Computational Predictions Dynamic Tracking And Evolutionary Analysis Of Antibiotic Resistance Through The Mining Of Microbial Genomes And Metagenomic Data
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Computational Predictions Dynamic Tracking And Evolutionary Analysis Of Antibiotic Resistance Through The Mining Of Microbial Genomes And Metagenomic Data
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Author : Qi Zhao
language : en
Publisher: Frontiers Media SA
Release Date : 2022-04-27
Computational Predictions Dynamic Tracking And Evolutionary Analysis Of Antibiotic Resistance Through The Mining Of Microbial Genomes And Metagenomic Data written by Qi Zhao and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-04-27 with Science categories.
Progress In Soil Microbiome Research
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Author : Javid Ahmad Parray
language : en
Publisher: Springer Nature
Release Date : 2024-11-21
Progress In Soil Microbiome Research written by Javid Ahmad Parray and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-11-21 with Science categories.
This book focuses on the latest research in soil and microbiome, evaluating new and emerging innovations. Recent research has connected specific microbial taxa to plant productivity, and it is now possible to link changes in microbiome structure to the functioning of plants or crops due to advanced approaches. It provides: Insights into basic microbiome research. Focusing on its applications in agriculture. Soil bioremediation. Environmental restoration. It addresses the impact of global change on soil microbial diversity and ecosystem functions. We aim to tailor microbiome applications to individual host species better, improving treatment efficiency. The book will discuss microbiome dynamics in various environments and their potential to improve soil and plant health to meet growing food demands. It will also highlight the current developments in microbiome research and their implications for climate change. 1. Linking the dynamics of microbial communities to microbiome function. 2. Recent soil microbiome applications and harnessing for sustainable agriculture, food security, and environmental management 3. An advanced and elaborative view of the most recent microbiological research findings 4. Simple, insightful illustrations of current microbial biotechnology trends 5. Future advances in microbial biotechnology research for sustainable development
Insights In Systems Microbiology 2021
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Author : George Tsiamis
language : en
Publisher: Frontiers Media SA
Release Date : 2022-10-06
Insights In Systems Microbiology 2021 written by George Tsiamis and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-10-06 with Science categories.
Mechanisms Of Antibiotic Resistance
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Author : Jun Lin
language : en
Publisher: Frontiers Media SA
Release Date : 2015-06-01
Mechanisms Of Antibiotic Resistance written by Jun Lin and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-06-01 with Antibiotics categories.
Antibiotics represent one of the most successful forms of therapy in medicine. But the efficiency of antibiotics is compromised by the growing number of antibiotic-resistant pathogens. Antibiotic resistance, which is implicated in elevated morbidity and mortality rates as well as in the increased treatment costs, is considered to be one of the major global public health threats (www.who.int/drugresistance/en/) and the magnitude of the problem recently prompted a number of international and national bodies to take actions to protect the public (http://ec.europa.eu/dgs/health_consumer/docs/road-map-amr_en.pdf: http://www.who.int/drugresistance/amr_global_action_plan/en/; http://www.whitehouse.gov/sites/default/files/docs/carb_national_strategy.pdf). Understanding the mechanisms by which bacteria successfully defend themselves against the antibiotic assault represent the main theme of this eBook published as a Research Topic in Frontiers in Microbiology, section of Antimicrobials, Resistance, and Chemotherapy. The articles in the eBook update the reader on various aspects and mechanisms of antibiotic resistance. A better understanding of these mechanisms should facilitate the development of means to potentiate the efficacy and increase the lifespan of antibiotics while minimizing the emergence of antibiotic resistance among pathogens.
The Pangenome
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Author : Hervé Tettelin
language : en
Publisher: Springer Nature
Release Date : 2020-04-30
The Pangenome written by Hervé Tettelin and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-04-30 with Science categories.
This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
Genome Data Analysis
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Author : Ju Han Kim
language : en
Publisher: Springer
Release Date : 2019-04-30
Genome Data Analysis written by Ju Han Kim and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-30 with Computers categories.
This textbook describes recent advances in genomics and bioinformatics and provides numerous examples of genome data analysis that illustrate its relevance to real world problems and will improve the reader’s bioinformatics skills. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine learning algorithms using R and Python are demonstrated for gene-expression microarrays, genotyping microarrays, next-generation sequencing data, epigenomic data, and biological network and semantic analyses. In addition, detailed attention is devoted to integrative genomic data analysis, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and integrated management of biomolecular databases. The textbook is primarily intended for life scientists, medical scientists, statisticians, data processing researchers, engineers, and other beginners in bioinformatics who are experiencing difficulty in approaching the field. However, it will also serve as a simple guideline for experts unfamiliar with the new, developing subfield of genomic analysis within bioinformatics.
Metagenomics For Microbiology
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Author : Jacques Izard
language : en
Publisher: Academic Press
Release Date : 2025-09-01
Metagenomics For Microbiology written by Jacques Izard and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-09-01 with Science categories.
Metagenomics for Microbiology, Second Edition unveils the intricate and diverse world of microbial communities, emphasizing their critical roles in health, disease, and ecosystem functionality. This updated edition addresses the significant challenges in the field and introduces promising approaches to make metagenomics research more feasible. Through comprehensive revisions and over five new chapters, readers are equipped with the latest research data and analyses, advancing their understanding of microbial principles. Notably, this edition provides a robust foundation for the design and analysis of omics studies, focusing on technological underpinnings and practical applications. It remains an essential resource for characterizing microbial consortia. - Describes updated methodologies with best-practice prescription, from sample to data analysis, for current metagenomic studies - Updates on sample preparation, data production, data clean up, data analysis, statistics, and experimental biology, with accompanying descriptions - Includes a new chapter on long read applications using Nanopore technology - Provides a new chapter on probability distributions that underpin the structure of microbiome ecosystems - Covers bio surveillance of diseases and biodefense
Animal Genomics
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Author : Bhanu P. Chowdhary
language : en
Publisher: S. Karger AG (Switzerland)
Release Date : 2003
Animal Genomics written by Bhanu P. Chowdhary and has been published by S. Karger AG (Switzerland) this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003 with Medical categories.
This publication provides an update on the current status of gene maps in different livestock and pet/companion animal species. The findings summarized in species specific commentaries and original articles testify the rapid advances made in the field of animal genomics. Of significant interest is the fact that current investigations are providing headways for two important and exciting research fronts: targeted high-resolution mapping leading to the application of genomic information in addressing questions of economic and biological significance in animals, and the initiation of whole genome sequencing projects for some of the animal species. Like in humans and mice, this will set the stage for a new level of research and real time complex analysis of the genomes of these species. Animal Genomics signifies the beginning of a new era in this field and celebrates the achievements of the past 20 years of genomics research. It will be of special interest to researchers involved in genome analysis - both gross chromosomal as well as molecular - in various animal species, and to comparative and evolutionary geneticists.
Antimicrobial Resistance
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Author : Mihai Mareș
language : en
Publisher:
Release Date : 2021
Antimicrobial Resistance written by Mihai Mareș and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with Drug resistance in microorganisms categories.
Mining Selected Metagenomes Metatranscriptomes For Biosynthetic Gene Clusters And Antimicrobial Resistance Genes
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Author : Ahmed Yamany
language : en
Publisher:
Release Date : 2021
Mining Selected Metagenomes Metatranscriptomes For Biosynthetic Gene Clusters And Antimicrobial Resistance Genes written by Ahmed Yamany and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with COVID-19 (Disease) categories.
Abstract: Antimicrobial resistance is one of the serious global challenges in the current century. The fact that resistance genes transfer between bacteria, coupled with the fact that the world is connected through complex dynamics. Studying microbial behavior and understanding the different factors coffering microbial resistance to a broad spectrum of the available drug classes, parallel with a comprehensive analysis of the natural microbial products as the primary source of the novel antibiotics, might shed some light on solutions for this problem. Microbial environments harbor a wide range of secondary metabolites (SM) with different functional groups. SMs are not directly involved in vital microbial processes such as reproduction, growth, and development. However, these organic compounds, which exist in many different chemical structures, carry out a broad range of functions. Some bioactive SMs are widely used in drug development of various therapeutic classes such as antibacterial, anticancer, immunosuppressant, diabetic, and cholesterol-lowering agents. These bioactive compounds' metabolic pathways are encoded by co-localized genes collectively called Biosynthetic Gene Clusters (BGCs). The majority of the discovered bioactive natural products are from microbial strains that are cultivatable. However, the advancement in sequencing techniques, bioinformatics, and metagenomics opened unlimited opportunities to reach and study the uncultivatable microbial communities, which represent the more significant fraction of the underexplored microbial ecology. In this study, selected samples of seven selected metatranscriptomic/metagenomic datasets were subjected to assembly, taxonomic assignment to the reads, and assembled contigs. The aim of this study is two-fold. Firstly, the assembled contigs were then investigated by two primary distinct computational methods, namely antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) and deep-learning (deepBGC) methods. A comparative study was performed to determine the biosynthetic gene clusters (BGCs) present in each of the included samples and compare their taxonomic differences. Secondly, the assembled contigs were also analyzed to determine the antimicrobial resistance (AMR) genes present in each sample by using the Resistance Gene Identifier (RGI) algorithm, which is a part of the Comprehensive Antibiotic Resistance Database (CARD). A total of 65 samples from the seven selected v metagenomic and metatranscriptomic datasets were investigated by antiSMASH, deepBGC pipelines, and CARD in the present study. The different classes of detected BGCs and their corresponding microbial taxa and the antimicrobial resistance gene families and their corresponding resistance mechanisms against specific drug classes were reported. In the current study, we reported that the datasets with a large extent of variability (i.e. sex, age and illness state) due to the nature of their environments, such as host microbiome samples of patients in two ecosystems (COVID-19 & Atopic Dermatitis), gave the most variable number of BGC classes detected by antiSMASH, where 19 different classes detected in skin microbiome of AD patients and 16 different classes detected in gut microbiome of COVID-19 patients. On the other hand and due to the selection pressure on the microbial ecosystems by the wide use of antibiotics, gut microbiome of COVID-19 patients' and water sewage samples had more than 70% of the detected AMR gene families where gut microbiome of COVID-19 patients' sample alone reported to had more than 50% of AMR genes detected by CARD. In conclusion, ecological characteristics and microbial diversity in terms of composition and relative abundance dramatically affect the dynamics of secondary metabolites' production and transferring antimicrobial resistance genes between bacteria. Microbial strains with higher biosynthetic and antimicrobial resistance potentials were enriched in environments with a rich microbial diversity such as host microbiome (i.e., COVID-19 patients), with patterns of abundance of biosynthetic gene clusters and AMR genes fluctuating by taxonomy.