Understanding Microbial Biofilms: Fundamentals to Applications

Front Cover
Understanding Microbial Biofilms: Fundamentals to Applications
Copyright
Contents
Contributors
Preface
Section A: Introduction to biofilms
Chapter 1: Marine biofilms: Bacterial diversity and dynamics
1. Introduction
2. Biofilm development in the marine environment
2.1. Phase I-Reversible adhesion of bacteria
2.2. Phase II-Irreversible adsorption
2.3. Phase III-Microbial biofilm formation
2.4. Phase IV-Biofilm detachment and dispersal
3. Bacterial competition and cooperation in shaping the diversity and dynamics of marine biofilm
4. Microbial diversity of marine biofilms
5. Factors influencing the establishment of marine biofilms
6. Bacterial protection from harsh environmental conditions
7. Traditional and modern methods to study biofilm-forming community
8. Economic implications of marine biofilms
8.1. Biofouling
8.2. Biofouling in ship hulls
8.3. Biofouling in desalination plants
8.4. Biofouling in power plants
8.5. Biocorrosion
9. Advantages of marine biofilms
10. Conclusion
References
Chapter 2: Cyanobacterial biofilms: Perspectives from origin to applications
1. Introduction
2. Cyanobacterial biofilms
2.1. Cyanobacterial biofilm distribution and natural diversity
2.2. Phototroph-heterotroph interaction in biofilm
3. Factors influencing cyanobacterial biofilm formation
3.1. Physical factors
3.1.1. Irradiance
3.1.2. Shear forces and hydrophobicity
3.2. Molecular mechanisms and genetic factors
4. Impact of abiotic factors such as temperature, nutrients, and environmental conditions on cyanobacterial mats/biofilms
4.1. Effect of warming on light- and dark-grown microbial biofilms
4.2. Effect of phosphate and sulfide availability on cultured biofilms
4.3. Role of environmental conditions
5. Application and utilization of cyanobacterial biofilms
5.1. Agriculture and biofuel
5.2. Wastewater treatment and bioremediation
6. Conclusion and future perspectives
References
Chapter 3: From understanding bacterial interactions to developing bactericidal surfaces
1. Introduction
2. Effect of surface chemistry on bacterial interaction: Applications of analytical techniques
3. Effect of surface physical characteristics on bacterial adhesion: Applications of analytical techniques
4. Development of antimicrobial surfaces: Applications of analytical techniques
5. Conclusions
References
Further reading
Chapter 4: Microbial biofilms: Unravel their potential for agricultural applications under agro-ecosystem
1. Introduction
2. Bacterial biofilms in soil system
3. Bacterial interaction in biofilms under soil ecosystem
3.1. Cooperative interactions
3.2. Inter and intraspecies competition
4. Significance of biofilms in agroecosystem
4.1. Biofilms in soil health
4.2. Biofilms in crop health
5. Conclusion and future perspective
References
Chapter 5: Chemotaxis and rhizobacterial biofilm formation in plant-microbe interaction
1. Introduction to microbial interaction with plants
2. Chemotaxis: Underground communication of rhizobacteria with plant roots
3. Role of root exudates in chemotaxis
4. Recognition of chemoattractants and mechanism of chemotaxis
5. Colonization and biofilm formation of rhizobacteria on plant root
5.1. Role of quorum sensing in biofilm development
6. Significance of rhizobacterial chemotaxis and biofilm formation
7. Conclusion
References
Chapter 6: Variable pressure SEM and conventional high vacuum SEM protocols for biofilm imaging
1. Introduction
2. Conventional scanning electron microscopy (SEM) applied to biofilm imaging
3. SEM tailored protocol for biofilm
4. Variable-pressure scanning electron microscopy (VP-SEM) in biofilm studies
5. Conclusion
References
Chapter 7: Aspects of biofilms on medical devices
1. Introduction
2. Biofilm formation on medical devices
3. Biofilm models
4. Medical-device-related infections
4.1. Central venous catheters
4.2. Endotracheal tube
4.3. Urinary catheters
4.4. Orthopedic devices
5. Diagnosis of medical-device-related biofilms
6. Current treatments
6.1. Prevention
6.1.1. Antibacterial coatings
6.1.2. Surface modification of biomaterials
6.1.3. Disruption of biofilm formation and antibiotic enhancers
6.2. Diagnosis
6.2.1. Biosensors for early detection
6.3. Treatment
6.3.1. Bioacoustics effect
6.3.2. Antimicrobial photodynamic therapies
7. Future prospects
References
Section B: Biofilms in nature
Chapter 8: Metagenomic analysis of electroactive microorganisms in corrosion: Impact of the corrosive biofilms in the oil ...
1. Introduction
2. Electroactive microorganisms
3. Metagenomic approaches in studies of MIC
4. Corrosive biofilms on metal surfaces
5. Metagenomic studies of electroactive bacteria
5.1. Sulfate and nitrate reducers
5.2. Methanogens involved in metal corrosion
5.3. Other electroactive corrosive bacteria
6. Conclusions
Funding
Conflicts of interest/competing interests
Ethics approval
Consent to participate
Consent for publication
Availability of data and material (data transparency)
Code availability (software application or custom code)
References
Further reading
Chapter 9: Biofilms in dairy industry
1. Introduction
2. Microorganisms in milk and dairy products
2.1. Lactic acid bacteria (LAB)
2.2. Pathogenic microorganisms in dairy products
2.2.1. Escherichia coli
2.2.2. Salmonella spp.
2.2.3. Listeria monocytogenes
2.2.4. Staphylococcus aureus
2.2.5. Campylobacter jejuni
2.3. Spoilage microorganisms in dairy industry
3. Biofilms in the dairy industry
4. Biofilm by lactic acid bacteria
5. Production of biofilms by pathogenic microorganisms
5.1. Staphylococcus aureus biofilm
5.2. Listeria monocytogenes biofilm
6. Production of biofilm by spoilage bacteria in milk and dairy products
6.1. Pseudomonas spp.
6.2. Biofilm formation by spore formers
7. Prevention and control of biofilm in the dairy industry
8. Conclusion
References
Chapter 10: Microalgal biofilm and their prospective application for wastewater treatment and biofuel production
1. Introduction
2. Microalgal biofilm
3. The life cycle of algal biofilm
3.1. Adsorption
3.2. Consolidation
3.3. Colonization
3.4. Maturation
4. Substratum for microalgal biofilm
5. Microalgal biofilm and biomass production
5.1. Photobioreactor for production of microalgal biofilm
6. Application of microalgal biofilm
6.1. Microalgal biofilm used in wastewater treatment
6.2. The microalgal biofilm used in biofuel production
6.2.1. Improved microalgal biofuel production through molecular strategies
6.2.2. Biofuel production interactions with bacterial biofilms
7. Conclusion and future prospective
References
Chapter 11: Biochemical and molecular mechanisms of sulfate-reducing bacterial biofilms
1. Introduction
2. Exopolysaccharide
3. Signaling pathways
3.1. Quorum sensing (QS)
3.2. Cyclic-di-GMP
4. Flagellum
5. Chemotaxis
6. Functional categories of genes and proteins in SRB biofilm cells
6.1. Electron transfer
6.2. Stress response
6.3. Iron acquisition
7. Conclusion
References
Chapter 12: Biofilms and their role in corrosion in marine environments
1. Introduction
2. Problems with marine biofilms
3. Mechanisms of microbiologically influenced corrosion (MIC)
3.1. Chemical microbiologically influenced corrosion
3.2. Electrical microbiologically influenced corrosion
4. Taxa involved in marine MIC
5. Corrosion of steel materials
6. Potential for copper use to control marine corrosion of materials
7. Other microbial control approaches in marine systems
8. Conclusion
References
Further reading
Chapter 13: Natural biofilms: Structure, development, and habitats
1. Introduction
2. Structure of biofilms
3. Development of biofilms
4. Interactions in biofilms
5. Biofilms in marine habitats
6. Biofilm in extreme habitats
7. Biofilm in humans
8. Biofilms on animal surfaces
9. Biofilm in plants
10. Bacteriophages and biofilms
11. Conclusion
References
Section C: Biofilm lifestyle of various microorganisms and its control
Chapter 14: Role of biofilms in hospital-acquired infections (HAIs)
1. Introduction
1.1. Hospital-acquired pneumonia
2. Sites of infection
2.1. Bacteremia
2.2. Urinary tract infection
2.3. Pneumonia
2.4. Surgical wound infections/pressure ulcers/wound infections
3. Pathogenesis of attachment
4. Diagnosis of biofilm infection
5. Factors affecting biofilm formation within the clinical and hospital setting
5.1. Nutrients
5.2. Host response
5.3. pH
5.4. Temperature
5.5. Surfaces
6. Device-related infections
6.1. Infected pressure ulcers
6.2. Central venous catheters (CVCs)
6.3. Urinary catheters
6.4. Catheter-related bloodstream infections (CRBSIs)
6.5. Prosthetic heart valves
6.6. Orthopedic devices
7. Prevention strategies
7.1. Hand hygiene
7.2. Cleaning
7.3. Disinfection
7.4. Sterilization
7.5. Behaviors and practices affecting cleaning and hospital-acquired infection
7.6. Brass alloys: Copper-bottomed solutions against hospital-acquired infections
7.6.1. Brass alloys to reduce hospital-acquired infections (Fig. 4)
7.7. Copper alloy surfaces kill bacteria and reduce hospital-acquired infections
7.7.1. Methicillin-resistant Staphylococcus aureus (MRSA)
7.7.2. Vancomycin-resistant enterococci (VRE)
7.7.3. Escherichia coli O157:H7
7.7.4. Clostridium difficile
7.7.5. Influenza A
7.7.6. Norovirus
7.7.7. Enterococci
7.7.8. Antibiotic coating of devices
8. Conclusion
References
Chapter 15: Implication of Vibrio biofilms in human and seafood sector
1. Introduction
2. Biofilms
3. Biofilm formation
4. Genes involved in biofilm formation
5. Signaling cascade involved in biofilm formation
6. Factors affecting Vibrio biofilms
7. Resistance against antibiotics and drugs
8. Vibriosis in human and aquaculture
9. Seafood sector and economic losses
10. Control of Vibrio biofilm
10.1. Bacteriophages
10.2. Chemotherapeutics agents
10.3. Quorum sensing (QS) disruptors
10.4. Immune priming
10.5. Biogenic compounds
10.6. Algal technology
10.7. Probiotic, prebiotics, and synbiotics
11. Concluding remarks and future perspectives
References
Further reading
Chapter 16: Candida: Biofilm formation and antifungal resistance
1. Introduction
2. Candida and human disease
3. Candida biofilm formation
4. Factors affecting biofilm
5. Recent advances to inhibit C. albicans biofilm formation
6. Candida biofilms and Candida-bacterial interactions
7. Genomics of biofilm formation and antifungal resistance
8. Conclusion
References
Chapter 17: Removal and control of biofilms in wounds
1. Introduction
2. Biofilm in wounds
3. Importance of biofilm to wound infections and management
4. Strategies of biofilm management in wounds
4.1. Prevention
4.2. Removal
4.3. Treatments to kill the microbes
4.3.1. Phage therapy
4.3.2. Probiotic therapeutics
4.3.3. Blue light therapy
5. Current developments for biofilm management in wounds
5.1. Addressing the challenges of biofilms in wounds
5.2. Biofilm identification and wound monitoring
5.3. Methods for debridement
5.4. Antibiofilm agents
5.5. Antibiofilm wound dressings
5.6. Other antibiofilm treatments
5.6.1. Cold atmospheric plasma
5.6.2. Electrochemistry and electroceuticals
5.7. Treating the wound environment and stimulating the bodys response
5.7.1. Oxygen therapies
5.7.2. Vaccines
5.7.3. Human-derived treatments
6. Future prospects
References
Chapter 18: Microbial biofilms: A persisting public health challenge
1. Introduction
2. Biofilm formation and maturation
2.1. Reversible attachment
2.2. Irreversible attachment
2.3. Growth
2.3.1. Extracellular polymeric substances (EPS)
2.4. Maturation
2.5. Dispersal
3. Infections associated with biofilms
4. Molecular mechanism of biofilm formation
4.1. Pseudomonas
4.2. Escherichia coli
4.3. Staphylococcus aureus
4.4. Klebsiella pneumoniae
5. Components of biofilms
5.1. Curli
5.2. Cellulose
5.3. Flagellum
5.4. Alginate
5.5. eDNA
5.6. Proteins
5.7. Quorum sensing
6. Biofilm infections
6.1. Implant related infections
6.2. Nonimplant infections
6.2.1. Periodontitis
6.2.2. Cystic fibrosis
6.2.3. Osteomyelitis
6.2.4. Wound infections
6.2.5. Rhinosinusitis
6.2.6. Infective endocarditis
6.3. Immunological response
6.3.1. Staphylococcus spp.
6.3.2. Candida spp.
7. Therapies against biofilms
7.1. Nanoparticles in biofilm treatment
7.1.1. Nanoparticle based on magnetic field
7.1.2. Inorganic nanoparticles
7.1.3. Silver nanoparticles
7.1.4. Zinc oxide nanoparticle
7.1.5. Titanium oxide nanoparticles
8. Conclusion
References
Chapter 19: Biofilm in antibiotic resistance and pathogenesis in relation to foodborne infection and control strategies
1. Introduction
2. Formation and development of biofilm
3. Important foodborne bacteria and biofilm formation by them in food matrices
4. Role of biofilm in antibiotic resistance
5. Relation between quorum sensing and biofilm production
6. Approaches for biofilm control and its eradication
6.1. Physical approaches for the control and eradication of microbial biofilms
6.1.1. Ultrasonic waves and their utilization as antibiofilm agent
6.1.2. Electrical field (EF) and pulse electric field (PEF)
6.1.3. Plasma
6.1.4. Magnetic field (mf)
6.2. Chemical approaches for the control and eradication of microbial biofilms
6.2.1. Chemical or synthetic sanitizers and enzymes
6.2.2. Bacteriocins
6.3. Herbal approaches for the control and eradication of microbial biofilms
6.4. Biological approaches for the control and eradication of microbial biofilms
7. Conclusion and future recommendations
References
Chapter 20: Biofilms associated with biomedical implants and combating therapies
1. Introduction
2. Types of medical devices and their associated biofilm infections
2.1. Intravascular implants
2.1.1. Central venous catheters
2.1.2. Midline catheters
2.1.3. Pulmonary artery catheters
2.2. Cardiovascular implants
2.2.1. Coronary stents
2.2.2. Defibrillators and associated devices
2.2.3. Implantable cardiovascular monitors
2.2.4. Mechanical heart valves
2.3. Neurosurgical implants
2.3.1. Intracranial pressure devices
2.3.2. Neurological stimulators
2.3.3. Ommaya reservoirs
2.3.4. Ventricular shunts
2.4. Orthopedic implants
2.4.1. Fracture fixation devices
2.4.2. Joint prostheses
2.4.3. Spinal implants
2.5. Urological-Inflatable penile implants
2.5.1. Indwelling catheters
2.5.2. External catheters
2.5.3. Short-term catheters (intermittent catheters)
2.6. Dental implants
2.6.1. Endosteal (Endosseous) implants
2.6.2. Subperiosteal implants
2.7. Ophthalmological implants
2.7.1. Glaucoma tubes
2.7.2. Lacrimal stents
3. Various strategies to combat biofilms on medical devices
3.1. Biofilms in urinary catheters
3.2. Biofilms in dental caries
3.3. Biofilms in breast implants
3.4. Biofilms in ophthalmological implants
3.5. Biofilms in orthopedic implants
3.6. Biofilms in cardiovascular implants
3.7. Combating biofilms in neurosurgical implants
4. Conclusion
References
Further reading
Section D: Molecular and biochemical aspect of microbial biofilms
Chapter 21: Influence of bacterial cell wall modulating genes and enzymes on biofilm formation with special emphasis on t ...
1. Introduction
2. Genes associated with cell surface are also involved in biofilm formation
3. The genes with a role in peptidoglycan transpeptidation and transglycosylation processes are fundamental for biofilm f ...
3.1. Escherichia coli
3.2. Pseudomonas aeruginosa
3.3. Bacillus subtilis
3.4. Mycobacterium species
4. PBPs of other bacterial species and their role in biofilm formation
5. Cell wall teichoic acid may play a vital role in biofilm initiation and pathogenesis
6. Genes and operons involved in exopolysaccharide synthesis are required for biofilm formation
7. Role of cell surface appendages and their encoding genes in biofilm formation
7.1. Flagella
7.2. Pili
7.3. Lipopolysaccharides (LPSs)
8. Biotechnological implications of understanding surface genes related to biofilms
9. Summary and possible future directions involving cell-surface components
References
Further reading
Chapter 22: Small regulatory RNAs in microbial pathogenesis and biofilm formation: An emerging role as potential drug targets
1. Introduction
2. Small regulatory RNAs (sRNAs)
3. Biogenesis of sRNAs
4. Types of sRNAs
5. Mechanism of action of sRNAs
5.1. Regulatory function of sRNAs in bacteria
5.2. Base pairing of sRNA with target mRNA
5.2.1. cis-Encoded sRNA
5.2.2. trans-Encoded sRNA
5.3. Interaction of sRNA with protein
5.3.1. Hfq proteins
5.3.2. CsrA proteins
5.3.3. ProQ proteins
6. Detection methods of sRNAs
7. Small regulatory RNAs: A biological circuits in bacterial pathogenesis
7.1. Staphylococcus aureus
7.2. Mycobacterium tuberculosis
7.3. Escherichia coli O157:H7
7.4. Listeria monocytogenes
7.5. Salmonella enterica serovar Typhimurium
7.6. Legionella spp.
8. Effect of environmental cues on altered sRNA expression
8.1. Temperature
8.2. Osmolarity
8.3. Acidic/alkali environment
8.4. Nutritional immunity and nutrient uptake
9. Cellular pathways that are differentially regulated by the sRNAs
9.1. Cell division
9.2. Oxidative stress response
9.3. Quorum sensing
9.4. Virulence
9.5. Antibiotic resistance development
10. sRNAs with functions relevant to microbial biofilm formation
11. Regulatory small RNAs (sRNAs) among archaea
12. Conceptualization and implementation of methods for identification of sRNAs-based drug targets and therapeutic molecules
13. Conclusion and future perspectives
References
Chapter 23: Genetic basis of biofilm formation and their role in antibiotic resistance, adhesion, and persistent infectio ...
1. Introduction
2. How biofilms are formed in bacterial pathogens
3. Microstructure of biofilms and their composition
3.1. Staphylococcus aureus
3.2. Klebsiella pneumoniae
3.3. Pseudomonas aeruginosa
3.4. Enterococcus faecium
3.5. Enterobacter spp.
4. Role of biofilms in adhesion, antibiotic resistance, and chronic infections
4.1. Survival in stress conditions
4.2. Role of biofilms in adhesion and colonization
4.3. Antibiotic resistance, bacterial persistence, and chronic infections
5. Major genetic elements and molecular pathways involved in biofilm formation
6. Biofilms and virulence
7. Antibiofilm strategies
7.1. EPS targeting
7.2. Combination therapy
7.3. QS inhibition
7.4. Targeting the adhesion process
8. Diseases associated with biofilm
9. Summary and conclusion
References
Further reading
Chapter 24: The emergence of predominance in the constitutive microflora of dairy membrane biofilms
1. Introduction
2. The process of membrane fouling on dairy membrane
2.1. Factors influencing membrane fouling
2.2. Bacterial fouling
3. Constitutive microflora reported on filtration membranes
3.1. Microflora on RO membranes
3.2. Microflora on UF membranes
3.3. Resilient microflora on filtration membranes
3.4. Pathogens as part of biofilm microflora
4. The emergence of predominance within the biofilm over prolonged use of membranes
5. Factors influencing the emergence of predominance
6. A case study to demonstrate factors influencing predominance
6.1. Competitive exclusion
6.2. Antimicrobial inhibition
7. Implications of the emergence of predominance
7.1. Signaling molecules and biofilms (quorum sensing inhibition)
7.2. Antimicrobial peptides
7.3. Role of bacteriophages
7.4. Enzyme mediated disruption
8. Conclusions
References
Chapter 25: Molecular basis of cariogenic biofilm and infections
1. Introduction
2. Dental caries
3. Streptococcus mutans and the cariogenic biofilm
4. Virulence factors promoting oral biofilm formation
5. Survival of Streptococcus mutans in acidified cariogenic biofilm
6. Biofilm properties contributing to antibiotic resistance
7. Genetic regulation of S. mutans biofilm formation
7.1. Two-component signal transduction systems (TCS/TCSTS)
7.1.1. VicRK
7.1.2. CiaRH
7.1.3. LytST
7.1.4. LiaSR
7.2. Quorum sensing (QS)
8. Treatment against dental biofilm
8.1. Phytochemical and bioactive compounds
8.2. Nanoparticles as antibiofilm agents
8.3. Plant-based chemicals in conjunction with nanotechnology
8.4. Vaccines
9. Conclusion and future prospects
References
Section E: Biofilms and pathogenesis
Chapter 26: Salmonella biofilm and its importance in the pathogenesis
1. Introduction
2. Biofilm formation in other Gram-positive and Gram-negative bacteria
3. Salmonella and biofilm formation
4. Regulation of Salmonella biofilm formation
5. Role of biofilm in Salmonella pathogenesis
6. The role of biofilm in Salmonella Typhi pathogenesis
7. Conclusions
References
Chapter 27: Mycobacterial biofilm: Structure and its functional relevance in the pathogenesis
1. Introduction
2. Biofilm formation by bacteria
3. Structure and characteristics of mycobacterial biofilm
4. Biofilm formation by NTM
5. Biofilm formation by M. smegmatis
6. Biofilm formation by M. tuberculosis
7. Requirements for biofilm formation
8. Mycobacterial genes involved in biofilm formation
9. Functional relevance of biofilm formation by mycobacteria
10. Therapeutic implications of mycobacterial biofilm
11. Conclusion
References
Chapter 28: Streptococcus pneumoniae biofilms and human infectious diseases: A review
1. Introduction
2. Streptococcus pneumoniae-related infections
3. Role of Streptococcus pneumoniae biofilms in human infectious diseases
3.1. Otitis media
3.2. Pneumonia
3.3. Bronchitis
3.4. Medical indwelling device-related infections
3.5. Bacteremia
3.6. Meningitis
4. Streptococcus pneumoniae biofilms structure
5. Pneumococci biofilms properties
5.1. Antibiotic resistance
5.2. Increases gene transfer frequency
5.3. Persister cells
6. Conclusion
References
Chapter 29: Oral biofilms: Architecture and control
1. Introduction
2. Human oral microbiome
3. Oral microbial biofilms
4. Oral candidiasis
4.1. Candida albicans
4.2. Pathogenicity and virulence factors of C. albicans
4.2.1. Adhesion to epithelial cells
4.2.2. Biofilm formation
4.2.3. Yeast to hyphal transition
4.3. Denture stomatitis
4.4. Evolution of drug resistance in C. albicans
5. Dental caries
5.1. S. mutans in dental caries
5.2. Virulence factors of S. mutans
5.2.1. Adhesion
5.2.2. Polysaccharide production
5.2.3. Glucan-binding proteins
5.2.4. Acid production
5.2.5. Acid tolerance
5.2.6. Host factors in caries
5.3. Biofilm formation by S. mutans
5.4. Fluoride resistance in S. mutans
6. Early childhood caries (ECC)
6.1. Synergistic interaction of C. albicans and S. mutans in development of ECC
7. Biofilm-mediated antimicrobial resistance
8. Mechanism and risk factors associated with oral biofilm formation
8.1. Risk factors associated with formation of oral biofilms
9. Alternative strategies to combat biofilm-associated drug resistance in pathogens
9.1. Targeting biofilm
9.2. Bioactives to fight against biofilm and antimicrobial resistance
9.3. Combinatorial drug therapy
9.4. Antimicrobial peptides (AMPs)
9.4.1. Ideal properties of AMPs
9.4.2. AMPs against cariogenic pathogen S. mutans
9.4.3. Advantages of AMPs over antibiotics
10. Conclusion and prospects
References
Further reading
Chapter 30: Molecular mechanisms of Acinetobacter baumannii biofilm formation and its impact on virulence, persistence, a ...
1. Introduction
2. Biofilms of Acinetobacter baumannii
3. Microstructure of A. baumannii biofilms and its composition
4. Regulation of biofilm formation
5. Role of biofilms in virulence and pathogenesis
6. Biofilms and persistence of Acinetobacter baumannii
7. Novel antibiofilm treatment strategies
8. Summary and conclusions
References
Further reading
Chapter 31: Polymicrobial biofilms: Impact on fungal pathogenesis
1. Introduction
2. Polymicrobial interactions
2.1. Fungi-bacteria polymicrobial biofilms
2.2. Fungi-fungi polymicrobial biofilms
3. Factors affecting biofilm formation and development
4. Composition of mono and polymicrobial biofilms
5. Biofilms and diseases
5.1. Systemic infections
5.2. Upper and low airways
5.3. Oral cavity
5.4. Gastrointestinal tract
5.5. Medical devices
5.6. Wounds
6. Models of biofilm infection and interaction
7. Treatment challenges
7.1. Combined therapy
7.2. Nanotechnology
7.3. Photodynamic therapy (PDT)
7.4. Antimicrobial peptides (AMPs)
7.5. Quorum sensing molecules (QSMs)
References
Chapter 32: Molecular mechanism of biofilm formation of pathogenic microorganisms and their role in host pathogen interaction
1. Introduction
1.1. Microorganisms involved in biofilm formation
1.1.1. Gram-positive bacteria
1.1.2. Gram-negative bacteria
1.1.3. Fungal species in biofilm formation
2. Biofilm-associated diseases
2.1. Otitis media
2.2. Cholesteatoma
2.3. Infective endocarditis (IE)
2.4. Atherosclerosis
2.5. Sialolithiasis
2.6. Typhoid fever
2.7. Inflammatory bowel disease and colorectal cancer
2.8. Chronic rhinosinusitis (CRS)
3. Mechanism of biofilm formation
3.1. In Pseudomonas aeruginosa
3.2. In Candida albicans
3.3. Biofilm development
3.3.1. Biofilm dispersal
3.4. Role of transcription factor in biofilm formation
3.5. Quorum sensing mechanism in biofilm formation
3.5.1. Quorum sensing in Gram-negative bacteria
3.5.2. Quorum sensing in Gram-positive bacteria
3.5.3. Quorum sensing in fungal biofilm
4. Implications of biofilms during host-pathogen interaction
4.1. Bacterial
4.1.1. Pseudomonas aeruginosa
4.1.2. Enterococcus faecalis
4.1.3. Escherichia coli
4.1.4. Staphylococcus aureus
4.2. Fungi
4.2.1. Candida albicans
4.2.2. Aspergillus fumigatus
5. Conclusion and future prospect
References
Further reading
Chapter 33: Pathogenic biofilms in environment and industrial setups and impact on human health
1. Introduction
2. Development of environmental biofilms
3. Biofilm under environmental stress
4. Antibiotic resistance and tolerance in biofilm
5. Wastewater as hotspot of antibiotic resistance in environment
6. Pathogenic biofilms as serious concern in environment and in humans
6.1. Biofilm in drinking water system (DWDS)
6.2. Biofilm in food industry
6.3. Biofilm in dairy industry
7. Impact of biofilms in clinical settings
7.1. Biofilm-associated diseases in humans
8. Conclusion and future prospects
References
Chapter 34: Biofilm formation: A well-played game in bacterial pathogenesis
1. Introduction
2. Establishment and development of bacterial biofilm
2.1. Establishment of conditioning layer on substratum surface
2.2. Adsorption and accumulation of microbes on the preconditioned surface
2.3. Adhesion of microbes
2.3.1. Reversible adhesion
2.3.2. Irreversible adhesion
2.4. Initial colonization, division of microbes, and development of microcolony
2.5. Microbial interactions and biofilm maturation
2.5.1. The spatial and temporal structure of EPS matrix and emergence of variation
2.6. Maturation and dispersal
3. Biofilm heterogeneity and pathogenesis
4. Biofilms: Making acute infections chronic
4.1. Eukaryotic ECM-A conditioning layer for pathogens
4.2. Frustrated phagocytosis
4.3. Matrix support to cooperative virulence
4.4. EPS matrix giving rise to antimicrobial tolerance
4.5. EPS as a source for genetic alteration giving rise to antimicrobial resistance
4.6. EPS as a shield in unfavorable conditions and succession
4.7. Persister cells in biofilm
5. Relevance of biofilm disease in clinical practice
5.1. Nondevice-related chronic biofilm disease
5.1.1. Respiratory-system-related infections
Rhinosinusitis (RS)
Pharyngitis, laryngitis, and sore throat
Pertussis and other Bordetella infections
Cystic fibrosis (CF)
5.1.2. Infections related to digestive system
Periodontitis and gingivitis
Sialadenitis and sialolithiasis
Recalcitrant typhoid fever
Inflammatory bowel disease
Colorectal cancer
5.1.3. Infections related to auditory system
Otitis media
5.1.4. Infections related to the cardiovascular system
Infective endocarditis
Atherosclerosis
5.1.5. The integumentary system
Wound infections
5.1.6. The urinary system
Urinary tract infections (UTIs)
Bacterial prostatitis
5.1.7. The reproductive system
Bacterial vaginosis
Chronic endometritis
Mastitis
5.1.8. Skeletal system
Septic arthritis and osteomyelitis
5.2. Microbial contamination on medical implant-device-related biofilm disease
5.2.1. Biofilms associated with catheters
5.2.2. Biofilms associated with ventilation-associated pneumonia
5.2.3. Biofilms associated with orthopedic implants
5.2.4. Biofilms associated with cardiovascular implants
5.2.5. Biofilms associated with ocular implants
Biofilms on contact lenses
Biofilms associated with scleral buckles
Biofilms on conjunctival plugs and lacrimal intubation devices
5.3. Relevancy of Koch postulates in polymicrobial biofilm infections
6. Recent developments to overcome infectious biofilms and future prospects
References
Section F: Application of microbial biofilms
Chapter 35: Plant growth promoting Rhizobacteria and their biofilms in promoting sustainable agriculture and soil health
1. Introduction
2. Plant growth promoting rhizobacteria (PGPR)
2.1. Direct mechanisms
2.1.1. Nitrogen fixation
2.1.2. Phosphate solubilization
2.1.3. Siderophore production
2.1.4. Phytohormone production
Auxin
ACC (1-aminocyclopropane-1-carboxylate) deaminase
Cytokinins and gibberellins
2.2. Indirect mechanisms
2.2.1. Antagonistic role
2.2.2. Induced systemic response
3. PGPR biofilms
3.1. Formation of biofilm
3.1.1. Attachment of bacteria to the surface
3.1.2. Maturation of the biofilm
3.1.3. Detachment and return to the planktonic growth mode
3.2. Factors influencing biofilm formation
3.2.1. Surfaces
3.2.2. Temperature and moisture content
3.2.3. Salinity
3.2.4. Nutrient availability
3.2.5. Microbial products
QS signal molecules in biofilm formation
Antimicrobial peptides
Exopolysaccharides
3.2.6. Soil enzymes
3.3. Constituents of biofilm matrix
4. Role of rhizobacterial biofilm in agriculture
4.1. Importance of biofilm formation in plant growth promotion
4.2. Role of PGPR biofilms in mitigating abiotic stress
4.2.1. Salt stress amelioration
4.2.2. Drought stress amelioration
4.3. Role of biofilm in biocontrol
4.4. Role of biofilm in bioremediation
5. Future perspectives
6. Conclusion
References
Further reading
Chapter 36: Antagonistic Bacilli as prospective probiotics against pathogenic biofilms
1. Introduction
1.1. Biofilms
1.2. Biofilms in food industry
1.3. Biofilms onto food and food contact surfaces
2. Approaches to control pathogenic biofilms
2.1. Metal ions and antibiofilm strategies
2.2. Probiotics and postbiotics against pathogenic biofilms
3. Probiotic Bacilli supporting the health of host organism
3.1. Bacilli biofilms against pathogen biofilms
3.2. Bacillus subtilis, a potential probiotic model
4. Probiotic-prebiotic complex
4.1. Prebiotic degradation and SCFAs production as a measure to control pathogenic biofilms
4.2. SCFAs and histone deacetylase (HDAC) inhibition as a biofilm inhibition strategy
5. Promising functional foods
6. Pulcherrimin as an antibiofilm agent
7. Concluding remarks and future prospects
References
Chapter 37: Use of bacterial biofilms to produce high added-value compounds
1. Introduction
2. Production of recombinant proteins using biofilms
2.1. β-Galactosidase
2.2. Green fluorescent protein (GFP)
2.3. Other proteins
3. Production of added-value compounds in biofilms
3.1. Organic acids
3.2. Polysaccharides
3.3. Bioactive compounds
3.4. Alcohols and solvents
3.5. Miscellaneous
4. Conclusions and future remarks
References
Chapter 38: Biofilms as sustainable tools for environmental biotechnologies: An interdisciplinary approach
1. Introduction to biofilms in environmental biotechnology
1.1. Beneficial properties of the biofilm state
1.2. Biofilms in industrial processes
2. Relevance of interactions of biofilm components with contaminants
2.1. Biofilm matrix: Chemical structure
2.2. Bioavailability of xenobiotics in biofilm structure
2.3. Biofilm matrix complexing capacity and metal immobilization
3. Biofilm-dependent microbial survival strategies in polluted environments
4. Application of biofilms in bioremediation processes
4.1. In situ bioremediation mediated by biofilms
4.2. Ex situ bioremediation: Biofilm-based bioreactors
5. Biofilm monitoring in nature: Image acquisition and processing
6. Concluding remarks
References
Chapter 39: Use of biofilm bacteria to enhance overall microbial fuel cell performance
1. Introduction
2. MFC design and operation
3. Double-chamber MFC (DCMFC)
4. Single-chamber MFC (SCMFC)
5. Stacked MFC
6. Micro-sized MFC
7. Electroactive biofilms in MFC
8. Biofilm formation and regulation in MFC
9. Electrochemical characterization of biofilms
10. Biofilm morphology and viability
11. Microbial community analysis in MFC
12. Conclusion
References
Chapter 40: Industrial applications and implications of biofilms
1. Biofilms in perspective
1.1. Exopolymers
2. Biofilm formation
3. Industrial applications of biofilms
4. Biofilm bioreactors for beneficial applications
5. Types of biofilm reactors
5.1. Continuous stirred-tank reactor (CSTR)
5.2. Packed-bed reactors
5.3. Fixed-bed reactors
5.4. Upflow anaerobic sludge blanket reactors
6. Bioreactors and denitrification process
7. Biofilm reactors in wastewater treatment
8. Biofilms for gas and odor treatment
8.1. Biofilters
8.2. Bioscrubbers
9. Biofilm reactors in ethanol production
10. Biofilm bioreactors and production of biochemicals
11. Industrial ramifications of biofilms
12. Industrial biocorrosion problems
13. Microbial corrosion in industrial cooling water systems
14. Implications of biofilms and biocorrosion
15. Prevention and control of biofilms in industries
16. Control strategies for industrial cooling water systems
17. Conclusion
References
Index
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