Host Adaptation, Virulence, and Evolution. Volume 1 : Microbial Genomics / Javid Ahmad Parray, Niraj Singh, and Wen-Jun Li, editors.

Format:

Book

Contributor:

Parray, Javid Ahmad, editor.

Singh, Niraj, editor.

Li, Wen-Jun, editor.

Language:

English

Subjects (All):

Metagenomics.

Microbial genomics.

Communicable diseases.

Physical Description:

1 online resource (703 pages)

Edition:

First edition.

Place of Publication:

London, England : Academic Press, [2025]

Summary:

Microbial Genomics: Host Adaptation, Virulence, and Evolution covers different aspects of microbial genomics, metagenomics, and functional studies of microbes that have provided a significant understanding of microbial-host interactions, virulence function, host adaptation mechanisms, including microbial evolution.

Contents:

Front Cover

Host Adaptation, Virulence, and Evolution

Copyright Page

Contents

List of contributors

Preface

Acknowledgment

I. Microbial genomics - introduction

1 Microbial genomics and genome sequencing approaches

1.1 Introduction

1.1.1 Definition of microbial genomics

1.1.2 Importance of genome sequencing approaches

1.1.3 Techniques in microbial genomics

1.1.3.1 Polymerase chain reaction amplification

1.1.3.2 DNA sequencing methods

1.1.3.3 Metagenomics

1.2 Applications of microbial genomics

1.2.1 Understanding microbial diversity

1.2.2 Identification of pathogens

1.2.3 Drug discovery and development

1.2.4 Environmental monitoring and bioremediation

1.3 Challenges in microbial genomics

1.3.1 Data analysis and interpretation

1.3.2 Sample collection and preservation

1.3.3 Ethical considerations in genomic research

1.4 Future directions in microbial genomics

1.4.1 Single-cell genomics

1.4.2 Synthetic biology and genome editing

1.4.3 Integration of genomic data with other omics

References

2 Genomic determinants for host adaptation or host specificity

2.1 Introduction

2.2 Reports of host-range modification in Xanthomonas

2.3 Role of population genomics for understanding host specificity

2.4 Impact of pathogen/microbial associated molecular pattern recognition in host specificity and fitness of Xanthomonas pa...

2.5 Host jumps associated with changes in lipopolysaccharide

2.6 Type III secretion systems and their effector-mediated host specificity

2.7 Discussion and future prospects

3 Genomic studies reveal molecular mechanims underlying plant-microbe interaction

3.1 Introduction

3.2 Insight into plant-microbe interactions

3.2.1 Phyllosphere, the site of plant-microbe interactions.

3.2.2 Plant-microbe interaction in the rhizosphere

3.3 Unraveling molecular mechanisms in plant-microbe interactions

3.3.1 Molecular interactions of microbes with the host phyllosphere

3.3.2 Molecular interactions of microbes at the host rhizosphere

3.4 Conclusion and future perspectives

II. Plant microbiome

4 The genetic architecture of adaptation to the root microbiota in plants

4.1 Introduction

4.1.1 Beneficial role of plant-associated microbiota in root environments

4.1.1.1 Abutilon fruticosum

4.1.1.2 Arabidopsis thaliana

4.1.1.3 Acmispon strigosus and Lotus japonicus

4.1.1.4 Caragana jubata and C. roborovskyi

4.1.2 Cotton

4.1.2.1 Crocus sativus

4.1.2.2 Ferula sinkiangensis

4.1.2.3 Glycine max

4.1.2.4 Glycine max, Oryza sativa, T. aestivum, and Zea mays

4.1.2.5 Leymus chinesis and Kalimeris integrifolia

4.1.2.6 Medicago truncatula

4.1.2.7 Oryza sativa

4.1.2.8 O. sativa, O. rufipogon, and G. max, G. soja

4.1.2.9 Panicum miliaceum

4.1.2.10 Panicum virgatum

4.1.2.11 Picea abies

4.1.2.12 Pennisetum glaucum

4.1.2.13 Phaseolus vulgaris

4.1.2.14 Robinia pseudoacacia

4.1.2.15 Sedum takesimense and Campanula takesimana

4.1.2.16 Solanum lycopersicum

4.1.2.17 Solanum lycopersicum and Capsicum annuum

4.1.2.18 Triticum aestivum

4.1.2.19 Vachellia erioloba and V. sieberiana

4.1.2.20 Vigna unguiculata

4.1.2.21 Zea mays

4.1.3 Arabidopsis and tomato

4.1.4 Ephemeral desert plants

4.2 Conclusion

5 Genome sequences and genetic features of beneficial bacterial community for successful colonization in plants

5.1 Introduction

5.1.1 The range of beneficial bacteria

5.1.2 Analysis and sequencing of genomes

5.1.3 Activities conducted by plant-associated bacterial genes and pathways via -omics methods.

5.1.3.1 Plant immunity modulation and virulence

5.1.3.2 Interactions between microbes

5.1.3.3 Uptake of plant metabolites

5.1.3.4 Plant sensing, colonization, and persistence

5.2 Conclusion

6 Omics approaches to understanding plant microbiome gene function

6.1 Introduction

6.2 Pathogen invasion induces a defense response from the plant

6.3 Host susceptibility to disease triggered by pathogen

6.4 Host immune response to PAMPs and effectors

6.5 Role of salicylic acid, jasmonic acid, and ethylene in plant immune response

6.6 Evolution of virulence in pathogens

6.7 Prospect of multiomics in understanding the plant-microbe interaction

6.8 Multiomics approach for identification and characterization of microbiome

6.9 Conclusion

Acknowledgement

III. Genome editing prospecting and approaches

7 Progress and prospect in microbial genome editing

7.1 Introduction

7.2 Genome editing in microbes

7.2.1 Classical approach to gene editing in microbes

7.2.1.1 Suicide plasmids

7.2.1.2 Lambda Red system

7.2.1.3 ClosTron method

7.2.1.4 ZFNs and TALENs

7.2.2 CRISPR/Cas systems

7.2.2.1 Components of CRISPR/Cas

7.2.2.1.1 Cas proteins

7.2.2.1.2 Guide RNA

7.2.2.1.3 Protospacer adjacent motif

7.2.2.2 CRISPR/Cas mechanisms

7.2.2.3 Classification of CRISPR/Cas system

7.2.2.3.1 Class 1 CRISPR systems

7.2.2.3.2 Type I CRISPR systems

7.2.2.3.3 Type IV CRISPR systems

7.2.2.3.4 Class 2 CRISPR systems

7.2.2.3.5 Type II CRISPR systems

7.2.2.3.6 Type V CRISPR systems

7.2.2.3.7 Type VI CRISPR systems

7.2.2.4 CRISPR/Cas versus ZFNs and TALENs

7.2.2.5 CRISPR mechanism involving double-strand breaks

7.2.2.6 CRISPR mechanism independent of double-strand breaks

7.2.2.7 Other CRISPR based techniques: CRISPRi and CRISPRa.

7.3 Crispr/Cas system applications in microbial genome editing

7.4 Challenges and future direction

8 Microbial base editing: a powerful emerging technology for microbial genome engineering

8.1 Introduction

8.2 Microbial genome-engineering tools

8.3 Base editing: prokaryotic microorganisms

8.3.1 Escherichia coli

8.4 Streptomyces species

8.5 Corynebacterium glutamicum

8.6 Clostridium beijerinckii

8.7 Rhodobacter sphaeroides

8.8 Pseudomonas species

8.9 Pathogenic bacteria

8.10 Shewanella oneidensis

8.11 Base editing: prokaryotic microorganisms

8.11.1 Aspergillus niger

8.12 Yarrowia lipolytica

8.13 Saccharomyces cerevisiae

8.14 Bioinformatics tools for base editing

8.15 A new CRISPR/Cas-derived genome-engineering technology

8.16 Cytosine base editors and adenine base editors

8.17 Numerous uses have been investigated, such as molecular recording, combinatorial mutation, protein evolution, and gene inactivation

8.17.1 Applications of microbial base editing

8.18 Strategies to increase the scope of targeting and modify the base editing window

8.19 Future aspects

IV. Microbial virulanse and disease incidence

9 Genetic origins of microbial virulence

9.1 Introduction

9.1.1 Definition of microbial virulence

9.1.2 Importance of studying genetic origins

9.1.3 Overview of microbial virulence factors

9.2 Evolutionary perspectives

9.2.1 Role of natural selection in virulence evolution

9.2.1.1 Trade-off hypothesis

9.2.1.2 Selective pressures

9.2.1.3 Transmission routes

9.2.1.4 Host-pathogen dynamics

9.2.2 Genetic adaptations for host exploitation

9.2.2.1 Adaptations for host recognition and attachment

9.2.2.2 Evasion of host immune responses

9.2.2.3 Nutrient acquisition and metabolic adaptations.

9.2.2.4 Toxin production and damage

9.2.2.5 Biofilm formation and persistence

9.2.2.6 Horizontal gene transfer and adaptation

9.2.2.7 Quorum sensing and cooperative behaviors

9.2.2.8 Signal production and detection

9.2.2.9 Threshold-dependent gene regulation

9.2.2.10 Cooperative behaviors

9.2.3 Coevolution between pathogens and hosts

9.2.3.1 Host immune responses and pathogen evolution

9.2.3.2 Pathogen adaptations and host resistance

9.2.3.3 Selective pressures in natural populations

9.2.3.4 Emergence of novel pathogens and host shifts

9.2.3.5 Public health implications

9.3 Horizontal gene transfer: a microbial powerhouse for virulence evolution

9.3.1 Mechanisms of genetic exchange

9.3.2 Acquisition of virulence genes through horizontal transfer

9.3.3 Impact on microbial virulence evolution

9.4 Virulence genes and pathogenicity islands

9.4.1 Identification and characterization of virulence genes

9.4.2 Role of pathogenicity islands in microbial pathogenesis

9.4.3 Evolutionary significance of pathogenicity islands

9.5 Host-pathogen interactions

9.5.1 Recognition and invasion of host cells

9.5.2 Immune evasion strategies

9.5.3 Manipulation of host signaling pathways

9.6 Genetic regulation of virulence

9.6.1 Transcriptional control of virulence genes

9.6.2 Posttranscriptional and posttranslational regulation

9.6.3 Quorum sensing and virulence regulation

9.7 Comparative genomics and phylogenetics

9.7.1 Comparative analysis of virulence genes across species

9.7.2 Phylogenetic relationships and virulence evolution

9.8 Conclusion

10 Leprosy drug resistance: a review

10.1 Introduction

10.2 Virulence factors of Mycobacterium leprae

10.3 Therapeutic agents of resistance

10.3.1 History of drug resistance of leprosy bacilli.

10.3.2 Leprosy chemotherapy.

Notes:

Includes bibliographical references and index.

Description based on publisher supplied metadata and other sources.

Description based on print version record.

ISBN:

9780443315558

0443315558

OCLC:

1503846507