Small Animal Microbiomes and Nutrition

Robin Saar, Sarah Dodd

ISBN: 9781119862604 

August 2023 

Wiley-Blackwell 

384 Pages

DESCRIPTION

Comprehensive resource providing holistic coverage of the effect of body microbiomes on the health status of dogs and cats

Small Animal Microbiomes and Nutrition offers new perspective on the prevention and treatment of common health conditions in dogs and cats that arise from or result in dysbiosis of the body’s microbiomes, along with providing alternative first-line solutions of utilizing nutrients—less invasive procedures in comparison to prescription drugs to treat dysbiosis in the body’s microbiomes. This practical manual guides the reader through body systems that are commonly influenced by the microbiota in the microbiomes as well as accompanying dietary recommendations.

Initially, an overview of the body’s microbiome including common terminology and functions of microbiomes precede the chapters on development of the body’s microbiomes and factors influencing their diversity and density. The following three sections provide readers with a different perspective of commonly observed health conditions by focusing on the state of the microbiome and how the condition may be prevented and/or treated with the use of nutrients.

Written by a highly qualified author with significant experience in the field, Small Animal Microbiomes and Nutrition includes information on sample topics such as:

• Results of research on alternative diets and emerging ingredients’ effect on the microbiomes and how to have the discussions with pet parents

• Nutrition focused calculations, feeding directions, and templates for history, and recommendation for follow-up conversations with pet parents

• Factors affecting the diversity and density of the microbiomes, such as genetics, age, sex, environment, stress, antibiotic therapy, and nutrition

• Integumentary microbiomes, covering the skin's microbiome, dysfunctional barrier syndrome, atopy (atopic dermatitis), and key nutritional factors

Small Animal Microbiomes and Nutrition is an essential resource for students completing companion animal health courses in two- and four-year programs, particularly those in veterinary technology, veterinary technician, and animal health technology diplomas and degrees, and it is also highly useful for students in other veterinary and animal science focused programs. Additionally, this book is essential in veterinary practices as a reference guide to support the transition into the utilization of microbiome medicine.

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

ABOUT THE AUTHOR

Robin Saar, RVT, VTS (NUTRITION), Canada. Robin became a Registered Animal Health Technologist in 1996 and obtained her Veterinary Technician Specialty in Nutrition in 2019. Robin’s professional experience includes working in small and mixed animal practices as an RVT, and a Practice Manager, and she developed a nutrition program for a veterinary corporation. Robin has written multiple peer reviewed articles and chapters about nutrition and this is her first dedicated textbook. Her current role with AnimalBiome in the veterinary department, meets her interest in nutrition and microbiome health. Currently, Robin is the Education Director for the Canadian Academy of Veterinary Nutrition, is the President-Elect for the Academy of Veterinary Nutrition Technicians, and is a Member at Large at the American Academy of Veterinary Nutrition. She is currently completing her MSc in Animal Nutrition through Glasgow University. Her principle is “Nutrition is a part of every pet, every day.”

Dr. Sarah Dodd, BVSc, MSc, PhD, DECVCN, EBVS® European Specialist in Veterinary and Comparative Nutrition, member of European College of Veterinary and Comparative Nutrition. Dr. Dodd received her veterinary degree from Massey University, New Zealand, in 2016. This was followed by an MSc and a PhD in Clinical Studies and Population Medicine at the University of Guelph in 2018 and 2022, respectively. Whilst completing the academic degrees, Dr. Dodd simultaneously undertook first an internship then a residency with the European College of Veterinary and Comparative Nutrition and became board certified in 2022. She has authored a number of peer-reviewed publications (articles, abstracts, and textbook chapters), co-authored a textbook on Small Animal Microbiomes and Nutrition and reviews manuscripts for a number of journals. Dr. Dodd is a founding member and active fellow of the Canadian Academy of Veterinary Nutrition.