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Applications of Metagenomics
Agriculture, Environment, and Health
- 1st Edition - April 23, 2024
- Editors: Hrudayanath Thatoi, Sukanta Kumar Pradhan, Upendra Kumar
- Language: English
- Paperback ISBN:9 7 8 - 0 - 3 2 3 - 9 8 3 9 4 - 5
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 9 8 4 0 3 - 4
Applications of Metagenomics: Agriculture, Environment, and Health examines current metagenomics methods and their applications in soil, polluted environment sites, agricu… Read more
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Request a sales quoteApplications of Metagenomics: Agriculture, Environment, and Health examines current metagenomics methods and their applications in soil, polluted environment sites, agriculture production, and health care, with separate sections dedicated to each application area. Special attention is paid to the biotechnological study of novel microbial resources for social welfare. Beyond applications, the book discusses evolving next generation technology and techniques used for carrying out metagenomics studies, and in doing so highlights the latest research and advances in the field, along with ways to adapt these approaches for different study types across the biological sciences.Chapter topics range from metagenomics for studying root microbial communities to microbial diversity of the rhizosphere, fungal diversity, microbial biodiversity in forest environments, the human microbiome, and disease epidemiology, with one chapter dedicated to Covid-19 metagenomics.
- Offers tools to apply evolving next generation sequencing technologies in the detection of disease pathogens, bacteria, viruses, fungi, and parasites across various environments, as well as host response
- Includes separate sections dedicated to topics and current studies in environmental science, agriculture production and health care
- Features chapter contributions from international experts in the field
Basic and translational researchers in genomics, genetics, biochemistry, molecular biology, microbiology, cellular biology, pathology, agriculture, and environmental science, life science researchers, biotechnologists, developmental biologists, Clinicians and graduate students in the biosciences
- Cover image
- Title page
- Table of Contents
- Copyright
- Dedication
- List of contributors
- About the editors
- Preface
- Section I: Agriculture
- Chapter 1. Meta-omics approaches for understanding and exploring soil microbial communities for sustainable agriculture
- Abstract
- 1.1 Introduction
- 1.2 Effect of climate change on soil microbial communities
- 1.3 Meta-genomics and its application in sustainable agriculture
- 1.4 Meta-transcriptomics and its application in sustainable agriculture
- 1.5 Meta-proteomics and its application in sustainable agriculture
- 1.6 Metabolomics and its application in sustainable agriculture
- 1.7 Stable isotope probing–omics and its application in sustainable agriculture
- 1.8 Challenges for meta-omics approaches in microbiome studies
- 1.9 Conclusion
- References
- Chapter 2. Impact of long-term agricultural management practices on rhizospheric microbiome vis-à-vis soil and plant health
- Abstract
- 2.1 Introduction
- 2.2 Role of microbial diversity in soil health and plant productivity
- 2.3 Impact of agricultural management practices on rhizospheric microbiome
- 2.4 Conclusions
- References
- Chapter 3. Plant microbiome: trends and prospects for sustainable agriculture management
- Abstract
- 3.1 Introduction
- 3.2 Diversity and function of plant microbiomes
- 3.3 Impact of microbiomes on plant functions
- 3.4 Modulation and employment of the plant microbiomes
- 3.5 Plant microbiomes modulations by agricultural management
- 3.6 Applications of beneficial microbiome for crop improvement
- 3.7 Plant microbiomes improvement by using inoculants for sustainable productivity of plants
- 3.8 Different biological strategies to minimize fertilizer application
- 3.9 Microbiome engineering
- 3.10 Conclusions and prospects
- Acknowledgments
- References
- Chapter 4. Long-term application of compost influences soil and root microbial communities under diverse rice-based cropping systems
- Abstract
- 4.1 Introduction
- 4.2 Compost as soil amendments
- 4.3 Composting and recycling of organic matter
- 4.4 Composting process
- 4.5 Change in microbial community during composting period
- 4.6 Effect of compost on soil microbial properties
- 4.7 Long term effect of compost on root and soil microbial communities under rice-based cropping system
- 4.8 Conclusions
- References
- Section II: Health
- Chapter 5. Understanding the role of gut microbiome in response to dietary supplement of prebiotics with reference to aquaculture
- Abstract
- 5.1 Introduction
- 5.2 Classification
- 5.3 Applications of prebiotics
- 5.4 Metagenomics approaches for the identification of fish gut microbiota
- 5.5 Fish gut microbiome
- 5.6 Effect of prebiotic in immune response
- 5.7 Conclusion and future prospects
- References
- Chapter 6. Profiling of microbiome diversity in cattle: present status and future prospectives
- Abstract
- 6.1 Introduction
- 6.2 Methods used for microbiome study
- 6.3 Conclusion
- References
- Chapter 7. A metagenomic overview of microbial diversity and their impact on human health
- Abstract
- 7.1 Introduction
- 7.2 Microbiome dysbiosis in noncommunicable disease
- 7.3 Modulation of the microbiome in COVID-19 patients
- 7.4 Oral microbiome in caries and periodontal disease
- 7.5 Influence of microbiome in neurological development
- 7.6 Antibiotic-induced microbiome dysbiosis
- 7.7 Restoration of the gut microbiome with probiotics and prebiotics
- 7.8 Conclusion
- Acknowledgments
- References
- Chapter 8. Severity of severe acute respiratory syndrome coronavirus 2 and its impact on human health, with special reference to gut metabiome
- Abstract
- 8.1 Introduction
- 8.2 Evolution of SARS-CoV to SARS-CoV-2
- 8.3 Gut microbiome of a healthy human
- 8.4 Relation of COVID-19 and gut microbiome
- 8.5 Post COVID-19 complications and mucormycosis
- 8.6 Nutritional measures during and after COVID-19
- 8.7 Therapeutic role of nutritional supplements
- 8.8 Conclusion
- References
- Chapter 9. Metagenomics-based diagnosis support system for the surveillance of infectious disease in healthcare settings
- Abstract
- 9.1 Introduction
- 9.2 Protocol for clinical metagenomics next-generation sequencing
- 9.3 Bioinformatic expertise and software’s
- 9.4 Applications of clinical metagenomics
- 9.5 Metagenomics next-generation sequencing–based clinical decision support systems
- 9.6 Challenges
- 9.7 Metagenomics next-generation sequencing in the next decade
- References
- Section III: Environment
- Chapter 10. Genomic approaches for the investigation of seagrass rhizosphere microbiome and bioprospecting potential: a field study from Chilika Lagoon, Odisha, India
- Abstract
- 10.1 Introduction
- 10.2 Seagrass microbiome in relation to plant growth and benthic biogeochemistry
- 10.3 Molecular techniques to explore seagrass rhizosphere microbiome
- 10.4 Seagrass microbial ecology research in India: a case study from Chilika Lagoon
- 10.5 Bioprospecting applications of seagrass microbiome
- 10.6 Concluding remarks and future perspectives
- Acknowledgments
- References
- Chapter 11. Revisiting metagenome of South-Asian hot springs for exploration of biomolecules
- Abstract
- 11.1 Introduction
- 11.2 Microbial adaptability: surviving in hot springs
- 11.3 Metagenomics and hot springs: exploring the thermophilic reservoirs
- 11.4 Bioprospecting South-Asian hot springs using metagenomics
- 11.5 Strategies for improving the bioactivity of metagenome-derived molecules
- 11.6 Conclusion
- References
- Chapter 12. Metagenomic insights of microbial diversity in mangrove forest environment
- Abstract
- 12.1 Introduction
- 12.2 The microbiome of mangrove rhizosphere
- 12.3 Microbiome in polluted mangrove sediments
- 12.4 Diversity of extreme halophiles
- 12.5 Industrial and pharmaceutical significant biomolecules
- 12.6 Antibiotic-resistant genes in mangrove sediments
- 12.7 Antimicrobial compounds from mangrove environment
- 12.8 Conclusion
- Acknowledgments
- References
- Chapter 13. Distinct biotic and abiotic factors influencing microbial diversity of soil: metagenomic tools and approaches employed
- Abstract
- 13.1 Introduction
- 13.2 Factors driving the microbial diversity of soil
- Acknowledgments
- References
- Further reading
- Section IV: Bioinformatics
- Chapter 14. Applications and limitations of bioinformatics pipelines and tools for metagenomic study
- Abstract
- 14.1 Introduction
- 14.2 Pipelines and parameters used for metagenomic analysis
- 14.3 QIIME2 (Quantitative Insights into Microbial Ecology)
- 14.4 MG-RAST
- 14.5 MEGAN
- 14.6 Strength and weakness of QIIME2, MGRAST, and MEGAN
- 14.7 Conclusion
- Acknowledgment
- References
- Chapter 15. Bioinformatics methods and tools in metagenomics
- Abstract
- 15.1 Introduction
- 15.2 Application of metagenomics
- 15.3 Methods involved in metagenomics study
- 15.4 Conclusion
- Acknowledgment
- References
- Further reading
- Chapter 16. Advances in microbial ecology illustration using metagenomics and bioinformatics approaches
- Abstract
- 16.1 Introduction
- 16.2 Influence of microbial ecology on environment and human health
- 16.3 Impact on microbial association toward balancing or equilibrating the ecosystem (microbial flora and microbial fauna and human microbiomes)
- 16.4 Quantification of microbial ecology and its limitations
- 16.5 Impact of metagenomics on microbial ecology with special emphasis on advanced tools
- 16.6 Advantages and challenges of metagenomics to balance microbial ecology
- 16.7 Conclusion
- Acknowledgments
- References
- Chapter 17. Metagenomics and bioinformatics in microbial ecology: current status and beyond
- Abstract
- 17.1 Introduction
- 17.2 Metagenomics and its development
- 17.3 Sequence-based metagenomics
- 17.4 Function-based metagenomics analysis
- 17.5 Recent advancement
- 17.6 Additional approaches for the fulfilment of Metagenomics void
- Acknowledgments
- References
- Index
- No. of pages: 472
- Language: English
- Edition: 1
- Published: April 23, 2024
- Imprint: Academic Press
- Paperback ISBN: 9780323983945
- eBook ISBN: 9780323984034
HT
Hrudayanath Thatoi
Prof. H.N Thatoi is serving as the Director of Center for Industrial Biotechnology Research (CIBR) at Siksha ‘O’ Anusandhan (SOA) University. Prior to that he served as a Professor in the Department of Biotechnology of Maharaja Sriram Chandra Bhanja Deo University. He has obtained his MSc, MPhil, and PhD in Botany from Utkal University. His major research interests and areas include sustainable production of renewable energy, mushroom diversity and bioactivity, Bioremediation, Structural and Computational biology, Nanotechnology, etc. To date, he is credited with the publication of 25 books and more than 326 research papers in national and international journals, proceedings of conferences and book chapters, and has been awarded with two patents. He serves as member of several scientific societies and editorial boards of reputable national and international journals. Dr. Thatoi is a Functional Area Expert in Ecology and Biodiversity and is accredited by QCI, NABET, MoEF, Govt. of India.
Affiliations and expertise
Professor and Director, Center for Industrial Biotechnology Research (CIBR), Siksha 'O' Anusandhan (SOA) UniversitySP
Sukanta Kumar Pradhan
Dr. Sukanta K. Pradhan is serving as HOD in the Department of Bioinformatics of Odisha University of Agriculture and Technology (OUAT). He obtained his B.Sc(Ag) and M.Sc(Bioinformatics) from OUAT and Ph.D (Biotechnology) from Ravenshaw University. He is also working as the Director, OUAT Data Centre. The teaching and research interest of Dr. Pradhan includes Genomics, Metagenomics, Transcriptomics, Bioinformatics, Biotechnology, and Microbiology. He has successfully implemented several research projects funded by DBT Govt. of India, RKVY Govt. of Odisha, DST Govt. of Odisha. Till date, Dr. Pradhan is credited with publication of 58 research papers in reputed national and international journals and 8 book chapters. He serves as member of several scientific societies of national repute. So far, he has guided 01 Ph.D. scholar and 53 M.Sc students for their thesis and dissertation works. He has visited USA and Bangkok to attend International Conferences on Computational Biology.
Affiliations and expertise
Head, Department of Bio-informatics, Orissa University of Agriculture and Technology, Bhubaneshwar, Odisha, IndiaUK
Upendra Kumar
Dr. Upendra Kumar is working as Senior Scientist at ICAR-National Rice Research Institute, Cuttack (Odisha), India. Meanwhile, he has served as Visiting Scientist at CSIRO, Adelaide, Australia twice (2016 & 2023). His research work is a blend of basic and applied nature, covering major aspects of Microbiology in relation to plant and soil health. Till date he has led several internal and external projects granted by ICAR, RKVY, DST, DBT, NASF etc. with funding amount of more than 15 Cr. He has more than 17 years experience in rice research and published more than 509 articles (journals, books, book chapters, technology bulletins, popular articles, e-publications etc) and also guided more than 15 MSc and PhD students. The cumulative impact factor of his publication is about 267. He has also developed more than 12 technology/product like liquid and carrier-based rice-specific bioinoculants for nutrient, pest and microbial decomposition of rice straw. He has also developed the Azolla-based biofertilizer (sporocarp), livestock feed and microbial-growth medium. He has also constructed liquid biofertilizer production unit at NRRI, Cuttack for the first time. He has developed csaXpert mobile app and characterized the microbial resources in relation to nitrogen fixation, nitrification and denitrification under varying nutrient and climatic conditions in rice-based cropping systems and deposited these microbial cultures in authentic repositories. Through these works, he has been conferred with the Edita David Memorial-2014 (AZRA, Bhubaneswar), Best Scientist Award Twice from ICAR-NRRI, Cuttack (2017 & 2023), AZRA Fellow-2018, Lal Bahadur Shastri Outstanding Young Scientist Award 2020 (ICAR, New Delhi), Nanaji Deshmukh ICAR Award for Outstanding Interdisciplinary Team Research in Agriculture and allied Sciences-2020 (ICAR, New Delhi) and Fellow of Association of Rice Research Workers (ARRW)-2020, SCON recognition Award-2021 and Young Scientist Awards Twice (GAP, 2018 & AZRA, 2022).
Affiliations and expertise
Scientist, National Rice Research Institute, Bidyadharpur, Cuttack, Odisha, India