Small Animal Microbiomes and Nutrition 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.
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
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.
