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1 Infectious Microecology1

1.1 ConceptionofInfectious Microecology2

1.1.1 Defmition2

1.1.2 Classification of Normal Microbiota α2

1.2 History of Infectious Microecology5

1.2.1 The Embryonic Stage of Microecology5

1.2.2 The Lag Phase of Microecology6

1.2.3 The Developmental Stage of Microecology6

1.2.4 The Establishment and Development of Infectious Microecology7

1.3 The Subject Characteristics of Infectious Microecology8

1.3.1 Subiect Relations8

1.3.2 Subject Core9

1.3.3 Infectious Microecology Is a Basic Subject9

1.3.4 Infectious Microecology Is an Applied Subject10

1.4 The Classification of Infection11

1.4.1 Types of Infection11

1.4.2 The Evolution of Infection13

1.4.3 The Outcome of Infection13

1.5 Microecological Characteristics of Infection13

1.5.1 Microecology Helps to Build and Maintain the Host's Immune Systems14

1.5.2 Dynamic Balances between Microecology and Host15

1.5.3 Many Infections are Correlated with Microecological Imbalance15

1.6 The Microecological Mechanism of Infection16

1.6.1 Occurrence of Infection16

1.6.2 Development of Infection17

1.6.3 Outcome of Infection17

1.7 Prevention and Control of Infections Using Infectious Microecology Theories18

1.7.1 The Revolution in Infection Prevention and Control Strategy18

1.7.2 Mechanisms for Preventing and Controlling Infections with Microecological Modulators19

1.7.3 Frequently Used Microecological Modulators19

1.7.4 Prospects of Infection Prevention and Control Using Infectious Microecology Theories19

References20

2 Human Microbiota and Its Function23

2.1 Metabolic Functions24

2.2 Trophic Functions27

2.3 Interaction between Gut Bacteria and Host Immunity27

2.4 Protective Functions:The Barrier Effect28

References29

3 Infectious Microecology and Immunology33

3.1 Infection and Immunity33

3.1.1 Immunity Response to Microbes34

3.1.2 Immune Responses to Extracellular Bacteria34

3.1.3 Immune Responses to Intracellular Bacteria35

3.1.4 Immune Responses to Fungi36

3.2 Infectious Microecology and Immunology36

3.2.1 Intestinal Microbes and Intestinal Barrier37

3.2.2 Intestinal Microecology and Host Immunity39

3.3 Hepatic Microecology and Immunity42

3.3.1 Liver Involvement in Innate Immunity42

3.3.2 Liver Involvement in Adaptive Immunity45

3.4 Liver's Immune Privilege46

References49

4 Microecology Disturbance and Infection59

4.1 Microecology Disturbance59

4.1.1 Concept of Microecology Disturbance60

4.1.2 Classification of Microecology Disturbance60

4.1.3 Influencing Factors of Microecology Disturbance64

4.2 Infection68

4.2.1 The Concept of Infection69

4.2.2 Types of Infection70

4.2.3 Etiologic Agent of Infection71

4.2.4 Epidemic Links of Infection74

4.3 The Relation between Microecology Disturbance and Infection75

4.3.1 Traditional Biological Pathogeny Theory76

4.3.2 Ecological Pathogeny Theory76

4.3.3 The Significance of Infection76

4.3.4 Microdysbiosis Induces Infection Diseases78

4.3.5 Mechanism of Microorganisms and Host79

References80

5 Nosocomial Infections and Bacterial Resistance83

5.1 Nosocomial Infections84

5.1.1 Introduction84

5.1.2 Epidemiology of Nosocomial Infections85

5.1.3 Pathogens of Nosocomial Infections89

5.1.4 Common Nosocomial Infections91

5.1.5 Prevention of Nosocomial Infections99

5.2 Bacterial Resistance103

5.2.1 Prevalence of Bacterial Resistance103

5.2.2 Mechanisms of Bacterial Resistance110

5.2.3 Strategies to Control Bacterial Resistance124

References124

6 Microbial Culture and Its Clinical Application133

6.1 Conventional Microbial Culture and Clinical Application133

6.1.1 Clinical Blood Culture133

6.1.2 Clinical Body Fluids Culture135

6.1.3 Clinical Urine Culture136

6.1.4 Culture of Specimens from Gastrointestinal Tract137

6.2 Requirements for Collection of Cultural or Non-Cultural Specimens137

6.2.1 Conventional Principles for Collection and Transportation of Specimens Used for Culture137

6.2.2 Special Conditions for Collecting Specimens Used for'Non-Routine'Culture139

6.2.3 Inoculating Samples in an Optimal Media:Selection of the Culture Media140

6.3 Clinical Choice ofMicrobial Culture or Non-Culture142

6.3.1 Overview of Microbial Culture and Non-Culture Based Methods142

6.3.2 Clinical Indication of Microbial Culture and Non-Culture144

6.4 Interpretation of the Microbial Culture Results146

6.4.1 Interpreting the Positive Results of the Microbial Culture147

6.4.2 Interpreting the Negative Results of the Microbial Culture149

References150

7 Molecular Microecological Techniques153

7.1 Introduction154

7.2 Size Pattern Analysis—T-RFLP Polymorphism Analysis of 16S rRNA Genes156

7.3 Melting Pattern Analysis—PCR-DGGE Analysis of 16S rRNA Genes159

7.4 FISH165

7.5 Microarray Applications in Microbial Ecology Research168

7.6 Cloning Library Construction and Sequencing172

7.7 Next-Generation Sequencing Techniques for Microbial Ecology Research174

7.8 Conclusion180

References180

8 Metabonomic Phenotyping for the Gut Microbiota and Mammal Interactions189

8.1 Mammals Are'Superorganisms'189

8.2 Co-Metabolisms and the Mammal-Microbiome Interactions190

8.3 Metabonomic Phenotyping for Mammals191

8.4 Future Perspectives194

References194

9 Bioinformatics for Genomes and Metagenomes in Ecology Studies203

9.1 Introduction to Advances in Microbial Ecology203

9.2 16S rDNA in Ecology Studies204

9.3 16S rDNA Gene Analysis205

9.4 Metagenomics207

9.5 Recent Applications of Environmental Metagenomic Sequencing208

9.6 Analysis of Viral Communities209

9.7 Assembly of Sequence Data209

9.8 Assembly:Strategies211

9.9 Assembly:Future Directions212

9.10 Fragment Recruitment215

9.11 Taxonomic Classification216

9.12 MGTAXA216

9.13 High Performance Computing217

9.14 Functional Annotation218

9.15 Analysis of Eukaryotes in Ecology Studies218

9.16 Challenges Presented by Data Volume(Computational and Storage Requirements,Cloud Computing Solutions)219

9.17 Future Directions221

References222

10 Ecology of Oral Infectious Diseases227

10.1 Ecological Basis228

10.1.1 Oral Biotic Area229

10.1.2 Normal Oral Microflora231

10.1.3 Saliva and Dental Plaque Biofilm244

10.2 Oral Infectious Diseases253

10.2.1 Dental Caries253

10.2.2 Pulpal and Periapical Diseases267

10.2.3 Periodontal Disease273

10.2.4 Maxillofacial Infectious Diseases285

10.2.5 Oral Mucosal Infections287

10.2.6 Secondary Infection from the Wearing of Dentures290

References291

11 Gastrointestinal Infectious Microecology293

11.1 Microbiota in Health293

11.1.1 Normal Microbiota in the Stomach293

11.1.2 Normal Microbiota in the Intestine294

11.1.3 Physiological Functions of Gastrointestinal Microbiota295

11.1.4 Factors Affecting Gastrointestinal Microecological Balance of the Host296

11.2 Helicobacter Pylori and Gastroduodenal Disease298

11.2.1 Helicobacter Pylori and Chronic Gastritis298

11.2.2 Helicobacter Pylori and Peptic Ulcer298

11.2.3 Helicobacter Pylori and Gastric Cancer299

11.2.4 Diagnosis for H. Pylori Infection299

11.2.5 Treatment301

11.3 Inflammatory Bowel Disease301

11.3.1 Role of Microbiota301

11.3.2 Immune Response302

11.3.3 Clinical Findings and Diagnosis302

11.3.4 Treatment303

11.4 Infectious Diarrhea304

11.4.1 Diarrhea Caused by Toxins304

11.4.2 Diarrhea Caused by Invasive Pathogens305

11.4.3 Diarrhea Caused by Viruses305

11.4.4 Diagnosis305

11.4.5 Treatment306

11.5 Irritable Bowel Syndrome306

11.5.1 Etiology307

11.5.2 Clinical Findings and Diagnosis308

11.5.3 Treatment309

11.6 Antibiotic-Associated Diarrhea309

11.6.1 Pathogenesis309

11.6.2 Clinical Findings and Diagnosis310

11.6.3 Treatment311

11.7 Colorectal Cancer311

11.7.1 Pathogenesis312

11.7.2 Symptoms313

11.7.3 Diagnosis313

11.7.4 Treatment314

11.8 Gastrointestinal Tuberculosis314

References315

12 Infectious Microecology in Liver Disease317

12.1 An Overview ofInfectious Microecology in Liver Disease318

12.1.1 Liver Anatomy and Enterohepatic Recycling318

12.1.2 Gut-Liver Axis318

12.1.3 The Role of Kupffer Cells in Liver Disease319

12.1.4 Endotoxin Activates Kupffer Cells in Liver Disease319

12.1.5 Pathogenesis of Bacterial Translocation in Liver Disease321

12.2 Gut Microflora in the Pathogenesis of the Complications of Cirrhosis322

12.2.1 Bacterial Infections in Cirrhosis323

12.2.2 Sources and Types of Bacterial Infection in Cirrhosis323

12.2.3 Bacteria Translocation in the Pathogenesis of Spontaneous Bacterial Peritonitis in Cirrhosis324

12.2.4 Gut Flora and the Hyperdynamic Circulatory State in Cirrhosis324

12.2.5 The Gut Flora and Hepatic Encephalopathy325

12.3 Modulation of Intestinal Microbiota as a Therapeutic Strategy of Liver Disease326

12.3.1 Manipulation of Gut Flora and Its Effect on Infections in Cirrhosis326

12.3.2 Manipulation of Gut Flora and Its Effect on Infections in Liver Transplants329

References329

13 Biliary Infection,Pancreatic Infection and Microecology333

13.1 Biliary Infection and Microecology333

13.1.1 Microecology Foundation of Biliary Tract System334

13.1.2 Biliary Infection and Microecology338

13.1.3 Microecology Treatment of Biliary Tract Infection343

13.2 Pancreatic Infection and Microecology349

13.2.1 Microecology Foundation of the Pancreas350

13.2.2 Pancreatic Infection and Microecology351

13.2.3 Microecology Therapies for Pancreatic Infection359

References367

14 Infectious Microecology in Urinary Tract and Reproductive System377

14.1 Introduction377

14.2 Infections of the Urinary Tract378

14.2.1 Definitions378

14.2.2 Classification379

14.3 Diagnosis380

14.3.1 Upper Urinary Tract Infection(UUTI)381

14.3.2 Lowerr Urinaru Tract Infections (LUTI)390

14.3.3 Factors Increasing Morbidity and/or Mortality395

14.4 Prostatitis and Related Disorders396

14.4.1 Epidemiology397

14.4.2 Pathophysiology398

14.4.3 Clinical Presentation and Diagnostic Evaluation398

14.4.4 Causative Pathogens in Prostatitis399

14.4.5 Treatment of Bacterial Prostatitis400

14.4.6 Conclusions403

References403

15 Infectious Microecology in the Diseases of the Respiratory System411

15.1 Ecological Space and Microecological Characteristics of the Respiratory System411

15.1.1 Non-Specific Defense Mechanism411

15.1.2 Specific Defense Mechanism413

15.2 Microecology and Microecology Changes in Respiratory System Infection414

15.3 Microecology of Respiratory System Fungal Infection416

15.3.1 Pulmonary Candidiasis416

15.3.2 Pulmonary Aspergillosis417

15.3.3 Pulmonary Cryptococcosis417

15.3.4 Pulmonary Coccidioidomycosis418

15.4 Microecology of Respiratory System Viral Infection418

15.5 Microecology of Respiratory System Mycobacterial Infection419

15.5.1 Pulmonary Tuberculosis420

15.5.2 Non-Tuberculous Mycobacterial Disease424

15.6 Main Measures of Microecological Prevention/Treatment and Respiratory System Ecological Prevention/Treatment in Anti-Infective Therapy426

References428

16 Infectious Microecology of Skin431

16.1 Histological Structures of Skin431

16.1.1 Epidermis432

16.1.2 The Dermis433

16.1.3 Subcutaneous Tissue434

16.1.4 Cutaneous Appendages:The Adnexa434

16.2 Functions of Skin436

16.2.1 Biological Barrier Function of Skin436

16.2.2 Immune Function of Skin437

16.2.3 Functions of the Sweat Gland and Sebaceous Gland439

16.2.4 Nutritional Metabolism of Skin441

16.2.5 Thermo-Regulation of Skin442

16.3 Characteristics of Cutaneous Microecology443

16.3.1 Normal Microbial Community of the Skin443

16.3.2 Influential Factors of Cutaneous Normal Microflora448

16.3.3 Physiological Function of Normal Cutaneous Microfloras454

16.4 Microecological Disturbance and Cutaneous Disorders455

16.4.1 Bacteria and Cutaneous Diseases455

16.4.2 Fungi and Cutaneous Diseases457

16.4.3 Virus and Cutaneous Diseases463

16.4.4 Warts466

16.5 Ecological Prevention and Treatment of Cutaneous Diseases468

16.5.1 Protect the Macroecological Environment468

16.5.2 Improve the Microecological Environment468

16.5.3 Use Antibiotics Appropriately470

16.5.4 Apply the Microecological Reagents470

16.6 Prospects473

References474

17 Infectious Microecology of the Hematological System477

17.1 Defensive Function of Blood477

17.1.1 Cellular Components of Blood478

17.1.2 Non-Cellular Components of Blood479

17.2 Molecular Ecology and Hematological Disease480

17.2.1 Apoptosis and Hematological Disease481

17.2.2 Oncogenes,Tumor Suppressor Genes and Signal Conducting Molecules487

17.2.3 Telomere Telomerase491

17.3 Microecological Changes and Hematologic Diseases493

17.3.1 Helicobacter Pylori and Primary Gastric Lymphoma493

17.3.2 Microecological Changes and Erythrocyte Disorders495

17.3.3 Microecological Changes and Leukocyte Diseases499

17.3.4 Infection and Bleeding Disorders502

17.4 Treatment of Hematologic Diseases and Infective Microecology507

17.4.1 Predisposing Factors and Pathogens507

17.4.2 The Principles of Treatment509

17.5 Molecular Ecological Treatment510

17.5.1 Genic Ecological Treatment510

17.5.2 Immune Ecological Treatment513

References515

18 Infectious Microecology in Solid-Organ Transplantation519

18.1 Screening of Donor and Recipient Prior to Solid-Organ Transplantation520

18.1.1 Donor-Derived Infections520

18.1.2 Recipient-Derived Infections521

18.2 Timeline ofInfection Post-Transplantation522

18.2.1 Early Period(1-4 weeks)523

18.2.2 Intermediate Period(1-6 months)523

18.2.3 Late Period (After 6 months)523

18.3 Prevention of Infection in Solid-Organ Transplantation524

18.3.1 Viral Infections524

18.3.2 Bacterial Infections527

18.3.3 Fungal Infections528

18.3.4 Parasitic Infections530

References531

19 Microecology of Infections Associated with Surgery and Trauma533

19.1 Main Pathogenic Bacteria Associated with Surgical and Trauma-Related Infections534

19.1.1 Changes to the Spectrum of the Pathogenic Bacteria534

19.1.2 Predominant Pathogenic Bacteria538

19.1.3 Primary Pathogenic Factors541

19.2 Post-Surgery-and Post-Trauma-Related Wound Infections542

19.2.1 Etiology and Pathogenesis of Wound Infections543

19.2.2 Prevention and Treatment of Wound Infections543

19.3 Intra-Abdominal Infections Associated with Surgery and Trauma547

19.3.1 Acute Peritonitis Resulting from Surgery and Trauma547

19.3.2 Intra-Abdominal Abscesses after Surgery and Trauma549

19.4 Enterogenic Infections Associated with Post-Surgery and Trauma550

19.4.1 Intestinal Barrier Function551

19.4.2 Intestinal Barrier Function and Bacterial Translocation554

19.4.3 Clinical Manifestations of Enterogenic Infections556

19.4.4 Prevention and Treatment of Enterogenic Infections557

19.5 Preventionand Prognosis of Surgical and TraumaticInfections558

19.5.1 Prevention of Post-Surgical and Post-Traumatic Infections559

19.5.2 Conventional Treatments Associated with Surgery and Wound Infections561

19.5.3 Complications of Severe Surgical and Wound Infections Prevention and Treatment of Sepsis and MOF563

19.5.4 Future Directions566

References566

20 Infective Microecology of Chemotherapy and Radiotherapy569

20.1 Mechanisrn of Chemotherapy and Radiotherapy569

20.1.1 Chemotherapy569

20.1.2 Radiotherapy572

20.2 Chemotherapy and Radiotherapy Effect on Microecology574

20.2.1 Cancer Patients and Microecology574

20.2.2 Microdysbiosis in Cancer Patients578

20.3 Microecology of Infection Caused by Radiotherapy and Chemotherapy580

20.3.1 Prevention and Treatment of Infection-Related Chemotherapy Toxicity581

20.3.2 Prevention and Treatment of Infection-Related Radiotherapy Toxicity582

20.3.3 Prevention and Treatment of Cancer Patients Infection584

20.3.4 Microecological Control of Cancer Patients587

20.4 Prospects589

References590

21 Infectious Microecology in Immunodeficiency Diseases593

21.1 HIV Immune Deficiency,Old View594

21.2 Immune Activation in HIV Infection595

21.3 Breakdown of Mucosal Immunity596

21.4 Solving the Problem from the Microecological Viewpoint598

21.5 HIV-1 Infection in Mucosa Scope600

21.6 Through Microbiota and Beyond601

21.7 Probiotics and HIV604

References605

22 Microecology Intervention in Prevention and Treatment of Infectious Diseases611

22.1 Theoretical Basis of Microecological Prevention and Treatment611

22.1.1 The Principle of Microecology Balance612

22.1.2 Principles of Biological Antagonism612

22.1.3 Biological Oxygen Consumption Hypothesis613

22.1.4 Immune Activating613

22.1.5 Nutritional Effect613

22.1.6 Three Circulations Theory614

22.1.7 Continuous Succession Effect614

22.2 Microecological Modulators615

22.2.1 Probiotics Definitions615

22.2.2 Characteristics and Classification of Probiotics616

22.2.3 Bio-Safety of Probiotics617

22.2.4 Bifidobacterium Products619

22.2.5 Lactobacillus Products620

22.2.6 Bacillus Products622

22.2.7 Saccharomyces Preparations623

22.2.8 Enterococcus Preparations624

22.2.9 Clostridium Butyricum Preparation625

22.3 Prebiotics Preparation625

22.3.1 Definition626

22.3.2 Oligosaccharide as Prebiotics627

22.3.3 Physiological Function628

22.4 Application of Probiotics and Prebiotics631

22.4.1 Gastrointestinal Tract Infection Diseases Prevention631

22.4.2 Constipation Treatment632

22.4.3 Prevention and Treatment of Hepatic Diseases633

22.4.4 Prevention of Hypercholesterolemia635

22.4.5 Treatment of Irritable Bowel Syndrome635

22.4.6 Prevention and Treatment of Vaginal Infection Diseases636

22.4.7 Application in Pediatric Diseases and Infant Care636

22.4.8 Application in Antitumor637

References638

23 Future Development of Infectious Microecology639

23.1 Evolving View of Infectious Disease639

23.2 Advances in Molecular Ecological Techniques640

23.3 Normal Human Microbiota641

23.4 Interactions between Infectious Diseases and Microbiota642

23.4.1 Disturbance of Normal Microbiota by Therapy642

23.4.2 Microbiota and Viral Infection643

23.4.3 Microbiota and Autoimmunity Disease644

23.5 Therapy644

23.5.1 Probiotics or Prebiotics644

23.5.2 Other Bacteriologic Therapy645

23.5.3 The Role of Microbiota in Drug Metabolism646

23.6 Summary and Prospects646

References647

Index649