Microbial Biofilms

Challenges and Advances in Metabolomic Study

1st Edition - June 10, 2023
Editors: Sanket Joshi, Dibyajit Lahiri, Rina Rani Ray, MubarakAli Davoodbasha
Language: English
Paperback ISBN:
9 7 8 - 0 - 3 2 3 - 9 5 7 1 5 - 1
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 9 5 7 1 6 - 8

Microbial Biofilms: Challenges and Advances in Metabolomic Study is a volume in the Advances in Biotechnology and Bioengineering Series. The volume covers the metabolomic char… Read more

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Microbial Biofilms: Challenges and Advances in Metabolomic Study is a volume in the Advances in Biotechnology and Bioengineering Series. The volume covers the metabolomic characteristics of bacterial biofilms and examines the techniques used in the analysis of the metabolomics of the biofilm, its formation, and related infections. The book includes the metabolomics study of various types of biofilms and details new strategies in targeting metabolic pathways for inhibiting the biofilm.

The book also describes various types of metabolomics studies like metabolomics of oral biofilm and metabolomics of biofilm by nosocomial microbes. It also points out the recent advancements on various aspects of metabolomics studies pertaining to biofilms, related infections, their pathogenesis, and present-day treatment strategies.

Microbial Biofilms: Challenges and Advances in Metabolomic Study
is a helpful resource to scientists and researchers engaged in biofilm studies, precisely on the metabolomic changes at molecular level occurring in the participating microorganisms. It is also fascinating and thought provoking for the clinicians and health professionals actively involved in the treatment of biofilm mediated chronic infections, since it depicts the pathogenic consequences of the small molecular interactions of the metabolites in biofilm.

Cover image
Title page
Table of Contents
Copyright
Dedication
List of contributors
Preface
Chapter 1. Microbial biofilms: issues and challenges
1. History and introduction
2. Denotation of biofilm
3. Biofilm matrix
4. Network of biofilm
5. Phases in biofilm formation
6. Role of biofilm
7. Supremacy of microbes in biofilm
8. Detrimental effect of biofilm
9. Mechanism of action in a biofilm network
10. Antibiotic resistance by biofilm
11. Antibiofilm approaches
12. Conclusion
Chapter 2. Genetics of microbial biofilm development
1. Introduction
2. Quorum sensing
3. Genetic control of biofilm formation
4. Genes required for various stages of biofilm formation in different bacteria
5. Biomathematical modeling: the genetic basis of biofilm development
6. CRISPR-based functional analysis of biofilm-forming genes in bacteria
7. Conclusion
Chapter 3. Introduction on genomic analysis of biofilms
1. Introduction
2. Biofilm formation
3. Extracellular polymeric substances
4. Quorum sensing
5. Antibiotic resistance
6. Central line-associated bloodstream infections
7. Model of biofilm infection
8. Identification of genes and proteins
9. Docking and combinatorial library
10. Advanced strategies to combat biofilms
Chapter 4. Metabolomic study of biofilm-forming natural microbiota of oral biofilm
1. Introduction
2. Formation of biofilm in the buccal cavity
3. Defining metabolome
4. Metabolomics of biofilms
5. Studying biofilm production by Staphylococcus aureus, Fusobacterium nucleatum, and Streptococcus mutans using a specific metabolomic approach
6. Conclusion
7. Future prospects
Chapter 5. From symbiosis to dysbiosis in gut-consequence includes metabolic syndrome
1. Introduction/keyhole view of gut dysbiosis and metabolic syndrome
2. The gut microbiome—our body's largest endocrine organ
3. What is symbiosis? How and why does it become dysbiosis
4. Current scenario—gut health imbalance and metabolic syndrome
5. What is the role of diet in gut symbiosis?
6. Move a little to get closer to gut symbiosis!
7. Sleep well to reap the benefits of gut symbiosis
8. Stress is harmful even to our gut microbiome!
9. What is my take-home message?
Chapter 6. Metabolomic study of biofilm-forming natural microbiota of skin biofilm
1. Introduction
2. Skin and biofilm production
3. Metabolites of skin biofilms
4. Natural microbiota of skin biofilms
5. Therapeutic strategies to combat biofilm formation
6. Future of metabolomics in cosmetics and skin care
Chapter 7. Metabolomic study of biofilm-forming natural microbiota of vaginal biofilm
1. Introduction
2. Natural microbiota of vagina
3. Metabolome of vagina
4. Bacterial vaginosis—pathogenesis
5. Metabolome alteration and biofilm formation in bacterial vaginosis
6. Diagnosis and treatment for bacterial vaginosis
Chapter 8. Metabolome analysis for host–microbiota interactions
1. Introduction
2. Use of metabolic networks of bacteria for studying metabolic communications
3. Construction of metabolic networks from annotated genomes
4. GEM application in gut microbiota modeling
5. Dysbiosis simulation and therapies by use of metabolic networks
6. Conclusion
Chapter 9. Multispecies metabolomics interactions resulting in the development of resistance
1. Introduction
2. Formation of multispecies biofilm
3. Exopolysaccharides
4. Extracellular proteins
5. Extracellular DNA
6. Mechanisms for multispecies biofilm formation
7. Quorum sensing signal molecules
8. Extracellular polymeric substances
9. Biofilm-regulating genes
10. Metabolomics in biofilm
11. Microbial interaction in multispecies biofilms
12. Competitive interaction
13. Cooperative interaction
14. Horizontal gene transfer
15. Other interaction
16. General mechanism of multispecies biofilms for antibiotic resistance
17. Penetration power of antibiotic
18. Persisters
19. Efflux pumps
20. Antibiotic-degrading enzymes
21. Adaptive response
22. Multispecies interactions
23. Conclusion and future prospects
Chapter 10. Natural phytochemicals: a potential alternative antibiofilm agent
1. Introduction to biofilms—formation and habitat
2. Phytochemicals, types, examples, and their varied uses
3. Quorum sensing and biofilm inhibitors from phytochemicals
4. Biofilm-imposed challenges
5. Phytochemical mechanism for inhibition
6. Future perspective of novel phytochemical strategies
7. Conclusion
Chapter 11. Medical devices–associated biofilm infections and challenges in treatment
1. Introduction
2. Medical devices and their uses
3. Major threatening consequences of biofilm formation on medical devices
4. Molecular mechanism behind biofilm formation on medical devices
5. Problems in the diagnosis of medical device–associated biofilm infections
6. Novel approaches for combating biofilms on medical devices
7. Conclusion
Chapter 12. NMR-based metabolomics study of microbial biofilm
1. Introduction
2. Bacterial biofilm
3. Steps involved in biofilm formation
4. Molecular analysis of biofilm formation
5. Genomic analysis of the bacterial biofilms
6. Analysis of bacterial biofilm using NMR-based metabolomics
7. Metabolite assays by NMR
8. In vitro metabolite profiling of microbial biofilm
9. Difference between NMR metabolomics of planktonic and biofilm modes of growth
10. In Pseudomonas
11. In Staphylococcus
12. In Salmonella
13. In Acinetobacter baumannii
14. In oral plaque-forming bacteria
15. Evaluation of fast 2D NMR for metabolomics
16. 1D, 2D, and solid-state NMR techniques for metabolomics
17. Conclusions
Chapter 13. Isotope labeling LC-MS for metabolomics of biofilm study and tracer-based biofilm metabolomics analysis
1. Introduction
2. Stable isotopes in metabolomics
3. Strategies used in stable isotope labeling to assist metabolomics using LC-MS
4. Liquid chromatography–mass spectrometry
5. LC-MS in metabolomics of biofilm
6. Tracer-based biofilm metabolomics analysis
7. Conclusion
Chapter 14. Lipidomics profiling of microbial biofilm
1. Introduction
2. Why should we concerned about biofilms?
3. What is lipidomics?
4. Importance of lipidomics in biofilms
5. Lipid nomenclature
6. Extraction method
7. Separation technique
8. Mass spectrometry–based lipidomics analysis
9. Application in dental plaque, Candida albicans, vaginal biofilm
Chapter 15. Functional metabolomics approaches in determining the inhibition of biofilm
1. Introduction
2. Formation of biofilm
3. What is metabolomics?
4. Metabolic remodulation triggers biofilm formation
5. Inhibition of biofilm
6. Prevention of biofilm formation through targeting quorum sensing mechanism
7. Metabolomics in drug targeting
8. Metabolomics based on nuclear magnetic resonance
9. Comparison of NMR-and MS-based metabolomics
10. Determination of biofilms using metabolomics based on nuclear magnetic resonance
11. Effect of xylitol and fluoride on metabolome profile of oral biofilm
12. Metabolic dysregulation of Staphylococcus aureus biofilm by carnosol
13. Conclusion
Chapter 16. Reprogramming the metabolomics of biofilms
1. Introduction
2. Data analysis
3. Pathway and network analysis of metabolomic data
4. Methodologies for reprogramming metabolomics
Chapter 17. Dysbiosis of microbiome: a risk factor for cancer, metabolic and inflammatory diseases
1. Introduction
2. Host—microbiota interaction
3. Microbiota—health and diseased condition
4. Healthy microbial profile—bacteriotherapy
5. Fecal transplantation
6. Conclusions
Chapter 18. Strategies to reduce microbial biofilm in medical prosthesis and other devices
1. Introduction
2. Tooth implant
3. Bone implant
4. Pacemaker
5. Naturally dissolving suture
6. Synthetic skin/tissue/ligament
7. Prevention and control
8. Discussion
9. Conclusion
Chapter 19. Targeting microbial biofilms using genomics-guided drug discovery
1. Introduction
2. Genomic approaches to study biofilm formation
3. Transcriptomic approaches to study biofilm formation
4. Proteomic approaches to study biofilms
5. Drug discovery
6. Genomics-guided drug discovery
Chapter 20. Biofilms: a sociomicrobiological nexus
1. Introduction to biofilms
2. Stages and complexity of a biofilm
3. Competition in biofilms
4. Coordination and cooperation in biofilms
5. Role of mutations in biofilm
6. Genetic study of biofilm formation in vitro by the introduction of genes such as green fluorescent protein
7. Conclusion
Chapter 21. In silico and in vivo methods for designing antibiofilm agents against Pseudomonas aeruginosa and Staphylococcus aureus
1. Introduction
2. Biofilms
3. Biofilms and human diseases
4. Antibiofilm strategies
5. Antibiofilm studies
6. Recent advances
Chapter 22. Biofilm: a threat to medical devices
1. Introduction
2. Biofilm formation strategy on medical devices
3. Biofilm and abiotic medical implants
4. Role of biofilm in disease
5. Prevention and control strategy for biofilm on medical devices
6. Early detection of biofilm formation in medical implants
7. Treatment approach for biofilm colonization on medical devices
8. Conclusion
Chapter 23. Biofilm formation in acute and chronic respiratory infections caused by nosocomial gram-negative bacteria
1. Introduction
2. Biofilms: what are they?
3. Biofilm biogenesis
4. Biofilms and nosocomial infections
5. Role of biofilms in nosocomial infections with reference to chronic respiratory infections
6. Current inhalation treatments for chronic infections caused by pulmonary biofilms
7. Conclusion
Acknowledgments
Index

Sanket Joshi

Dr. Sanket Joshi is currently a Professor at the Amity Institute of Microbial Technology, Amity University, Rajasthan, India. He has academic teaching and research experience of about 16 years, and industrial R&D experience of about 4 years in India and Oman. While working in Indian pharma companies, he undertook several turnkey projects. His current research interests encompass energy (In-situ/ex-situ microbial enhanced light/heavy oil recovery; chemical enhanced oil Recovery; biofuels), microbial products (biosurfactants, biopolymers, R&D and scale-up), and environmental bioremediation (crude oil pollution; analysis, mitigation and control of souring by Sulfate reducing bacteria; HPAM contaminated sites). He has about 125 scientific publications in international journals, book chapters, and conference proceedings, and two books to his credit. He is an Academic/Associate Editor for: Frontiers in Microbiology, PeerJ, Ecotoxicology (Springer), Petroleum Science and Technology (Springer), Biotech (Springer), and Open Biotechnology Journal; guest editor for Frontiers in Microbiology, Sustainability, Scientifica, and Open Biotechnology Journal.

Affiliations and expertise

Professor, Amity Institute of Microbial Technology, Amity University, Rajasthan, India

Dibyajit Lahiri

Dibyajit Lahiri is at present is working as Associate Professor in the Department of Biotechnology, University of Engineering & Management, Kolkata. His research interest is precisely on biofilm isolated from human prosthesis and its inhibition by various novel phyto and nano compounds. He is keen to explore the molecular mechanism behind the removal of biofilm by natural compounds. His research arena also encompasses computational drug development by using of bioinformatic. His work is regularly being presented and appreciated before a number of experts of National and International repute. He has more than 100 publications. Dr. Lahiri has edited 5 books. He is also in the role of associate editors of various journals of international reputes.

Affiliations and expertise

Associate Professor, Department of Biotechnology, University of Engineering and Management, Kolkata, India

Rina Rani Ray

Rina Rani Ray is Associate Professor and Head, Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal. Her research interest focuses on the diverse field of microbial biotechnology. She has been in academics and research for more than 25 years and worked in several institutes of repute. She started her research career in the field of microbial enzyme technology. She successfully completed a number of research projects funded by different sponsoring agencies like UGC, DST and DRDO and is working a project sponsored by DBT, WB. She has published around 80 research papers in various peer reviewed national and international journals and is on the editorial board and a regular reviewer of many journals. At present, her research group is working on the positive and negative aspects of biofilm. She is the member of various scientific associations and was nominated fellows of Zoological Society, India and Academy for Environment and Life Sciences, India.

Affiliations and expertise

Associate Professor and Head, Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, India

MubarakAli Davoodbasha

Dr. D. MubarakAli PhD completed his master and doctoral degree in the department of Microbiology, Bharathidasan University, Tiruchirappalli, India. He was worked as Research Professor in Division of Bioengineering, Incheon National University (INU) and Research Associate in Centre for Surface Technology and Applications (CeSTA), Korea Aerospace University, Republic of Korea. He worked also as Scientist in Central Inter-Disciplinary Research Facility (DSIR-recognized), Puducherry (UT), India; Research Associate – III in National Repository for Microalgae and Cyanobacteria – Freshwater. He published nearly 91 peer-reviewed articles; 5 book chapters and holds 2 International and 2 National Patents. He has deposited 85 gene sequences in GenBank (NCBI). He is serving as an Editor in Biocatalysis and Agricultural Biotechnology (Elsevier), Guest Editor in Sustainability (MDPI) and Guest Editor in Pharmaceutical Nanotechnology (Bentham & Sciences). Presently, Assistant Professor in School of Life Science, B.S. Abdur Rahman Crescent Institute of Science and Technology, Chennai where teaching and guiding Ph.D., M.Tech., M.Sc and B.Tech students.

Affiliations and expertise

Assistant Professor, School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and Technology, India