Small Animal Microbiomes and NutritionComprehensive resource providing holistic coverage of the effect of body microbiomes on the health status of dogs and catsSmall 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 factorsSmall 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 xviiAbout the Companion Website xixSection I Understanding a Microbiome 11 Common Definitions 31.1 Microbiome 31.2 Microbiota 41.3 Pathogens 51.4 Symbiosis 81.5 Dysbiosis 111.6 Probiotics 121.7 Prebiotics 151.8 Synbiotics 161.9 Biological Markers (Biomarkers) and Their Measurement 161.9.1 Genes, the Genome, and Genomics 171.9.2 Metabolites, the Metabolome, and Metabolomics 191.9.2.1 Metabonomics 221.9.3 The Proteome and Proteomics 23Glossary 23References 252 Functions of the Gastrointestinal Microbiome 322.1 What Is the Gastrointestinal Microbiome? 322.2 Metabolic Functions 322.2.1 Short-Chain Fatty Acids 332.2.2 Gases 352.2.3 Amino Acids 352.2.4 Vitamins and Minerals 362.3 Structural Functions 372.3.1 Tight Junctions and Intestinal Permeability 372.4 Protective Functions 382.4.1 Bacteriocins 382.4.2 Quorum-Sensing 392.4.3 Immune Response 392.5 Participation in Bidirectional Axis Communication 392.6 Chapter Summary 39References 403 The Origin and Development of the Gastrointestinal Microbiome 443.1 In Utero 443.2 Factors Influencing the Initial Colonization of Microbiota 453.2.1 Presentation at Birth 463.2.2 Environmental Exposure 473.2.3 Diet Type and Method of Feeding 473.2.4 Age 483.3 Dysbiosis During Microbiome Development 493.4 Key Nutritional Factors 533.4.1 Maternal Colostrum and Maternal Milk 533.4.2 Prebiotics 533.4.3 Non-maternal Colostrum 543.4.4 Commercial Milk Replacer 553.5 Chapter Summary 55References 554 Factors Affecting the Diversity and Density of the Microbiomes 594.1 Physiological Factors 604.1.1 Genetics 604.1.2 Age 604.1.3 Sex 624.1.4 Nutrition 624.1.5 Environment 644.2 Pathophysiological Factors 654.2.1 Stress 654.2.2 Pharmaceutical Therapy 654.2.2.1 Antimicrobials 654.2.2.2 Other Pharmaceuticals 674.3 Chapter Summary 67References 685 Essential Nutrients and the Microbiota 735.1 Protein 745.1.1 Quantity 755.1.2 Quotient 755.1.3 Quality 765.2 Carbohydrates 775.2.1 Simple Carbohydrates 775.2.2 Complex Carbohydrates 785.2.2.1 Solubility 795.2.2.2 Fermentability 795.3 Fat 825.4 Vitamins and Minerals 825.4.1 Vitamins 835.4.1.1 Fat-Soluble Vitamins 835.4.1.2 Water-Soluble Vitamins 845.4.2 Minerals 865.5 Processing and Digestibility of Nutrients 875.6 Chapter Summary 88References 896 Current Methods for Microbiome Analysis 966.1 Introduction 966.2 Why is it Important to Characterize the Microbiome? 996.3 Sample Collection and Preservation Methods 1006.4 Current Methods for Microbiome Analysis 1016.4.1 Microscopy 1036.4.2 Cultivation 1036.4.3 Molecular Methods 1046.4.3.1 Quantitative PCR Panels 1046.4.3.2 Amplicon Sequencing: 16S, 18S, and ITS 1066.4.3.3 Metagenomic Sequencing 1066.4.3.4 Metabolomics 1076.5 Chapter Summary 108References 1087 Microbiome- Centric Management of Dysbiosis 1127.1 Key Nutritional Factors 1137.2 Probiotics 1147.3 Fecal Microbiota Transplantation 1157.4 Bacteriophages 1177.5 Chapter Summary 118References 118Section II The Microbiome's Involvement in Body Systems 1278 The Immune System 1298.1 Innate and Adaptive Immunity 1298.1.1 Innate Immune System 1298.1.1.1 Physical Barriers 1308.1.1.2 Cellular Protection 1308.1.1.3 Humoral Immune Response 1318.1.2 Adaptive Immune System 1318.1.2.1 Lymphocytes 1318.1.2.2 Antibodies 1328.1.3 Immune System Maturation 1328.2 The Microbiome's Involvement in Immunity 1328.2.1 Germ- Free Animals 1338.2.2 Intestinal Permeability's Association with the Immune System 1338.2.3 Cancer's Association with the Immune System and GI Microbiome 1348.2.3.1 Immunotherapy 1358.3 Supportive Nutrients 1368.3.1 Prebiotics 1368.3.2 Probiotics 1378.3.3 Postbiotics 1378.3.3.1 Short Chain Fatty Acids 1378.3.3.2 Colostrum (Bovine) 1378.4 Chapter Summary 138References 1399 The Endocannabinoid System 1419.1 Endocannabinoid System 1419.2 The Endocannabinoidome Axis 1429.3 Chapter Summary 145References 14610 Respiratory System Microbiome 14810.1 The Respiratory System Microbiome 14810.2 Factors Affecting Diversity and Density 14910.3 Diseases Associated with Dysbiosis 15210.3.1 Asthma 15310.3.2 Bacterial Pneumonia 15310.3.3 Upper Respiratory Infection 15410.4 Key Nutritional Factors 15510.4.1 Probiotics 15510.4.2 Minerals, Vitamins, and Antioxidants 15510.4.3 Omega 3 Fatty Acids 15610.5 Chapter Summary 156References 15711 Oral Microbiomes 15911.1 The Oral Microbiome 15911.2 Factors Affecting Diversity and Density 16011.3 Diseases Associated with Dysbiosis and Inflammation 16211.3.1 Periodontal Disease 16211.3.1.1 Stomatitis 16411.3.1.2 Glossitis 16411.3.2 Systemic Antimicrobials 16411.4 Key Nutritional Factors 16411.5 Chapter Summary 165References 16612 Aural Microbiome 16712.1 The Aural Microbiome 16712.2 Factors Affecting Diversity and Density 16812.2.1 Influencing Factors 16812.2.2 Biofilms 16812.3 Diseases Associated with Dysbiosis 17012.4 Key Nutritional Factors 17312.5 Chapter Summary 173References 17413 Integumentary Microbiomes 17513.1 The Cutaneous Microbiome 17513.2 Factors Affecting Diversity and Density 17613.2.1 Environment 17613.2.2 Diet and the Gut Microbiome 17813.2.3 Pharmaceuticals 17813.3 Diseases Associated with Dysbiosis 17813.3.1 Dysfunctional Barrier Syndrome 17813.3.2 Atopic Dermatitis 18113.4 Key Nutritional Factors 18213.4.1 Protein 18213.4.2 Essential Fatty Acids 18313.4.3 Fiber 18313.4.4 Vitamins 18413.4.5 Minerals 18413.5 Chapter Summary 184References 18514 Hepatic Circulation and Bile Acid Involvement with Microbiomes 18914.1 Hepatic Circulation and Bile Acid Metabolism 18914.1.1 Primary Bile Acids 19014.1.1.1 Conjugation of Primary Bile Acids 19014.1.2 The Function of the Gallbladder and Micelles 19014.1.3 Recycling of Bile Acids 19114.1.4 Secondary Bile Acids 19214.2 Microbiota's Role in Bile Acid Metabolism 19214.2.1 Deconjugation 19214.2.2 Dehydroxylation 19314.2.3 Oxidation and Epimerization 19314.2.4 Re- Conjugation 19414.3 Bile and Bile Acids Fundamental Roles in the Regulation of Various Physiological Systems 19514.3.1 Digestion 19514.3.2 Metabolism 19514.3.3 Cell Signaling 19514.3.4 Microbiome Composition 19514.3.5 Immune Homeostasis 19514.3.6 Exogenous and Endogenous Substrate Disposal 19614.3.7 Circulatory System Support 19614.4 Nutrients in Bile 19614.4.1 Fats (Cholesterol) 19614.4.2 Proteins 19614.4.3 Vitamins 19714.4.4 Other 19714.5 Liver-Gut-Brain Axis 19714.6 Bile Acid Dysmetabolism 19914.6.1 Diseases Associated with Bile Acid Dysmetabolism 20114.6.1.1 Aging 20114.6.1.2 Diabetes Mellitus 20214.6.1.3 Bile Acid Diarrhea 20314.7 Key Nutritional Factors 20314.7.1 Water 20314.7.2 Fat 20414.7.3 Protein 20414.7.4 Carbohydrates 20414.7.5 Fiber 20514.7.6 Probiotics 20514.8 Chapter Summary 206References 20715 Gastrointestinal Microbiomes 21015.1 The Gastrointestinal Microbiome 21015.1.1 The Pharyngeal Microbiome 21015.1.2 The Esophageal Microbiome 21115.1.3 The Gastric Microbiome 21215.1.4 The Intestinal Microbiome 21315.2 The GI Microbiome's Role in the Production of Vitamins 21715.3 Conditions Affected by or Associated with the GI Microbiome 21715.3.1 Chronic Enteropathies 21915.3.1.1 Antibiotic- Responsive Enteropathy 21915.3.1.2 Food- Responsive Enteropathy 22015.3.1.3 Inflammatory Bowel Disease 22015.3.2 Dietary Hypersensitivity and Atopy 22115.3.3 Obesity 22315.3.4 Diabetes Mellitus 22315.3.5 Neoplasia 22415.3.6 Congestive Heart Failure 22515.3.7 Chronic Kidney Disease 22515.4 Chapter Summary 226References 22616 Neurological Interactions with Microbiomes 23416.1 The Nervous System 23516.2 The Gut-Brain Communication Axis 23716.2.1 Enteroendocrine and Neuroendocrine Cells 23716.2.2 Microbial Metabolites 23816.2.2.1 Gastrotransmitter - Gas Metabolites 23916.2.2.2 Short- Chain Fatty Acids 24016.2.2.3 Neurotransmitters 24216.2.2.4 GI Microbiota- Derived Cellular Components 24416.2.3 The Importance of Barrier Function 24416.3 Anxiety 24516.4 Cognitive Dysfunction 24716.5 Psychobiotics 24916.6 Nutrients 25016.6.1 Simple Carbohydrates 25016.6.2 Fat and Essential Fatty Acids 25016.6.2.1 Medium- Chain Triglycerides (MCT) 25016.6.2.2 Omega 3 Fatty Acids 25116.6.3 Vitamin and Mineral "Brain Blend" 25116.6.4 Fiber Sources - Oligosaccharides 25216.7 Chapter Summary 252References 25417 Urinary System 25817.1 GI-Renal Axis 25817.2 Urobiome 26117.2.1 Urinary Tract Infections 26117.2.2 Biofilm in the Bladder 26417.3 Defenses Against Urinary Tract Infections 26517.3.1 Innate Immune System's Role 26517.3.1.1 Bacterial Interference 26517.3.1.2 Pilicides and Curlicides 26617.4 Key Nutritional Factors 26617.4.1 Mannose (D- Mannose) 26617.5 Chapter Summary 267References 267Section III Emerging Ingredients and Alternative Diets 26918 Raw Ingredient Diets 27318.1 Raw vs Cooking 27418.1.1 Starches and Vegetables 27418.1.2 Meat (Protein) 27518.2 Comparing Extruded, Canned, and Raw 27718.3 Antimicrobial Resistance 27918.4 Fermented Products 28218.5 Chapter Summary 283References 28419 Grain and Gluten- Free Diets 28819.1 Grains 28819.1.1 Nutrients from Grains 28919.1.1.1 Fiber 28919.1.1.2 Lipids 28919.1.1.3 Phenolics 29019.1.2 Obesity's Relationship to Grains 29019.1.3 Processing's Effect on Grain Nutrient Profile 29119.2 Gluten 29119.3 Chapter Summary 291References 29220 Cannabinoids 29320.1 Regulations on Cannabis Products 29320.2 By- products of the Plant as an Ingredient Source 29420.3 Concerns About the Health and Safety of Cannabis Products in Animal Feed 29520.4 Cannabidiol Supplementation Effects on the Microbiome 29520.5 Antimicrobial Effects of Cannabis 29720.6 Current Diets on the World Pet Food Market 29820.7 Chapter Summary 298References 29821 Insects 30121.1 Black Soldier Fly Larvae 30121.1.1 Adjustable Nutrient Profile 30221.1.2 Natural Decomposers 30221.1.3 Non- Disease Vector Species 30221.1.4 Reduce Pathogen and Other Vermin on Decaying Matter 30221.1.5 Production of Antimicrobial Peptides 30221.1.6 BSFL GI Microbiome 30321.1.7 Probiotics for BSFL 30321.2 Heavy Metal and Mycotoxin Accumulation in Insects 30421.3 Chitin 30421.4 The Effects on the Host GI Microbiome 30521.5 Chapter Summary 307References 307Section IV Communication and Nutrition Plans for Pet Parents 31122 Communicating with Pet Parents 31322.1 From the Pet Parent Perspective 31322.2 How the Brain Processes New Information 31422.2.1 The Protection Motivation Theory 31422.2.1.1 Receipt of Knowledge 31422.2.1.2 Threat Appraisal 31622.2.1.3 Coping Appraisal 31622.2.1.4 Behavior or Intention 31722.3 Improving Action Results 31822.3.1 Steps to Create a Successful Action Plan 31822.3.1.1 Step 1 Identify the Threat 31822.3.1.2 Step 2 Develop a Plan 31822.4 Supporting Pet Parents Through the Decision- Making Process 31922.4.1 Dr. Google 31922.4.2 Provide Learning Tools 32022.4.3 Understanding Financial Constraints 32022.5 Improving Conversations 32222.5.1 Lose the Judgment - Validate Pet Parents Emotions 32222.6 Providing Continuing Support to Pet Parents 32322.6.1 Staying in Touch 32322.6.2 How Often to Request Contact 32522.7 Chapter Summary 325References 32623 Documenting a Nutrition History 32823.1 How to Ask the Right Questions 32823.1.1 Closed- Ended Questions 32823.1.2 Open- Ended Questions 32923.1.3 Probing Questions 32923.1.4 Using Appropriate Tone 33023.1.5 Timing Is Everything 33023.2 Nutrition Questionnaire 33023.2.1 What to Include in a Nutrition History 33123.2.1.1 A More In- Depth History Form Should Inquire about 33223.3 Chapter Summary 333References 33424 Dietary Treatment Plans 33524.1 Pet Parents Want Veterinary Nutrition Recommendations 33524.2 Increasing the Value of Nutrition Plans 33524.3 Components of a Nutrition Plan 33624.3.1 Diet Recommendation 33724.3.2 Caloric Goals 33724.3.2.1 Main Meal(s) 33724.3.2.2 Treat Goals 33724.3.3 Timeline 33724.3.3.1 Action Plan 33824.3.3.2 Information About the Pet's Condition or Life Stage 33824.4 Chapter Summary 338References 33925 Calculations for the Nutrition Consultation 34025.1 Energy Requirements 34025.1.1 Resting Energy Requirements 34025.1.2 Maintenance Energy Requirements 34225.1.3 Calculation for Growth 34225.1.4 Calculating for Pregnancy 34225.1.5 Calculating for Lactation 34325.2 Calculating kcal/cup or kcal/can from Energy Requirement 34325.2.1 Formulations 34425.2.1.1 Calculating Diet 1 kcal where a Set Percentage of the can/cup or Multiple cans(cups) Volumes are Predetermined 34425.3 Calculating kcal per day by Weight (grams) 34425.4 Calculating Calories from Nutrients and Metabolizable Energy 34525.4.1 Calculating NFE 34525.4.2 Calculating % of kcals from the Macronutrients 34525.4.3 Calculating Metabolizable Energy 34525.5 Calculating Percentage of Body Weight Loss 34625.6 Calculating Energy Requirements for a Critical Care Patient 34625.7 Calculating Water Requirements 34725.8 Calculating Metabolic Water 34725.9 Feeding and Transition Plan Formulations 34725.9.1 Calculating Meals by kcal per Meal 34725.9.2 Calculating Meals by Volume per Meal 34725.10 Creating a Feeding Plan 34825.10.1 General Guidelines for Diet Transitions 34825.10.2 Immediate Diet Transition (For Critical Care and Initial Calorie Restricted Diet Changes) 34825.11 Chapter Summary 348References 350Index 351