1 Infectious Microecology

1.1 ConceptionofInfectious Microecology

1.1.1 Defmition

1.1.2 Classification of Normal Microbiota α

1.2 History of Infectious Microecology

1.2.1 The Embryonic Stage of Microecology

1.2.2 The Lag Phase of Microecology

1.2.3 The Developmental Stage of Microecology

1.2.4 The Establishment and Development of Infectious Microecology

1.3 The Subject Characteristics of Infectious Microecology

1.3.1 Subiect Relations

1.3.2 Subject Core

1.3.3 Infectious Microecology Is a Basic Subject

1.3.4 Infectious Microecology Is an Applied Subject

1.4 The Classification of Infection

1.4.1 Types of Infection

1.4.2 The Evolution of Infection

1.4.3 The Outcome of Infection

1.5 Microecological Characteristics of Infection

1.5.1 Microecology Helps to Build and Maintain the Host's Immune Systems

1.5.2 Dynamic Balances between Microecology and Host

1.5.3 Many Infections are Correlated with Microecological Imbalance

1.6 The Microecological Mechanism of Infection

1.6.1 Occurrence of Infection

1.6.2 Development of Infection

1.6.3 Outcome of Infection

1.7 Prevention and Control of Infections Using Infectious Microecology Theories

1.7.1 The Revolution in Infection Prevention and Control Strategy

1.7.2 Mechanisms for Preventing and Controlling Infections with Microecological Modulators

1.7.3 Frequently Used Microecological Modulators

1.7.4 Prospects of Infection Prevention and Control Using Infectious Microecology Theories

References

2 Human Microbiota and Its Function

2.1 Metabolic Functions

2.2 Trophic Functions

2.3 Interaction between Gut Bacteria and Host Immunity

2.4 Protective Functions:The Barrier Effect

References

3 Infectious Microecology and Immunology

3.1 Infection and Immunity

3.1.1 Immunity Response to Microbes

3.1.2 Immune Responses to Extracellular Bacteria

3.1.3 Immune Responses to Intracellular Bacteria

3.1.4 Immune Responses to Fungi

3.2 Infectious Microecology and Immunology

3.2.1 Intestinal Microbes and Intestinal Barrier

3.2.2 Intestinal Microecology and Host Immunity

3.3 Hepatic Microecology and Immunity

3.3.1 Liver Involvement in Innate Immunity

3.3.2 Liver Involvement in Adaptive Immunity

3.4 Liver's Immune Privilege

References

4 Microecology Disturbance and Infection

4.1 Microecology Disturbance

4.1.1 Concept of Microecology Disturbance

4.1.2 Classification of Microecology Disturbance

4.1.3 Influencing Factors of Microecology Disturbance

4.2 Infection

4.2.1 The Concept of Infection

4.2.2 Types of Infection

4.2.3 Etiologic Agent of Infection

4.2.4 Epidemic Links of Infection

4.3 The Relation between Microecology Disturbance and Infection

4.3.1 Traditional Biological Pathogeny Theory

4.3.2 Ecological Pathogeny Theory

4.3.3 The Significance of Infection

4.3.4 Microdysbiosis Induces Infection Diseases

4.3.5 Mechanism of Microorganisms and Host

References

5 Nosocomial Infections and Bacterial Resistance

5.1 Nosocomial Infections

5.1.1 Introduction

5.1.2 Epidemiology of Nosocomial Infections

5.1.3 Pathogens of Nosocomial Infections

5.1.4 Common Nosocomial Infections

5.1.5 Prevention of Nosocomial Infections

5.2 Bacterial Resistance

5.2.1 Prevalence of Bacterial Resistance

5.2.2 Mechanisms of Bacterial Resistance

5.2.3 Strategies to Control Bacterial Resistance

References

6 Microbial Culture and Its Clinical Application

6.1 Conventional Microbial Culture and Clinical Application

6.1.1 Clinical Blood Culture

6.1.2 Clinical Body Fluids Culture

6.1.3 Clinical Urine Culture

6.1.4 Culture of Specimens from Gastrointestinal Tract

6.2 Requirements for Collection of Cultural or Non-Cultural Specimens

6.2.1 Conventional Principles for Collection and Transportation of Specimens Used for Culture

6.2.2 Special Conditions for Collecting Specimens Used for'Non-Routine'Culture

6.2.3 Inoculating Samples in an Optimal Media:Selection of the Culture Media

6.3 Clinical Choice ofMicrobial Culture or Non-Culture

6.3.1 Overview of Microbial Culture and Non-Culture Based Methods

6.3.2 Clinical Indication of Microbial Culture and Non-Culture

6.4 Interpretation of the Microbial Culture Results

6.4.1 Interpreting the Positive Results of the Microbial Culture

6.4.2 Interpreting the Negative Results of the Microbial Culture

References

7 Molecular Microecological Techniques

7.1 Introduction

7.2 Size Pattern Analysis—T-RFLP Polymorphism Analysis of 16S rRNA Genes

7.3 Melting Pattern Analysis—PCR-DGGE Analysis of 16S rRNA Genes

7.4 FISH

7.5 Microarray Applications in Microbial Ecology Research

7.6 Cloning Library Construction and Sequencing

7.7 Next-Generation Sequencing Techniques for Microbial Ecology Research

7.8 Conclusion

References

8 Metabonomic Phenotyping for the Gut Microbiota and Mammal Interactions

8.1 Mammals Are'Superorganisms'

8.2 Co-Metabolisms and the Mammal-Microbiome Interactions

8.3 Metabonomic Phenotyping for Mammals

8.4 Future Perspectives

References

9 Bioinformatics for Genomes and Metagenomes in Ecology Studies

9.1 Introduction to Advances in Microbial Ecology

9.2 16S rDNA in Ecology Studies

9.3 16S rDNA Gene Analysis

9.4 Metagenomics

9.5 Recent Applications of Environmental Metagenomic Sequencing

9.6 Analysis of Viral Communities

9.7 Assembly of Sequence Data

9.8 Assembly:Strategies

9.9 Assembly:Future Directions

9.10 Fragment Recruitment

9.11 Taxonomic Classification

9.12 MGTAXA

9.13 High Performance Computing

9.14 Functional Annotation

9.15 Analysis of Eukaryotes in Ecology Studies

9.16 Challenges Presented by Data Volume(Computational and Storage Requirements,Cloud Computing Solutions)

9.17 Future Directions

References

10 Ecology of Oral Infectious Diseases

10.1 Ecological Basis

10.1.1 Oral Biotic Area

10.1.2 Normal Oral Microflora

10.1.3 Saliva and Dental Plaque Biofilm

10.2 Oral Infectious Diseases

10.2.1 Dental Caries

10.2.2 Pulpal and Periapical Diseases

10.2.3 Periodontal Disease

10.2.4 Maxillofacial Infectious Diseases

10.2.5 Oral Mucosal Infections

10.2.6 Secondary Infection from the Wearing of Dentures

References

11 Gastrointestinal Infectious Microecology

11.1 Microbiota in Health

11.1.1 Normal Microbiota in the Stomach

11.1.2 Normal Microbiota in the Intestine

11.1.3 Physiological Functions of Gastrointestinal Microbiota

11.1.4 Factors Affecting Gastrointestinal Microecological Balance of the Host

11.2 Helicobacter Pylori and Gastroduodenal Disease

11.2.1 Helicobacter Pylori and Chronic Gastritis

11.2.2 Helicobacter Pylori and Peptic Ulcer

11.2.3 Helicobacter Pylori and Gastric Cancer

11.2.4 Diagnosis for H. Pylori Infection

11.2.5 Treatment

11.3 Inflammatory Bowel Disease

11.3.1 Role of Microbiota

11.3.2 Immune Response

11.3.3 Clinical Findings and Diagnosis

11.3.4 Treatment

11.4 Infectious Diarrhea

11.4.1 Diarrhea Caused by Toxins

11.4.2 Diarrhea Caused by Invasive Pathogens

11.4.3 Diarrhea Caused by Viruses

11.4.4 Diagnosis

11.4.5 Treatment

11.5 Irritable Bowel Syndrome

11.5.1 Etiology

11.5.2 Clinical Findings and Diagnosis

11.5.3 Treatment

11.6 Antibiotic-Associated Diarrhea

11.6.1 Pathogenesis

11.6.2 Clinical Findings and Diagnosis

11.6.3 Treatment

11.7 Colorectal Cancer

11.7.1 Pathogenesis

11.7.2 Symptoms

11.7.3 Diagnosis

11.7.4 Treatment

11.8 Gastrointestinal Tuberculosis

References

12 Infectious Microecology in Liver Disease

12.1 An Overview ofInfectious Microecology in Liver Disease

12.1.1 Liver Anatomy and Enterohepatic Recycling

12.1.2 Gut-Liver Axis

12.1.3 The Role of Kupffer Cells in Liver Disease

12.1.4 Endotoxin Activates Kupffer Cells in Liver Disease

12.1.5 Pathogenesis of Bacterial Translocation in Liver Disease

12.2 Gut Microflora in the Pathogenesis of the Complications of Cirrhosis

12.2.1 Bacterial Infections in Cirrhosis

12.2.2 Sources and Types of Bacterial Infection in Cirrhosis

12.2.3 Bacteria Translocation in the Pathogenesis of Spontaneous Bacterial Peritonitis in Cirrhosis

12.2.4 Gut Flora and the Hyperdynamic Circulatory State in Cirrhosis

12.2.5 The Gut Flora and Hepatic Encephalopathy

12.3 Modulation of Intestinal Microbiota as a Therapeutic Strategy of Liver Disease

12.3.1 Manipulation of Gut Flora and Its Effect on Infections in Cirrhosis

12.3.2 Manipulation of Gut Flora and Its Effect on Infections in Liver Transplants

References

13 Biliary Infection,Pancreatic Infection and Microecology

13.1 Biliary Infection and Microecology

13.1.1 Microecology Foundation of Biliary Tract System

13.1.2 Biliary Infection and Microecology

13.1.3 Microecology Treatment of Biliary Tract Infection

13.2 Pancreatic Infection and Microecology

13.2.1 Microecology Foundation of the Pancreas

13.2.2 Pancreatic Infection and Microecology

13.2.3 Microecology Therapies for Pancreatic Infection

References

14 Infectious Microecology in Urinary Tract and Reproductive System

14.1 Introduction

14.2 Infections of the Urinary Tract

14.2.1 Definitions

14.2.2 Classification

14.3 Diagnosis

14.3.1 Upper Urinary Tract Infection(UUTI)

14.3.2 Lowerr Urinaru Tract Infections (LUTI)

14.3.3 Factors Increasing Morbidity and/or Mortality

14.4 Prostatitis and Related Disorders

14.4.1 Epidemiology

14.4.2 Pathophysiology

14.4.3 Clinical Presentation and Diagnostic Evaluation

14.4.4 Causative Pathogens in Prostatitis

14.4.5 Treatment of Bacterial Prostatitis

14.4.6 Conclusions

References

15 Infectious Microecology in the Diseases of the Respiratory System

15.1 Ecological Space and Microecological Characteristics of the Respiratory System

15.1.1 Non-Specific Defense Mechanism

15.1.2 Specific Defense Mechanism

15.2 Microecology and Microecology Changes in Respiratory System Infection

15.3 Microecology of Respiratory System Fungal Infection

15.3.1 Pulmonary Candidiasis

15.3.2 Pulmonary Aspergillosis

15.3.3 Pulmonary Cryptococcosis

15.3.4 Pulmonary Coccidioidomycosis

15.4 Microecology of Respiratory System Viral Infection

15.5 Microecology of Respiratory System Mycobacterial Infection

15.5.1 Pulmonary Tuberculosis

15.5.2 Non-Tuberculous Mycobacterial Disease

15.6 Main Measures of Microecological Prevention/Treatment and Respiratory System Ecological Prevention/Treatment in Anti-Infective Therapy

References

16 Infectious Microecology of Skin

16.1 Histological Structures of Skin

16.1.1 Epidermis

16.1.2 The Dermis

16.1.3 Subcutaneous Tissue

16.1.4 Cutaneous Appendages:The Adnexa

16.2 Functions of Skin

16.2.1 Biological Barrier Function of Skin

16.2.2 Immune Function of Skin

16.2.3 Functions of the Sweat Gland and Sebaceous Gland

16.2.4 Nutritional Metabolism of Skin

16.2.5 Thermo-Regulation of Skin

16.3 Characteristics of Cutaneous Microecology

16.3.1 Normal Microbial Community of the Skin

16.3.2 Influential Factors of Cutaneous Normal Microflora

16.3.3 Physiological Function of Normal Cutaneous Microfloras

16.4 Microecological Disturbance and Cutaneous Disorders

16.4.1 Bacteria and Cutaneous Diseases

16.4.2 Fungi and Cutaneous Diseases

16.4.3 Virus and Cutaneous Diseases

16.4.4 Warts

16.5 Ecological Prevention and Treatment of Cutaneous Diseases

16.5.1 Protect the Macroecological Environment

16.5.2 Improve the Microecological Environment

16.5.3 Use Antibiotics Appropriately

16.5.4 Apply the Microecological Reagents

16.6 Prospects

References

17 Infectious Microecology of the Hematological System

17.1 Defensive Function of Blood

17.1.1 Cellular Components of Blood

17.1.2 Non-Cellular Components of Blood

17.2 Molecular Ecology and Hematological Disease

17.2.1 Apoptosis and Hematological Disease

17.2.2 Oncogenes,Tumor Suppressor Genes and Signal Conducting Molecules

17.2.3 Telomere Telomerase

17.3 Microecological Changes and Hematologic Diseases

17.3.1 Helicobacter Pylori and Primary Gastric Lymphoma

17.3.2 Microecological Changes and Erythrocyte Disorders

17.3.3 Microecological Changes and Leukocyte Diseases

17.3.4 Infection and Bleeding Disorders

17.4 Treatment of Hematologic Diseases and Infective Microecology

17.4.1 Predisposing Factors and Pathogens

17.4.2 The Principles of Treatment

17.5 Molecular Ecological Treatment

17.5.1 Genic Ecological Treatment

17.5.2 Immune Ecological Treatment

References

18 Infectious Microecology in Solid-Organ Transplantation

18.1 Screening of Donor and Recipient Prior to Solid-Organ Transplantation

18.1.1 Donor-Derived Infections

18.1.2 Recipient-Derived Infections

18.2 Timeline ofInfection Post-Transplantation

18.2.1 Early Period(1-4 weeks)

18.2.2 Intermediate Period(1-6 months)

18.2.3 Late Period (After 6 months)

18.3 Prevention of Infection in Solid-Organ Transplantation

18.3.1 Viral Infections

18.3.2 Bacterial Infections

18.3.3 Fungal Infections

18.3.4 Parasitic Infections

References

19 Microecology of Infections Associated with Surgery and Trauma

19.1 Main Pathogenic Bacteria Associated with Surgical and Trauma-Related Infections

19.1.1 Changes to the Spectrum of the Pathogenic Bacteria

19.1.2 Predominant Pathogenic Bacteria

19.1.3 Primary Pathogenic Factors

19.2 Post-Surgery-and Post-Trauma-Related Wound Infections

19.2.1 Etiology and Pathogenesis of Wound Infections

19.2.2 Prevention and Treatment of Wound Infections

19.3 Intra-Abdominal Infections Associated with Surgery and Trauma

19.3.1 Acute Peritonitis Resulting from Surgery and Trauma

19.3.2 Intra-Abdominal Abscesses after Surgery and Trauma

19.4 Enterogenic Infections Associated with Post-Surgery and Trauma

19.4.1 Intestinal Barrier Function

19.4.2 Intestinal Barrier Function and Bacterial Translocation

19.4.3 Clinical Manifestations of Enterogenic Infections

19.4.4 Prevention and Treatment of Enterogenic Infections

19.5 Preventionand Prognosis of Surgical and TraumaticInfections

19.5.1 Prevention of Post-Surgical and Post-Traumatic Infections

19.5.2 Conventional Treatments Associated with Surgery and Wound Infections

19.5.3 Complications of Severe Surgical and Wound Infections Prevention and Treatment of Sepsis and MOF

19.5.4 Future Directions

References

20 Infective Microecology of Chemotherapy and Radiotherapy

20.1 Mechanisrn of Chemotherapy and Radiotherapy

20.1.1 Chemotherapy

20.1.2 Radiotherapy

20.2 Chemotherapy and Radiotherapy Effect on Microecology

20.2.1 Cancer Patients and Microecology

20.2.2 Microdysbiosis in Cancer Patients

20.3 Microecology of Infection Caused by Radiotherapy and Chemotherapy

20.3.1 Prevention and Treatment of Infection-Related Chemotherapy Toxicity

20.3.2 Prevention and Treatment of Infection-Related Radiotherapy Toxicity

20.3.3 Prevention and Treatment of Cancer Patients Infection

20.3.4 Microecological Control of Cancer Patients

20.4 Prospects

References

21 Infectious Microecology in Immunodeficiency Diseases

21.1 HIV Immune Deficiency,Old View

21.2 Immune Activation in HIV Infection

21.3 Breakdown of Mucosal Immunity

21.4 Solving the Problem from the Microecological Viewpoint

21.5 HIV-1 Infection in Mucosa Scope

21.6 Through Microbiota and Beyond

21.7 Probiotics and HIV

References

22 Microecology Intervention in Prevention and Treatment of Infectious Diseases

22.1 Theoretical Basis of Microecological Prevention and Treatment

22.1.1 The Principle of Microecology Balance

22.1.2 Principles of Biological Antagonism

22.1.3 Biological Oxygen Consumption Hypothesis

22.1.4 Immune Activating

22.1.5 Nutritional Effect

22.1.6 Three Circulations Theory

22.1.7 Continuous Succession Effect

22.2 Microecological Modulators

22.2.1 Probiotics Definitions

22.2.2 Characteristics and Classification of Probiotics

22.2.3 Bio-Safety of Probiotics

22.2.4 Bifidobacterium Products

22.2.5 Lactobacillus Products

22.2.6 Bacillus Products

22.2.7 Saccharomyces Preparations

22.2.8 Enterococcus Preparations

22.2.9 Clostridium Butyricum Preparation

22.3 Prebiotics Preparation

22.3.1 Definition

22.3.2 Oligosaccharide as Prebiotics

22.3.3 Physiological Function

22.4 Application of Probiotics and Prebiotics

22.4.1 Gastrointestinal Tract Infection Diseases Prevention

22.4.2 Constipation Treatment

22.4.3 Prevention and Treatment of Hepatic Diseases

22.4.4 Prevention of Hypercholesterolemia

22.4.5 Treatment of Irritable Bowel Syndrome

22.4.6 Prevention and Treatment of Vaginal Infection Diseases

22.4.7 Application in Pediatric Diseases and Infant Care

22.4.8 Application in Antitumor

References

23 Future Development of Infectious Microecology

23.1 Evolving View of Infectious Disease

23.2 Advances in Molecular Ecological Techniques

23.3 Normal Human Microbiota

23.4 Interactions between Infectious Diseases and Microbiota

23.4.1 Disturbance of Normal Microbiota by Therapy

23.4.2 Microbiota and Viral Infection

23.4.3 Microbiota and Autoimmunity Disease

23.5 Therapy

23.5.1 Probiotics or Prebiotics

23.5.2 Other Bacteriologic Therapy

23.5.3 The Role of Microbiota in Drug Metabolism

23.6 Summary and Prospects

References

Index