The OHMR contains the most extensive set of stool metagenomes from companion animals spanning several publicly available datasets and new study populations, in addition to hundreds of reference human stool metagenomes. At the OHMR’s initial launch, we analyzed thousands of pet and human metagenomes, identifying unique and shared microbial features across humans, dogs, and cats. This analysis revealed host-specific adaptations and functional differences, such as variations in metabolic and antibiotic resistance genes. The OHMR can help enhance our understanding of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.
– “Similarity of the dog and human gut microbiomes in gene content and response to diet” by Coelho et al (2018). This study catalogued the gene content from 129 dog gut metagenomes and found that the dog microbiome is more similar to the human microbiome, relative to that of pigs or mice. Further, a dietary intervention (high protein/low carbohydrate and low protein/high carbohydrate diets) demonstrated that diet significantly impacts the dog microbiome taxonomically and functionally, with effects mirroring those found in humans.
– To capture features of the microbiome during early life, we included two published developmental datasets from “Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens” by Deusch et al. (2014) and “A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development” by Deusch et al. (2015).
– We also included a dataset from an international population of shelter and stray dogs published in Yarlagadda et al.’s “Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes“, further diversifying our collection of companion animal microbiome samples beyond animals from Westernized households.
The OHMR provides nearly 2,000 newly sequenced metagenomic stool samples from cats and dogs, spanning a variety of ages, diets, housing types (facility vs. private household), and clinical diagnoses. For example, approximately 850 of these samples were collected from animals undergoing different dietary interventions, allowing us to measure metabolic processes important for pet health. Nearly 150 of the newly sequenced OHMR samples are from animals enrolled in a developmental study aimed at understanding microbiome changes from early age to adulthood. This diverse sampling of pets with varied phenotypes and interventions enables us to capture unique microbial features potentially associated with health outcomes.
There are active areas of research surrounding One Health topics aimed at improving the health of pets and humans.
– Assess the functional landscape (metagenomics, metatranscriptomics, metabolomics) of the companion animal microbiome. Even in the human microbiome, the function of several genes and the chemical activity of microbial metabolic byproducts remain unknown. This is even more true for less characterized microbial communities such as the companion animal microbiome. Several of these uncharacterized functional features, the microbial “dark matter”, are likely associated with pet health.
– The food provided by an owner is typically the only source of nutrition for cats and dogs. Relative to humans, the nutrient composition consumed by pets is consistent, which means the energy substrates provided to the gut microbiome are consistent. Changes to diet elicit changes to the microbiome, making companion animals good candidates for understanding how diet can impact microbial metabolism. Moreover, diet is often the first line of therapy chosen by veterinarians to treat several clinical diagnoses. More work is needed to understand how the microbiome interacts with diet and how changes to microbial chemistry impact the health of our pets.
– In humans, the microbiome in early life is important for things like allergy development. Less is know about which microbial features of the microbiome during the early life of pets might predict the development of disease. More generally, biomarkers (in this context, features of the microbiome such as microbes or their byproducts) of disease are important to understand in pets, as they cannot communicate their symptoms. Population-scale microbiome studies in companion animals will help us identify biomarkers of disease.
– The One Health concept is largely concerned with antimicrobial resistance in humans and animals. The gut microbiome in animals can be a reservoir for AMR and the extent of transmission between owners and their pets is unknown. On the other hand, microbial transmission (pet<->pet and human<->pet) of beneficial microbes and its impact on pet and owner health is also unknown. Through longitudinal studies that employ phylogenetic analyses, we can better understand which microbes, and their genes, are transmitted and how they adapt in different host environments.
– Animals are good candidates to explore the use of therapeutic aids (such as prebiotics and fecal microbiome transplantation) to help restore the microbiome after antibiotics as things like diet are easier to control in animals relative to humans.
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