Table Of Contents

Preface xvii

About the Companion Website xix

Section I Understanding a Microbiome 1

1 Common Definitions 3

1.1 Microbiome 3

1.2 Microbiota 4

1.3 Pathogens 5

1.4 Symbiosis 8

1.5 Dysbiosis 11

1.6 Probiotics 12

1.7 Prebiotics 15

1.8 Synbiotics 16

1.9 Biological Markers (Biomarkers) and Their Measurement 16

1.9.1 Genes, the Genome, and Genomics 17

1.9.2 Metabolites, the Metabolome, and Metabolomics 19

1.9.2.1 Metabonomics 22

1.9.3 The Proteome and Proteomics 23

Glossary 23

References 25

2 Functions of the Gastrointestinal Microbiome 32

2.1 What Is the Gastrointestinal Microbiome? 32

2.2 Metabolic Functions 32

2.2.1 Short-Chain Fatty Acids 33

2.2.2 Gases 35

2.2.3 Amino Acids 35

2.2.4 Vitamins and Minerals 36

2.3 Structural Functions 37

2.3.1 Tight Junctions and Intestinal Permeability 37

2.4 Protective Functions 38

2.4.1 Bacteriocins 38

2.4.2 Quorum-Sensing 39

2.4.3 Immune Response 39

2.5 Participation in Bidirectional Axis Communication 39

2.6 Chapter Summary 39

References 40

3 The Origin and Development of the Gastrointestinal Microbiome 44

3.1 In Utero 44

3.2 Factors Influencing the Initial Colonization of Microbiota 45

3.2.1 Presentation at Birth 46

3.2.2 Environmental Exposure 47

3.2.3 Diet Type and Method of Feeding 47

3.2.4 Age 48

3.3 Dysbiosis During Microbiome Development 49

3.4 Key Nutritional Factors 53

3.4.1 Maternal Colostrum and Maternal Milk 53

3.4.2 Prebiotics 53

3.4.3 Non-maternal Colostrum 54

3.4.4 Commercial Milk Replacer 55

3.5 Chapter Summary 55

References 55

4 Factors Affecting the Diversity and Density of the Microbiomes 59

4.1 Physiological Factors 60

4.1.1 Genetics 60

4.1.2 Age 60

4.1.3 Sex 62

4.1.4 Nutrition 62

4.1.5 Environment 64

4.2 Pathophysiological Factors 65

4.2.1 Stress 65

4.2.2 Pharmaceutical Therapy 65

4.2.2.1 Antimicrobials 65

4.2.2.2 Other Pharmaceuticals 67

4.3 Chapter Summary 67

References 68

5 Essential Nutrients and the Microbiota 73

5.1 Protein 74

5.1.1 Quantity 75

5.1.2 Quotient 75

5.1.3 Quality 76

5.2 Carbohydrates 77

5.2.1 Simple Carbohydrates 77

5.2.2 Complex Carbohydrates 78

5.2.2.1 Solubility 79

5.2.2.2 Fermentability 79

5.3 Fat 82

5.4 Vitamins and Minerals 82

5.4.1 Vitamins 83

5.4.1.1 Fat-Soluble Vitamins 83

5.4.1.2 Water-Soluble Vitamins 84

5.4.2 Minerals 86

5.5 Processing and Digestibility of Nutrients 87

5.6 Chapter Summary 88

References 89

6 Current Methods for Microbiome Analysis 96

6.1 Introduction 96

6.2 Why is it Important to Characterize the Microbiome? 99

6.3 Sample Collection and Preservation Methods 100

6.4 Current Methods for Microbiome Analysis 101

6.4.1 Microscopy 103

6.4.2 Cultivation 103

6.4.3 Molecular Methods 104

6.4.3.1 Quantitative PCR Panels 104

6.4.3.2 Amplicon Sequencing: 16S, 18S, and ITS 106

6.4.3.3 Metagenomic Sequencing 106

6.4.3.4 Metabolomics 107

6.5 Chapter Summary 108

References 108

7 Microbiome- Centric Management of Dysbiosis 112

7.1 Key Nutritional Factors 113

7.2 Probiotics 114

7.3 Fecal Microbiota Transplantation 115

7.4 Bacteriophages 117

7.5 Chapter Summary 118

References 118

Section II The Microbiome’s Involvement in Body Systems 127

8 The Immune System 129

8.1 Innate and Adaptive Immunity 129

8.1.1 Innate Immune System 129

8.1.1.1 Physical Barriers 130

8.1.1.2 Cellular Protection 130

8.1.1.3 Humoral Immune Response 131

8.1.2 Adaptive Immune System 131

8.1.2.1 Lymphocytes 131

8.1.2.2 Antibodies 132

8.1.3 Immune System Maturation 132

8.2 The Microbiome’s Involvement in Immunity 132

8.2.1 Germ- Free Animals 133

8.2.2 Intestinal Permeability’s Association with the Immune System 133

8.2.3 Cancer’s Association with the Immune System and GI Microbiome 134

8.2.3.1 Immunotherapy 135

8.3 Supportive Nutrients 136

8.3.1 Prebiotics 136

8.3.2 Probiotics 137

8.3.3 Postbiotics 137

8.3.3.1 Short Chain Fatty Acids 137

8.3.3.2 Colostrum (Bovine) 137

8.4 Chapter Summary 138

References 139

9 The Endocannabinoid System 141

9.1 Endocannabinoid System 141

9.2 The Endocannabinoidome Axis 142

9.3 Chapter Summary 145

References 146

10 Respiratory System Microbiome 148

10.1 The Respiratory System Microbiome 148

10.2 Factors Affecting Diversity and Density 149

10.3 Diseases Associated with Dysbiosis 152

10.3.1 Asthma 153

10.3.2 Bacterial Pneumonia 153

10.3.3 Upper Respiratory Infection 154

10.4 Key Nutritional Factors 155

10.4.1 Probiotics 155

10.4.2 Minerals, Vitamins, and Antioxidants 155

10.4.3 Omega 3 Fatty Acids 156

10.5 Chapter Summary 156

References 157

11 Oral Microbiomes 159

11.1 The Oral Microbiome 159

11.2 Factors Affecting Diversity and Density 160

11.3 Diseases Associated with Dysbiosis and Inflammation 162

11.3.1 Periodontal Disease 162

11.3.1.1 Stomatitis 164

11.3.1.2 Glossitis 164

11.3.2 Systemic Antimicrobials 164

11.4 Key Nutritional Factors 164

11.5 Chapter Summary 165

References 166

12 Aural Microbiome 167

12.1 The Aural Microbiome 167

12.2 Factors Affecting Diversity and Density 168

12.2.1 Influencing Factors 168

12.2.2 Biofilms 168

12.3 Diseases Associated with Dysbiosis 170

12.4 Key Nutritional Factors 173

12.5 Chapter Summary 173

References 174

13 Integumentary Microbiomes 175

13.1 The Cutaneous Microbiome 175

13.2 Factors Affecting Diversity and Density 176

13.2.1 Environment 176

13.2.2 Diet and the Gut Microbiome 178

13.2.3 Pharmaceuticals 178

13.3 Diseases Associated with Dysbiosis 178

13.3.1 Dysfunctional Barrier Syndrome 178

13.3.2 Atopic Dermatitis 181

13.4 Key Nutritional Factors 182

13.4.1 Protein 182

13.4.2 Essential Fatty Acids 183

13.4.3 Fiber 183

13.4.4 Vitamins 184

13.4.5 Minerals 184

13.5 Chapter Summary 184

References 185

14 Hepatic Circulation and Bile Acid Involvement with Microbiomes 189

14.1 Hepatic Circulation and Bile Acid Metabolism 189

14.1.1 Primary Bile Acids 190

14.1.1.1 Conjugation of Primary Bile Acids 190

14.1.2 The Function of the Gallbladder and Micelles 190

14.1.3 Recycling of Bile Acids 191

14.1.4 Secondary Bile Acids 192

14.2 Microbiota’s Role in Bile Acid Metabolism 192

14.2.1 Deconjugation 192

14.2.2 Dehydroxylation 193

14.2.3 Oxidation and Epimerization 193

14.2.4 Re- Conjugation 194

14.3 Bile and Bile Acids Fundamental Roles in the Regulation of Various Physiological Systems 195

14.3.1 Digestion 195

14.3.2 Metabolism 195

14.3.3 Cell Signaling 195

14.3.4 Microbiome Composition 195

14.3.5 Immune Homeostasis 195

14.3.6 Exogenous and Endogenous Substrate Disposal 196

14.3.7 Circulatory System Support 196

14.4 Nutrients in Bile 196

14.4.1 Fats (Cholesterol) 196

14.4.2 Proteins 196

14.4.3 Vitamins 197

14.4.4 Other 197

14.5 Liver–Gut–Brain Axis 197

14.6 Bile Acid Dysmetabolism 199

14.6.1 Diseases Associated with Bile Acid Dysmetabolism 201

14.6.1.1 Aging 201

14.6.1.2 Diabetes Mellitus 202

14.6.1.3 Bile Acid Diarrhea 203

14.7 Key Nutritional Factors 203

14.7.1 Water 203

14.7.2 Fat 204

14.7.3 Protein 204

14.7.4 Carbohydrates 204

14.7.5 Fiber 205

14.7.6 Probiotics 205

14.8 Chapter Summary 206

References 207

15 Gastrointestinal Microbiomes 210

15.1 The Gastrointestinal Microbiome 210

15.1.1 The Pharyngeal Microbiome 210

15.1.2 The Esophageal Microbiome 211

15.1.3 The Gastric Microbiome 212

15.1.4 The Intestinal Microbiome 213

15.2 The GI Microbiome’s Role in the Production of Vitamins 217

15.3 Conditions Affected by or Associated with the GI Microbiome 217

15.3.1 Chronic Enteropathies 219

15.3.1.1 Antibiotic- Responsive Enteropathy 219

15.3.1.2 Food- Responsive Enteropathy 220

15.3.1.3 Inflammatory Bowel Disease 220

15.3.2 Dietary Hypersensitivity and Atopy 221

15.3.3 Obesity 223

15.3.4 Diabetes Mellitus 223

15.3.5 Neoplasia 224

15.3.6 Congestive Heart Failure 225

15.3.7 Chronic Kidney Disease 225

15.4 Chapter Summary 226

References 226

16 Neurological Interactions with Microbiomes 234

16.1 The Nervous System 235

16.2 The Gut–Brain Communication Axis 237

16.2.1 Enteroendocrine and Neuroendocrine Cells 237

16.2.2 Microbial Metabolites 238

16.2.2.1 Gastrotransmitter – Gas Metabolites 239

16.2.2.2 Short- Chain Fatty Acids 240

16.2.2.3 Neurotransmitters 242

16.2.2.4 GI Microbiota- Derived Cellular Components 244

16.2.3 The Importance of Barrier Function 244

16.3 Anxiety 245

16.4 Cognitive Dysfunction 247

16.5 Psychobiotics 249

16.6 Nutrients 250

16.6.1 Simple Carbohydrates 250

16.6.2 Fat and Essential Fatty Acids 250

16.6.2.1 Medium- Chain Triglycerides (MCT) 250

16.6.2.2 Omega 3 Fatty Acids 251

16.6.3 Vitamin and Mineral “Brain Blend” 251

16.6.4 Fiber Sources – Oligosaccharides 252

16.7 Chapter Summary 252

References 254

17 Urinary System 258

17.1 GI–Renal Axis 258

17.2 Urobiome 261

17.2.1 Urinary Tract Infections 261

17.2.2 Biofilm in the Bladder 264

17.3 Defenses Against Urinary Tract Infections 265

17.3.1 Innate Immune System’s Role 265

17.3.1.1 Bacterial Interference 265

17.3.1.2 Pilicides and Curlicides 266

17.4 Key Nutritional Factors 266

17.4.1 Mannose (D- Mannose) 266

17.5 Chapter Summary 267

References 267

Section III Emerging Ingredients and Alternative Diets 269

18 Raw Ingredient Diets 273

18.1 Raw vs Cooking 274

18.1.1 Starches and Vegetables 274

18.1.2 Meat (Protein) 275

18.2 Comparing Extruded, Canned, and Raw 277

18.3 Antimicrobial Resistance 279

18.4 Fermented Products 282

18.5 Chapter Summary 283

References 284

19 Grain and Gluten- Free Diets 288

19.1 Grains 288

19.1.1 Nutrients from Grains 289

19.1.1.1 Fiber 289

19.1.1.2 Lipids 289

19.1.1.3 Phenolics 290

19.1.2 Obesity’s Relationship to Grains 290

19.1.3 Processing’s Effect on Grain Nutrient Profile 291

19.2 Gluten 291

19.3 Chapter Summary 291

References 292

20 Cannabinoids 293

20.1 Regulations on Cannabis Products 293

20.2 By- products of the Plant as an Ingredient Source 294

20.3 Concerns About the Health and Safety of Cannabis Products in Animal Feed 295

20.4 Cannabidiol Supplementation Effects on the Microbiome 295

20.5 Antimicrobial Effects of Cannabis 297

20.6 Current Diets on the World Pet Food Market 298

20.7 Chapter Summary 298

References 298

21 Insects 301

21.1 Black Soldier Fly Larvae 301

21.1.1 Adjustable Nutrient Profile 302

21.1.2 Natural Decomposers 302

21.1.3 Non- Disease Vector Species 302

21.1.4 Reduce Pathogen and Other Vermin on Decaying Matter 302

21.1.5 Production of Antimicrobial Peptides 302

21.1.6 BSFL GI Microbiome 303

21.1.7 Probiotics for BSFL 303

21.2 Heavy Metal and Mycotoxin Accumulation in Insects 304

21.3 Chitin 304

21.4 The Effects on the Host GI Microbiome 305

21.5 Chapter Summary 307

References 307

Section IV Communication and Nutrition Plans for Pet Parents 311

22 Communicating with Pet Parents 313

22.1 From the Pet Parent Perspective 313

22.2 How the Brain Processes New Information 314

22.2.1 The Protection Motivation Theory 314

22.2.1.1 Receipt of Knowledge 314

22.2.1.2 Threat Appraisal 316

22.2.1.3 Coping Appraisal 316

22.2.1.4 Behavior or Intention 317

22.3 Improving Action Results 318

22.3.1 Steps to Create a Successful Action Plan 318

22.3.1.1 Step 1 Identify the Threat 318

22.3.1.2 Step 2 Develop a Plan 318

22.4 Supporting Pet Parents Through the Decision- Making Process 319

22.4.1 Dr. Google 319

22.4.2 Provide Learning Tools 320

22.4.3 Understanding Financial Constraints 320

22.5 Improving Conversations 322

22.5.1 Lose the Judgment – Validate Pet Parents Emotions 322

22.6 Providing Continuing Support to Pet Parents 323

22.6.1 Staying in Touch 323

22.6.2 How Often to Request Contact 325

22.7 Chapter Summary 325

References 326

23 Documenting a Nutrition History 328

23.1 How to Ask the Right Questions 328

23.1.1 Closed- Ended Questions 328

23.1.2 Open- Ended Questions 329

23.1.3 Probing Questions 329

23.1.4 Using Appropriate Tone 330

23.1.5 Timing Is Everything 330

23.2 Nutrition Questionnaire 330

23.2.1 What to Include in a Nutrition History 331

23.2.1.1 A More In- Depth History Form Should Inquire about 332

23.3 Chapter Summary 333

References 334

24 Dietary Treatment Plans 335

24.1 Pet Parents Want Veterinary Nutrition Recommendations 335

24.2 Increasing the Value of Nutrition Plans 335

24.3 Components of a Nutrition Plan 336

24.3.1 Diet Recommendation 337

24.3.2 Caloric Goals 337

24.3.2.1 Main Meal(s) 337

24.3.2.2 Treat Goals 337

24.3.3 Timeline 337

24.3.3.1 Action Plan 338

24.3.3.2 Information About the Pet’s Condition or Life Stage 338

24.4 Chapter Summary 338

References 339

25 Calculations for the Nutrition Consultation 340

25.1 Energy Requirements 340

25.1.1 Resting Energy Requirements 340

25.1.2 Maintenance Energy Requirements 342

25.1.3 Calculation for Growth 342

25.1.4 Calculating for Pregnancy 342

25.1.5 Calculating for Lactation 343

25.2 Calculating kcal/cup or kcal/can from Energy Requirement 343

25.2.1 Formulations 344

25.2.1.1 Calculating Diet 1 kcal where a Set Percentage of the can/cup or Multiple cans(cups) Volumes are Predetermined 344

25.3 Calculating kcal per day by Weight (grams) 344

25.4 Calculating Calories from Nutrients and Metabolizable Energy 345

25.4.1 Calculating NFE 345

25.4.2 Calculating % of kcals from the Macronutrients 345

25.4.3 Calculating Metabolizable Energy 345

25.5 Calculating Percentage of Body Weight Loss 346

25.6 Calculating Energy Requirements for a Critical Care Patient 346

25.7 Calculating Water Requirements 347

25.8 Calculating Metabolic Water 347

25.9 Feeding and Transition Plan Formulations 347

25.9.1 Calculating Meals by kcal per Meal 347

25.9.2 Calculating Meals by Volume per Meal 347

25.10 Creating a Feeding Plan 348

25.10.1 General Guidelines for Diet Transitions 348

25.10.2 Immediate Diet Transition (For Critical Care and Initial Calorie Restricted Diet Changes) 348

25.11 Chapter Summary 348

References 350

Index 351