Summary of Gut Microbiome Research in Dogs and Wolves

Impact of Diet and Domestication on Canis Microbiome

Table of Contents

Background

Study 1: Differences in the Gut Microbiomes of Dogs and Wolves: Roles of Antibiotics and Starch

• Objectives and Methods
• Key Findings
  • Bacterial Composition and Diversity
  • Antibiotic Resistance
  • Starch Metabolism
• Conclusions

Study 2: Gut Microbiome of Captive Wolves is More Similar to Domestic Dogs than Wild Wolves Indicated by Metagenomics Study

• Objectives and Methods
• Key Findings
  • Bacterial Composition
  • Functional Diversity
• Conclusions

Study 3: The Fecal Microbiota of Dogs Switching to a Raw Diet Only Partially Converges to That of Wolves

• Objectives and Methods
• Key Findings
  • Microbial Shifts
  • Genus-Level Changes
  • Functional Predictions
• Conclusions

Study 4: The Gut Microbiome Buffers Dietary Adaptation in Bronze Age Domesticated Dogs

• Objectives and Methods
• Key Findings
  • Microbiome Structure
  • Starch Metabolism
  • Functional Adaptations
• Conclusions

Comprehensive Analysis and Conclusions

• Impact of Domestication and Diet
• Health Implications
• Conclusions

Background

The domestication of dogs from wolves has led to significant changes in their diet, living environment, and gut microbiota. This summary integrates findings from four research studies to provide a comprehensive understanding of how domestication, dietary changes, and captivity impact the gut microbiomes of dogs and wolves.

Study 1: Differences in the Gut Microbiomes of Dogs and Wolves: Roles of Antibiotics and Starch

Objectives and Methods: This study aimed to assess the gut bacterial diversity and function in domestic dogs compared with captive wolves. The researchers surveyed the gut bacterial diversity of 27 domestic dogs (fed commercial dog food) and 31 wolves (fed uncooked meat) using 16S rRNA sequencing. Additionally, faecal samples from 5 dogs and 5 wolves were collected for shotgun metagenomic sequencing to explore functional changes in their gut microbiome.

Key Findings:

1. Bacterial Composition and Diversity:
   • The gut microbiome of dogs exhibited higher microbial diversity compared to wolves.
   • Dogs’ gut microbiomes were dominated by the genera Lactobacillus and Allobaculum.
   • Wolves’ gut microbiomes were dominated by Clostridium sensu stricto 1.
   • The overall community structures of the microbiota in dogs and wolves were distinct.
2. Antibiotic Resistance:
   • Dogs’ gut microbiomes were enriched with bacteria resistant to clinical antibiotics, likely due to exposure from veterinary care.
   • Wolves’ gut microbiomes contained more bacteria resistant to antibiotics used in livestock, reflecting their diet of uncooked meat.
3. Starch Metabolism:
   • The gut microbiome of dogs had a higher abundance of glycosyl hydrolases related to starch digestion, indicating adaptation to a starch-rich diet.

Conclusions: The living environment and diet of dogs and captive wolves have led to increased numbers of bacteria with antibiotic resistance genes. Dogs’ gut microbiota have adapted to a starch-rich diet, aligning with their domestic lifestyle, which has implications for public health.

Study 2: Gut Microbiome of Captive Wolves is More Similar to Domestic Dogs than Wild Wolves Indicated by Metagenomics Study

Objectives and Methods: This study aimed to compare the species diversity and functional diversity of gut microbes in wild wolves, captive wolves, and domestic dogs. Shotgun sequencing was performed on samples from 3 wild wolves, 4 captive wolves, and 4 domestic dogs.

Key Findings:

1. Bacterial Composition:
   • Most abundant phyla in the gut of wolves and dogs were Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, and Actinobacteria.
   • Dominant genera included Bacteroides, Fusobacterium, Prevotella, Megamonas, Paraprevotella, Faecalibacterium, and Clostridium.
   • Wild wolves had a higher abundance of Bacteroides, while captive wolves and domestic dogs had higher abundances of Fusobacterium and Faecalibacterium, respectively.
2. Functional Diversity:
   • The gut microbiomes of domestic dogs and captive wolves were significantly enriched in carbohydrate metabolism pathways compared to wild wolves.
   • Enzyme analysis revealed 177 enzymes significantly more abundant in domestic dogs than in wild wolves, highlighting adaptation to carbohydrate-rich diets.
   • Captive wolves’ gut microbiomes were more similar to domestic dogs than to wild wolves, indicating the strong influence of captivity.

Conclusions: Captive wolves’ gut microbiomes have adapted to resemble those of domestic dogs more closely than wild wolves, primarily due to dietary and environmental factors. The study underscores the impact of captivity on gut microbiota composition and function.

Study 3: The Fecal Microbiota of Dogs Switching to a Raw Diet Only Partially Converges to That of Wolves

Objectives and Methods: This study investigated the dynamics of gut microbiota in dogs switching from a starch-rich, processed kibble diet to a raw meat diet, using wolves as a reference. Six American Staffordshire Terriers were switched from a kibble diet to a raw meat diet identical to that of the wolves, with samples collected at various intervals over 28 days.

Key Findings:

1. Microbial Shifts:
   • Switching to a raw meat diet initially increased the relative abundance of Fusobacteria and Bacteroidetes while decreasing Firmicutes.
   • By day 28, these differences were no longer significant, indicating transient changes.
2. Genus-Level Changes:
   • Faecalibacterium, Catenibacterium, Allisonella, and Megamonas decreased in dogs on the raw diet, aligning more closely with wolves’ gut microbiota.
   • Some microbial groups remained distinct between dogs and wolves, indicating persistent differences due to domestication.
3. Functional Predictions:
   • Carbohydrate metabolism was higher in wolves and dogs on the raw diet compared to dogs on kibble, reflecting dietary impacts.
   • The gut microbiota of dogs showed dynamic changes but retained distinct characteristics from wolves.

Conclusions: Dietary changes in dogs result in significant but often transient shifts in gut microbiota. While raw diets bring some microbial groups closer to those of wolves, distinct differences persist, suggesting deep-rooted effects of domestication on gut microbiota.

Study 4: The Gut Microbiome Buffers Dietary Adaptation in Bronze Age Domesticated Dogs

Objectives and Methods: The study explored the role of the gut microbiome during recent canine evolutionary history by sequencing the metagenome of 13 canine coprolites from a Bronze Age site in Solarolo, Italy.

Key Findings:

1. Microbiome Structure:
   • The microbiome of Bronze Age dogs shared features with both modern dogs and wild wolves, indicating a transitional state.
   • The microbiome composition suggested an omnivorous diet with evidence of starchy agricultural foods.
2. Starch Metabolism:
   • Solarolo dogs’ microbiomes were enriched in sequences encoding alpha-amylases, compensating for a low copy number of the host amylase gene.
   • This suggests that early domesticated dogs adapted to a starch-rich diet through microbial functionalities devoted to starch catabolism.
3. Functional Adaptations:
   • The Solarolo dogs’ microbiomes were enriched in genes involved in short-chain fatty acid (SCFA) production, supporting energy extraction from plant-based diets.
   • The microbiome showed adaptations to dietary shifts, complementing the delayed genomic response in host amylase gene expansion.

Conclusions: The gut microbiome of Bronze Age dogs played a crucial role in adapting to starch-rich diets, compensating for delayed genetic adaptations. This highlights the importance of the gut microbiome in the evolutionary history and dietary transitions of domesticated dogs.

Combined Analysis and Conclusions

Impact of Domestication and Diet:

• Domestication has led to increased microbial diversity and adaptation to starch-rich diets in dogs, supported by higher abundances of glycosyl hydrolases.
• Captivity and diet significantly influence gut microbiota. Captive wolves’ gut microbiomes are more similar to domestic dogs than to wild wolves, showing the profound impact of environment and diet over genetic factors.
• Antibiotic resistance genes are more prevalent in dogs due to exposure from veterinary care, while wolves’ resistance genes reflect their diet.
• The gut microbiome has played a crucial role in adapting to dietary changes throughout domestication, especially during the transition to agricultural diets.

Health Implications:

• The presence of antibiotic resistance genes in domestic dogs poses public health risks, emphasizing the need for careful management of antibiotic use in pets.
• Understanding gut microbiota adaptations provides insights into the health and nutritional needs of domestic and wild animals.

Conclusions: The research highlights the intricate interplay between genetics, diet, and environment in shaping the gut microbiota of dogs and wolves. Domestication and dietary habits have led to distinct microbial communities, with significant implications for animal health and public health. The findings underscore the importance of considering both genetic and environmental factors in managing the health and well-being of domestic animals. The gut microbiome has been a critical adaptive partner, enabling rapid responses to dietary changes and complementing the genomic adaptations in domesticated dogs, especially during the Neolithic transition to agricultural diets. This underscores the vital role of the gut microbiome in the evolutionary history and domestication of dogs.