Human and Animal Microbiome Engineering

1st Edition - October 23, 2024
Imprint: Academic Press
Editors: Dharumadurai Dhanasekaran, A. Sankaranarayanan, Priyanka Sarkar
Language: English
Paperback ISBN:
9 7 8 - 0 - 4 4 3 - 2 2 3 4 8 - 8
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 2 2 3 4 9 - 5

Human and Animal Microbiome Engineering provides both basic and detailed information about microbiome engineering for the health enhancement of humans and animal populatio… Read more

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Human and Animal Microbiome Engineering provides both basic and detailed information about microbiome engineering for the health enhancement of humans and animal populations. The book provides updated information about current research topics in this emerging field, including microbiome gene therapy, engineered probiotics, and smart living biotic machines for the release of therapeutics. The book is divided into 4 sections covering microbiome engineering application with a focus on future perspectives in human health and enhancement; microbiome engineering in human health and disease including real-world case studies; animal microbiome engineering essentials; and microbiome engineering for livestock improvement.

This is the perfect reference for researchers and scientists to further explore the relationship between host and microbiome and discover novel ideas about the concepts of microbiome engineering in the health enhancement of humans and animal populations.

Title of Book
Cover image
Title page
Table of Contents
Copyright
Contributors
About the editors
Preface
Section I. Microbiome engineering application and future perspectives
Chapter 1. Microbiome engineering in human health
1 Introduction
2 Microbiome regulation
3 Probiotics
4 Prebiotics
5 Antibiotics
6 Fecal microbiota transplantation
7 Engineered bacteria
8 Conclusion
Chapter 2. Microbiome and dietary antioxidants in human health enhancement
1 Introduction
2 What is the human microbiome?
2.1 Methods to measure the microbiome
3 What are antioxidants, probiotics, prebiotics, and synbiotics?
4 Human microorganisms, their pathogenic and their health enhancement and antioxidant potential
4.1 Bacteria
4.1.1 Bacteria, Actinobacteria
4.1.2 Bacteria, Bacteriodetes
4.1.3 Bacteria, Firmicutes
4.1.4 Bacteria, Proteobacteria
4.1.5 Other bacteria
4.2 Archaea
4.3 Eukarya
5 Human health as per the human gut microorganisms
5.1 A microorganism-based approach to human health
6 The microbiome and human health enhancement
Section II. Microbiome engineering in human health
Chapter 3. Gut microbiome engineering and diabetics
1 Introduction
2 Gut microbiome and its influencing factors on development
2.1 Overview
2.2 Early-life microbial colonization
2.3 Vertical transmission from mother to infant
2.4 Mode of birth (vaginal vs. cesarean)
2.5 Factors influencing microbial diversity
2.5.1 Diet and nutrition
2.5.2 Antibiotic use
2.6 Modulation of gut microbiota
2.6.1 Probiotics
2.6.2 Prebiotics
3 Gut microbe and ecosystem
3.1 Structure and components of ecosystem
3.2 Functions of gut microbiome
3.3 Bacterial association
3.4 Survival of microbiota
3.5 Challenges
4 Gut microbiota and host immunity
4.1 Preamble
4.2 Evolution of immunity
4.3 Immune system
4.4 Influencing factors
5 Gut microbiome and diabetes
5.1 An overview
5.2 Trends on treatment
5.3 Gut immunomodulation
5.4 Gut structuring immunity
5.5 Metabolites and immune reactions
5.6 Probiotic, prebiotics, synbiotics, and postbiotics interventions
5.7 Fecal microbiota transplantation (FMT)
5.8 Potential therapeutic benefits of bile acids and short-chain fatty acids in diabetes
5.9 Herbal medicine
5.10 Microbiome-modulating drugs
5.11 Engineering bacteria and phages
6 Challenges/limitations in controlling diabetics by gut microbiomes
6.1 Interindividual variability
6.2 Lack of long-term data
6.3 Limited Understanding of Mechanisms
6.4 Ethical considerations
7 Conclusion
Chapter 4. Skin microbiome: A therapeutic approach
1 Protective barrier
2 The role of keratinocytes with skin-associated microorganisms
3 The human skin's first contact with the microbiome
4 Role of the human skin microbiome
5 Change in the microbiome during aging
6 Advantages of the skin microbiome
7 Using fermentation products as probiotics
7.1 Staphylococcus epidermidis attracts mosquitoes
7.2 Staphylococcus epidermidis protects against skin pathogens
8 The relationship between skin diseases and the microbiome
9 The microbiome as a therapeutic
10 Conclusion
Chapter 5. Microbiome engineering and cancer therapy
1 Introduction
2 Brief history of microbial engineering
2.1 Natural fermentation period
2.2 Establishment of microbial pure culture technology
2.3 Establishment of microbial ventilated stirring fermentation technology
2.4 Microbial metabolism control fermentation technology
2.5 Exploit microbial fermentation raw materials
2.6 Genetic engineering
2.7 Metabolic engineering
2.8 Microbial enzymes
3 Application of microbial engineering in cancer therapy
3.1 Interaction between immunotherapy and microorganisms
3.1.1 Effectiveness of microorganisms and immunopharmaceuticals
3.1.2 Toxicity of microorganisms and immune drugs
3.2 Interactions between chemotherapy and microorganisms
3.2.1 Microorganisms and chemotherapy toxicity
3.2.2 Microorganisms and the efficacy of chemotherapy
3.3 Cancer modulation through microbial therapy
3.3.1 Genetic engineering
3.3.2 Microbiome transplantation
3.3.3 Prebiotics and postbiotics
3.3.4 Dietary modification
3.3.5 Antibiotics
3.3.6 Targeting TME microbes
3.3.7 Phage
3.3.8 Engineered microorganisms
3.3.9 Drug carriers
3.3.10 Intratumoral microbiota
3.3.11 Marine microbial metabolites of antitumor active substances
4 Assessment of the utility of microbial engineering in cancer therapy
4.1 Effectiveness and prospects of microbial immunotherapy
4.2 Potential and challenges of microbial drugs in cancer therapy
4.2.1 Potential of microbial drugs in cancer therapy
4.2.2 Challenges of microbial drugs in cancer therapy
4.3 Advantages and challenges of microbial drug delivery and delivery systems
4.3.1 Advantages of microbial drug carrier and delivery systems
4.3.2 Challenges of microbial drug carrier and delivery systems
5 Combined application of microbial engineering and other cancer therapies
5.1 Microbial immunotherapy combination
5.1.1 Microbial immunotherapy combined with chemotherapy
5.1.2 Microbial immunotherapy combined with radiotherapy
5.1.3 Microbial immunotherapy combined with targeted therapy
5.2 Microbial drug therapy combinations
5.2.1 Combined application of microbial drug therapy and chemotherapy
5.2.2 Combination of microbial drug therapy and surgery
5.2.3 Combined application of microbial drug therapy and gene therapy
6 Role of microbial engineering in cancer prevention
6.1 Regulation of the gut microbiota
6.2 Development of novel microbial vaccines
6.3 Development of novel anticancer drugs
6.4 Cancer detection and diagnosis
7 Clinical applications of microbial engineering
7.1 Synthetic biology
7.2 Antibiotic
7.3 Probiotics
8 Conclusion
9 Prospect of microbial engineering
Chapter 6. Phage-based tools to modulate gut bacteria for the development of a sustainable microbiome community
1 Introduction
1.1 Ways to specifically target unwanted gut bacteria
1.2 Phages as microbiota modulators
1.3 The limitations of phages and the help of emerging technologies
1.4 Innovative approaches have emerged to study phages that were previously difficult to culture
2 Advancement in phage-based tools due to the use of synthetic biology
3 Conclusion
Chapter 7. Advanced biotechnological processes to develop innovative probiotics with the ability to modulate intestinal microbiota
1 Introduction
2 Bacterial ghost
3 Probiotics/parabiotics for use as BG
4 Bioactive compounds for BG
5 Intestinal microbiota
6 Conclusions
Chapter 8. Oral microbiome and human health
1 Introduction
2 Development of the oral microbiome
3 The human microbiome project
4 Functions of the oral microbiome
5 Oral bacterial microbiome
6 Oral microbiome and diseases
6.1 Periodontitis
6.2 Dental caries
6.3 Halitosis
7 Oral bacteria and systemic diseases
7.1 Tumor
7.2 Diabetes mellitus
7.3 Cardiovascular diseases
7.4 Respiratory diseases
7.5 Bacteremia
7.6 Alzheimer’s disease
7.7 Preterm birth
8 Oral fungal, viral, protozoan, and archaeal microbiome
8.1 Fungal microbiome
8.2 Viral microbiome
8.3 Protozoan microbiome
8.4 Archeal microbiome
9 Conclusion
Chapter 9. The gut-brain axis and schizophrenia: Unraveling the role of gut microbiome in mental health
1 Introduction
2 Gut microbiota
2.1 Overview of gut microbiota and composition
2.2 Factors influencing gut microbial diversity and stability
2.2.1 Diet
2.2.2 Genetics
2.2.3 Method of delivery during birth
2.2.4 Infants feeding
2.2.5 Infections
2.2.6 Antibiotics
3 Interconnected pathways of microbiota-gut-brain axis
4 Influence of intestinal microflora on neurodevelopment
4.1 Gut microbiota and development of the BBB
4.2 Gut microbiota and myelination
4.3 Gut microbiota and maturation of microglia
4.4 Gut microbiota and neurogenesis
5 Evidence of altered gut microbiota pattern in schizophrenia
5.1 Dysbiosis of gut microbiota and neurotransmitter imbalance in schizophrenia
5.2 Gut microbiota dysbiosis and immune dysregulation in schizophrenia
6 Antipsychotics treatment and changes in gut microbiota diversity in schizophrenia
7 Gut microbiota interventions in schizophrenia
8 Conclusion and future perspective
Chapter 10. Artificial intelligence algorithms of patients with irritable Bowel syndrome
1 Introduction
2 Artificial in gastroenterology
3 Application of AI in therapeutics of gastric diseases
4 Role of AI in irritable Bowel syndrome
5 Implementation of first-generation AI in the treatment of IBS
6 Implementation of second-generation AI toward IBS treatment
7 Implementation of AI-based personalized diet for irritable Bowel syndrome
8 Future prospects of AI toward gastrointestinal disorders
9 Conclusion
Chapter 11. Case study: Oral microbiome
1 Introduction
2 Microbial diversity in the oral cavity
2.1 Microbial diversity across oral regions
2.1.1 Microbial roles and interactions
2.1.2 Commensals and potential pathogens
2.1.3 Impact characteristics of microbial dysbiosis in dental caries
2.1.4 Periodontal diseases- microbial contributions and impact
2.2 Candida overgrowth and oral candidiasis: Fungal dynamics in the oral microbiome
2.2.1 Mechanisms of Candida overgrowth
2.2.2 Impact of oral candidiasis
2.2.3 Beyond the mouth: Oral microbiome and systemic connections
2.2.4 Methodological insights: Tools for studying the oral microbiome
2.2.5 Functional pathways of the oral microbiome: Insights from genomic analysis
2.2.6 Personalized approaches to oral health management
2.2.7 Novel interventions: Probiotics, prebiotics, and therapeutic strategies
2.2.8 Future horizons: Advancements and unexplored frontiers
3 Conclusion
Chapter 12. Case study: Colonic microbiome in inflammatory bowel disease
1 Introduction
2 Methods
3 DNA extraction
4 DNA quality control
5 Library preparation
5.1 16SrRNA gene amplification
5.2 Nanopore sequencing
5.3 Data analysis
6 Raw data processing
7 Taxonomy classification
8 Diversity analysis
9 Rarefaction analysis
9.1 Results
10 Discussion and conclusion
Chapter 13. Case study: Reproductive organ microbiome of women
1 Introduction
2 Composition of the female reproductive tract microbiotas
2.1 The vaginal microbiota
2.2 The upper reproductive tract microbiotas
3 Factors that influence the composition of female reproductive tract microbiota
4 Vaginal microbiome and associated pathologies
4.1 Bacterial vaginosis
5 Endometrial microbiome
5.1 Chronic endometritis
5.2 Endometriosis
5.3 The microbiota of ovarian follicles
5.4 Placental and amniotic fluid microbiome
5.5 Pregnancy
5.6 Preeclampsia
6 Strategies to restore the female reproductive tract microbiota to improve reproductive health
7 Conclusion
Chapter 14. Case study of gallbladder diseases and microbiome
1 Introduction
2 Microbiome of healthy gallbladder
3 Diseases associated with gall bladder and biliary tract
3.1 Cholecystitis
3.1.1 Acute cholecystitis
3.1.2 Chronic cholecystitis
3.2 Choledocholithaisis
3.3 Mirizzi syndrome
3.4 Cholangiocarcinoma
3.5 Gall bladder cancer
4 Microbiome associated with gallbladder cancer and gallstones
4.1 Xanthogranuomatous cholecystitis (XGC) and gallstones
4.2 Chronic cholecystitis (CC) and gallstones
5 Case studies from different parts of the world
5.1 India
5.2 China
5.3 Western Nepal
5.4 Iran
5.5 Chile
5.6 Spain
6 Conclusion
Section III. Microbiome engineering in livestock improvement
Chapter 15. Microbiome engineering to improve animal health
1 Introduction
2 Microbiome engineering
2.1 Changes in microbiome composition by host-mediated selection
2.2 Host-selective microbiome engineering approaches
3 Animal microbiome engineering
3.1 Supplement with probiotics or prebiotics
3.2 Microbiota transplantation re-establishment the microbiome
3.3 Phage therapy
4 Future and challenges of microbiome engineering in improving animal health
5 Conclusion
Chapter 16. Gastrointestinal microbiome engineering in pig
1 Introduction
2 Pig gut microbiome
3 Composition of intestinal microbiota
4 Influence of gut microbiome on the host
4.1 Host sensing of microbial patterns and microbiota engineering
5 Gastro intestinal microbiome engineering
5.1 Probiotics
5.2 Prebiotics
5.3 Postbiotics
5.4 Enzymes
5.5 Fecal microbiota transplantation (FMT)
5.6 Dietary manipulation
5.7 Synthetic biology
6 Applications of pig gut microbiome engineering
6.1 Disease resistance
6.2 Immunomodulation
6.3 Alternative antibiotics
6.4 Feed supplementation and growth enhancement
6.5 Stress tolerance
7 Conclusion
Chapter 17. Microbiome engineering and ruminants
1 Introduction
1.1 The concept of the microbiome
1.2 Conceptual purpose and method of microbiome engineering
1.3 Characteristics of the gastrointestinal tract in ruminants—Digestive characteristics
1.4 Ruminant microbiome
1.5 Effect of the microbiome on ruminant performance
1.5.1 Effect of the rumen microbiome on ruminant
1.5.2 Impact of the hindgut gut microbiome on ruminant
2 Effects of early microbial colonization on ruminants
3 Application of microbiome engineering in ruminants
3.1 Application in its gastrointestinal tract—Probiotics
3.1.1 Probiotics and immunomodulation
3.1.2 Probiotics and secretion of antimicrobial substances
3.1.3 Probiotics and competitive rejection of pathogens
3.2 Application in ruminant unique organ—Rumen
3.2.1 Discovery of rumen microbial enzymes
3.2.2 Transformation of rumen microbial enzymes
4 Conclusion
Chapter 18. Animal feed and gut microbiome engineering toward the maintenance of animal health
1 Introduction
2 Animal feed and gut microbiome alleviates diarrhea of young animal
3 Animal feeding and gut microbiome maintain perinatal health
4 Animal feeding and gut microbiome improve mastitis
5 Conclusion
Chapter 19. Biotechnological approaches in fish gut microbiome
1 Introduction
2 Fish gut microbiome
2.1 Taxonomic composition of gut microbiota
2.2 Functional profiling of microbial communities
3 Biotechnological tools in microbiome analysis
3.1 Metabolomics and microbiome engineering
4 Diet-induced changes in fish gut microbiome
4.1 Environmental factors shaping microbial communities
5 Fish gut microbiome and its secondary metabolites
6 Biotechnological applications
6.1 Probiotics and disease management
6.2 Enhancing nutrient utilization and growth
7 Challenges and future directions
7.1 Addressing biotechnological limitations
8 Prospects for sustainable aquaculture
8.1 Enhancing feed efficiency
8.2 Selective breeding programs
8.2.1 Integrated multitrophic aquaculture
8.2.2 Recirculating aquaculture systems
8.3 Aquaponics
8.3.1 Certification and standards
8.3.2 Technology and innovation
8.3.3 Ecosystem health monitoring
9 Conclusion
Chapter 20. Gastrointestinal microbiome engineering in prawn breeding
1 Introduction
2 Habitat of prawn
3 Normal microflora of prawn
4 Gut microbial communities of freshwater prawn
4.1 Gut microbiome against aquatic pathogens
4.2 Microbiome in the early developmental stages of shrimp
4.3 Autonomous aquaculture farming system
4.4 Low productivity in traditional monitoring method
5 Strategies for future development
5.1 Improvement in marketing and processing
6 Prawn fertilization process
7 Prawn culture methods
7.1 Polyculture
7.2 Integrated rice-prawn culture
7.3 Aquaponics
8 Problems in prawn cultivation
9 Emerging technologies for prawn breeding
9.1 Biofloc technology
9.2 Bio-filters
9.3 IOT technology
10 Conclusion
Chapter 21. Fecal microbiota transplantation for the control of Cdifficile infection in animals
1 Pathogenesis of C. difficile
2 Epidemiology of C. difficile in animals
3 Host susceptibility to CDI in animals
4 From pasture to table, C. difficile infection may be a potential zoonotic disease
5 Fecal microbiota transplantation: An emerging strategy to combat C. difficile infection in animals
6 Conclusion and future trends
Chapter 22. Next-generation probiotics and animal health
1 Introduction
2 Use of probiotic for animal health
3 How probiotics work?
4 Next-generation probiotics
5 The current examples of NGP for animals
6 Conclusion
Index

Dharumadurai Dhanasekaran

Dr. Dhanasekaran Dharumadurai is an Associate Professor in the School of Life Sciences, Bharathidasan University. He has experience in fields of actinobacteriology and mycology. He has 16 years teaching experience and was awarded the UGC-Raman Post-Doctoral Fellowship from the University Grant Commission. His current research focus is microbiome profiling. He has filed two Indian patents, deposited 139 nucleotide sequences and 7 metagenome sequences, bacterial draft genome sequence in GenBank, and 5 bioactive compounds in Pubchem. He is a member of the American Society for Microbiology, North American Mycology Association, International Society for symbiosis, Mycological Society of India, National Academy of Biological Sciences, Society for Alternatives to Animal Experiments, Society of Chemical and Synthetic Biology, Microbiologist Society.

Affiliations and expertise

Assistant Professor, Department of Microbiology, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India

A. Sankaranarayanan

Dr. A. Sankara narayanan is an Associate Professor and Head in the Department of Life Sciences, Sri Sathya Sai University for Human Excellence, Kalaburagi, Karnataka, India, from June 2021 onwards. His current research focus is on Microbiome studies, fermented food products and Environmental Microbiology. He has published so far 17 books under different international publishers, 60 chapters and 80 research articles in International and National journals of repute, guided 5 PhDs, 16 MPhil, scholars, and operated 5 funded projects in Microbiology. From 2002 to 2015, he worked as an Assistant Professor and Head, Department of Microbiology, K.S.R. College of Arts and Science, Tiruchengode, Tamil Nadu and in August 2015–May 2021 he was associated with Uka Tarsadia University, Surat, Gujarat, India. He has been awarded with the Indian Academy of Sciences (IASc), National Academy of Sciences (NAS), and The National Academy of Sciences (TNAS) sponsored summer research fellowship for young teachers consecutively for 3 years and his name is included as a Mentor in DST-Mentors/Resource persons for summer/ winter camps and other INSPIRE initiatives, Department of Science and Technology, Govt. of India, New Delhi. He is a grant reviewer in the British Society for Antimicrobial Chemotherapy (BSAC), UK. He is an active member in Editorial boards of various National and International Journals. He is Doctoral Committee member, Board of Study member in Microbiology in various colleges and Universities in India, and Reviewer in many International reputed Journals. One among of his edited book received Outstanding Academic Title (OAT) Award from one of the International Publishers in the year 2020. This OAT Award represents the highest calibre of scholarly titles, overall excellence in presentation and importance relative to other literature in the field. His name was included in the World Scientists and University Rankings for the Year 2023; ranking list is released by AD Scientific Index.

Affiliations and expertise

Associate Professor and Head of Life Sciences, Sri Sathya Sai University for Human Excellence, Kamalapur Navanihal, Kalaburagi District, India

Priyanka Sarkar

Dr. Priyanka Sarkar completed her PhD in Bioengineering and Technology, jointly from Institute of Advanced Study in Science and Technology (IASST) and Gauhati University in 2019. After which, she completed her Post Doctoral training at Asian Healthcare Foundation, Asian Institute of Gastroenterology (AIG Hospitals). Since her PhD, her research has delved into the intricate relationship between the gut microbiome (the community of microorganisms residing in our gut) and its impact on human health, particularly focusing on chronic diseases and immune function. She has longstanding interests in decoding the cross-talk between gut microbiome and host health. She has published more than 12 research papers in these areas of research and has contributed to 4 book chapters and 2 review articles in the field of microbiome. She has been serving as a reviewer in many journals. She has been honoured with international and national awards for her research works [DST-SERB Core Research Grant (2021, as a co-PI), Young Scientist Awards (2021)]. She has successfully completed research projects from national funding agencies such as SERB-DST, and guided students for their doctoral and master’s degrees.

Affiliations and expertise

Wellcome-Trust/DBT (Indian Alliance) Lab; Institute of Translational Research; Asian Healthcare foundation; Asian Institute of Gastroenterology (AIG), Hyderabad, Telangana, India

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Human and Animal Microbiome Engineering

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Dharumadurai Dhanasekaran

A. Sankaranarayanan

Priyanka Sarkar

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