Understanding the Microbiome

October 7, 2021 - 7 minutes read

Our Inside Precision series is a deep dive into the physiological and biochemical research being conducted by the Dog Aging Project. The aim of the Precision Cohort study is to provide an in-depth and precise (hence the name) investigation of the physiological processes that underlie health and aging in a wide range of dogs.

Read more in this series to learn about the researchers on our team who are working with biological samples.

One poorly understood factor that may have a great impact on our dogs’ well-being in general and aging processes specifically is the gut microbiome. In this post, we will explain what we mean by gut microbiome, how we study it, and what we hope to discover by analyzing it as part of the Precision Cohort study in the Dog Aging Project.

What is the gut microbiome?

The gut microbiome refers to the community of microorganisms (mainly bacteria) residing in the gastrointestinal tract, or “gut” of various animals. This microbiome is extensively studied in humans and is known to harbor hundreds of different species, collectively supporting a myriad of capabilities and functions.

In humans, the gut microbiome has been shown to be related to an ever increasing list of medical conditions, ranging from inflammatory bowel diseases, obesity, diabetes, neurological conditions, liver cirrhosis, colorectal cancer and more. A growing body of evidence also points to a tight link between the microbiome and aging, demonstrating that microbiome composition shifts with age and might affect aging processes through a variety of mechanisms.

Though studies of the dog microbiome are not as common, we do know that there are many similarities between the gut microbiomes of dogs and humans. Additionally, we know that the dog microbiome is extremely variable and may be influenced by a wide range of factors, including breed, diet, age, living environment, health condition, and likely aging as well.

We don’t yet know the exact mechanisms by which these microbes have such a substantial effect on our health and the health of our dogs, but microbiome research is considered a promising avenue for developing novel diagnostic and therapeutic approaches for a wide variety of health related conditions.

How do we study the microbiome?

A typical analysis of the gut microbiome starts with the collection of fecal samples from the subjects of interest. Traditionally, microbiologists had to then cultivate the microbiota in the lab, isolate species, and study them individually. Today, however, all genomic DNA can be extracted from a sample and sequenced using “next generation sequencing” (NGS) technologies, resulting in data about the entire community of organisms in a sample, including those never before cultured in the lab! We call this new and exciting field metagenomics, the analysis of all genetic content recovered directly from environmental samples (and in our case, canine fecal samples).

After reading all DNA content into large files, bioinformatic tools are applied to make sense of the data. Most commonly, these tools help us identify which bacterial species are present in each sample, what are their relative abundances, and what genes do they encode. Multiple analyses and tools can be used to also address additional study-specific questions.

Importantly, though metagenomics research has been around for a while, new technologies, methodologies, and tools are being constantly developed and published. Advances in these areas are constantly improving our ability to more accurately describe which microbes are there and what they are doing. Often, metagenomics by itself is not enough to elucidate complex interactions between the microbiome and the host, and so additional -omic technologies are applied.

The Precision Cohort study includes metabolomics, the study of biochemical processes that involve small molecules produced during cell metabolism called metabolites. This research will provide further insight into these complex interplays. Stay tuned for more in-depth posts about our metabolomic research in the Inside Precision series.

What do we hope to achieve by studying the microbiome of dogs in the Precision Cohort?

This one-of-a-kind cohort of companion dogs in the Dog Aging Project will allow us to investigate how aging processes and aging-related diseases are reflected in the community of gut microbes, within and across breeds. After collecting fecal samples and profiling the microbiome for a wide diversity of dogs, we will explore whether the composition of microbes in the canine gut, and their genes, are predictive of aging status, and whether they can be used as a diagnostic tool for canine health and disease.

In our research, we hope to answer the questions: Does the microbiome change with age? If so, how? Does the functional capacity of the microbiome (how the microbiome functions) change along with changes in the species composition of the microbiome (which species are present)? Lastly, how do aging-related drugs impact the microbiome composition and function?

The Dog Aging Project provides a genuinely unique opportunity to explore the unresolved and mysterious relationship between the microbiome and aging, paving the way for novel diagnostic and even therapeutic approaches. Dog poop has never seemed as exciting as it does now, right?!

Muller, Efrat

Efrat Muller
Research Team

Cover photo by cottonbro.