the rapidity increasing incidence rate of bacterial and fungal infections with multi-resistant pathogens, the metabolic changes associated with host-pathogen interactions offer one of the most promising starting points for developing novel antibiotics. . Part one of this comprehensive guide describes the metabolic adaptation of pathogenic microbes in humans, while part two points to routes for the development of novel antibiotics. This is volume six of the book series on drug discovery in infectious diseases by Paul Selzer.

Recent Advances on Model Hosts

Recent Advances on Model Hosts
Author: Eleftherios Mylonakis
Publisher: Springer Science & Business Media
Total Pages: 135
Release: 2011-12-01
Genre: Science
ISBN: 1441956387

Most studies of bacterial or fungal infectious diseases focus separately on the pathogenic microbe, the host response, or the characterization of therapeutic compounds. Compartmentalization of pathogenesis-related research into an analysis of the “pathogen”, the “host,” or the “antimicrobial compound” has largely been dictated by the lack of model systems in which all of these approaches can be used simultaneously, as well as by the traditional view that microbiology, immunology, and chemical biology and pharmacology are separate disciplines. An increasing number of workers from different fields have turned to insects, fish, worms and other model hosts as facile, ethically expedient, relatively simple, and inexpensive hosts to model a variety of human infectious diseases and to study host responses and innate immunity. Because many of these hosts are genetically tractable, they can be used in conjunction with an appropriate pathogen to facilitate the discovery of novel features of the host innate immune response. This book provides a series of reports from the 1st International Conference on Model Hosts. This first of its kind meeting focused on invertebrate, vertebrate and amoeboid systems used for the study of host-pathogen interactions, virulence and immunity, as well as on the relevance of these pathogenesis systems and mammalian models. Importantly, a common, fundamental set of molecular mechanisms is employed by a significant number of microbial pathogens against a widely divergent array of metazoan hosts. Moreover, the evolutionarily conserved immune responses of these model hosts have contributed important insights to our understanding of the innate immune response of mammals. This book provides a series of reports from the 1st International Conference on Model Hosts. This first of its kind meeting focused on invertebrate, vertebrate and amoeboid systems used for the study of host-pathogen interactions, virulence and immunity, as well as on the relevance of these pathogenesis systems and mammalian models. Importantly, a common, fundamental set of molecular mechanisms is employed by a significant number of microbial pathogens against a widely divergent array of metazoan hosts. Moreover, the evolutionarily conserved immune responses of these model hosts have contributed important insights to our understanding of the innate immune response of mammals.

Application and Integration of Omics-powered Diagnostics in Clinical and Public Health Microbiology

Application and Integration of Omics-powered Diagnostics in Clinical and Public Health Microbiology
Author: Jacob Moran-Gilad
Publisher: Springer Nature
Total Pages: 240
Release: 2021-05-24
Genre: Science
ISBN: 3030621553

Various “omics” methods have recently revolutionized molecular diagnostics. Next-generation sequencing (NGS) makes it possible to sequence a human genome in just one day. Whole genome sequencing (WGS) greatly improves the ability to investigate the outbreaks of numerous pathogens. Metagenomics helps to analyze the microbiome, which aids greatly in identifying the pathogenesis of infectious diseases. Proteomic-based methods, namely matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF-MS), have a promising role in identifying myctobacteria and fungi, and predicting antimicrobial resistance. While there are numerous scientific publications on “omics” applications for microbiology, there are relatively few books that review this topic from a clinical diagnostics perspective. This book looks at this field from a holistic viewpoint, instead of limiting by type of “omics” technology, in order to cover the body of knowledge needed for practitioners and academics interested in clinical and public health microbiology. Additionally, it addresses the management, economical, regulatory and operational aspects of integrating these technologies into routine diagnostics.

The Microbiota in Gastrointestinal Pathophysiology

The Microbiota in Gastrointestinal Pathophysiology
Author: Martin H. Floch
Publisher: Academic Press
Total Pages: 444
Release: 2016-11-16
Genre: Science
ISBN: 0128040629

The Microbiota in Gastrointestinal Pathophysiology: Implications for Human Health, Prebiotics, Probiotics and Dysbiosis is a one-stop reference on the state-of-the-art research on gut microbial ecology in relation to human disease. This important resource starts with an overview of the normal microbiota of the gastrointestinal tract, including the esophagus, stomach, Ileum, and colon. The book then identifies what a healthy vs. unhealthy microbial community looks like, including methods of identification. Also included is insight into which features and contributions the microbiota make that are essential and useful to host physiology, as is information on how to promote appropriate mutualisms and prevent undesirable dysbioses. Through the power of synthesizing what is known by experienced researchers in the field, current gaps are closed, raising understanding of the role of the microbiome and allowing for further research. Explains how to modify the gut microbiota and how the current strategies used to do this produce their effects Explores the gut microbiota as a therapeutic target Provides the synthesis of existing data from both mainstream and non-mainstream sources through experienced researchers in the field Serves as a ‘one-stop’ shop for a topic that’s currently spread across a number of various journals

New Frontiers of Molecular Epidemiology of Infectious Diseases

New Frontiers of Molecular Epidemiology of Infectious Diseases
Author: Serge Morand
Publisher: Springer
Total Pages: 0
Release: 2014-11-28
Genre: Medical
ISBN: 9789400792524

Molecular epidemiology has recently broaden its focuses due to the development of molecular tools but also by incorporating advances of other fields such as mathematical epidemiology, molecular ecology, population genetics and evolution. Facing new risks of emerging and re-emerging infectious diseases that are threats for humans and their livestock, the objectives of molecular epidemiology include: - the development of molecular tools, genotyping and gene expression - the incorporation of concepts and results of population genetics of infectious diseases - the integration of recent advances in theoretical epidemiology and evolutionary ecology of diseases - a better understanding of transmission for the development of risk factors analyses. This book will demonstrate how the latest developments in molecular tools and in epidemiology can be integrated with studies of host-pathogen interactions. Besides a strong theoretical component, there will also be an emphasis on applications in the fields of epidemiology, public health, veterinary medicine, and health ecology. Students and researchers in the fields of epidemiology, animal and human health, evolutionary ecology, parasitology are the main potential readers of the book, as well as a broader audience from veterinary medicine and conservation.

Host-Pathogen Interactions

Host-Pathogen Interactions
Author: Steffen Rupp
Publisher: Humana Press
Total Pages: 428
Release: 2008-11-01
Genre: Science
ISBN: 9781603279895

In recent decades, infectious diseases, once believed to be fairly contained, have become a vital, resurgent field of research. In Host-Pathogen Interactions: Methods and Protocols, top experts examine the relationship between the host and the pathogen, crucial in the outcome of an infection and the establishment of disease or asymptomatic, commensal colonization by organisms. The step-by-step laboratory methods and protocols of this volume study host-pathogen interaction, with a focus on fungal, bacterial and parasitic pathogens, at a molecular level in order to reveal the mechanisms of infection and to identify the vulnerabilities of the pathogen of interest. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters feature brief subject introductions, lists of the necessary materials and reagents, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Host-Pathogen Interactions: Methods and Protocols serves as an easy entry point for all those investigating the factors responsible for the pathogenicity of microorganisms.

Systems Biology Approaches for Host-Pathogen Interaction Analysis

Systems Biology Approaches for Host-Pathogen Interaction Analysis
Author: Mohd. Tashfeen Ashraf
Publisher: Elsevier
Total Pages: 317
Release: 2024-02-16
Genre: Science
ISBN: 0323958915

System Biology Approaches for Microbial Pathogenesis Interaction Analysis aids biological researchers to expand their research scope using piled up data generated through recent technological advancement. In addition, it also opens avenues for bioinformatics and computer science researchers to utilize their expertise in biological meaningful ways. It also covers network biology approaches to decipher complex multiple host-pathogen interactions in addition to giving valuable coverage of artificial intelligence. The host-pathogen interactions are generally considered as highly specific interactions leading to a variety of consequences. The utilization of data science approaches has revolutionized scientific research including host-pathogen interaction analyses. Data science approaches coupled with network biology has taken host-pathogen interaction analysis from specific interaction to a new paradigm of understanding consequences of these interaction in the biological network. Unfortunately, basic biological researchers are mostly unaware of these advancements. In contrast, data scientists are not familiar with biological aspects of such data. System Biology Approaches for Microbial Pathogenesis Interaction Analysis will bridge these gaps through a new paradigm of understanding consequences of interaction in biological networks. Covers network biology approaches to decipher complex multiple host-pathogen interactions Gives the biological researcher insights into artificial intelligence, providing an additional competitive edge Provides a new paradigm for understanding the consequences of interactions in biological networks

Host-Microbe Interactions

Host-Microbe Interactions
Author:
Publisher: Academic Press
Total Pages: 346
Release: 2016-08-03
Genre: Science
ISBN: 0128096179

Host-Microbe Interactions, the latest volume in the Progress in Molecular Biology series, provides a forum for the discussion of new discoveries, approaches, and ideas in molecular biology. It contains contributions from leaders in their respective fields, along with abundant references. This volume is dedicated to the subject of host-microbe interactions. Provides the latest research on host-microbe interactions, including new discoveries, approaches, and ideas Contains contributions from leading authorities on topics relating to molecular biology Informs and updates on all the latest developments in the field