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