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The Microbiome

Independent Research: Is There a Core Microbiome in Healthy Dogs?

A 2024 study analysed faecal samples from 286 healthy or presumed-healthy pet dogs using full-length 16S sequencing. Researchers identified 23 bacterial species that together made up around three-quarters of the microbiome on average, while also showing that diet, body weight, age, sex and geography all contributed to variation between individual dogs.

Peer reviewed Open access
Independent Research: Is There a Core Microbiome in Healthy Dogs?
Year
2024
Study type
Peer-reviewed cross-sectional microbiome study
Sample
286 healthy or presumed-healthy companion dogs
Measured
Species-level faecal microbiome composition, diversity and associations with diet, age, body weight, sex, neuter status and geography
01

The research question

Dogs can have very different microbiomes.

Diet, age, size, environment and many other factors can influence which microorganisms are detected in an individual animal.

That creates an important question:

Is there nevertheless a group of bacterial species that commonly occurs in healthy dogs?

Rojas and colleagues investigated this using faecal samples from hundreds of companion dogs living in North America.

Unlike many earlier studies that identified bacteria mainly at genus level, the researchers used full-length 16S sequencing to achieve greater species-level resolution.

They also asked:

How much of the variation between healthy dogs can be explained by factors such as diet, body weight, age and geography?

02

What did the researchers do?

Faecal samples were originally collected from more than 3,700 companion dogs.

The researchers applied strict selection criteria to create a healthy reference population.

A total of 286 dogs were included in the main analysis.

Of these:

56 dogs were clinically verified as healthy

and

230 were presumed healthy based on owner information and screening criteria

Dogs were excluded if they had reported clinical signs, relevant physical conditions, recent antibiotic use, current medications or bacterial probiotic supplementation.

The dogs lived in homes across North America.

Their median age was four years and body weights ranged from 1.8 kg to 67.1 kg.

Faecal microbial DNA was analysed using full-length 16S ribosomal RNA sequencing.

The researchers then examined:

which bacterial species occurred consistently across healthy dogs

and

whether microbiome composition was associated with diet, body weight, age, sex, neuter status or geography

03

What did they measure?

The researchers examined several aspects of the microbiome.

Core bacterial species

They identified species appearing consistently across the healthy reference population.

Relative abundance

Researchers measured how much of the microbial community was represented by each species.

Alpha diversity

This assessed the richness and diversity present within individual dogs.

Beta diversity

This assessed how different one dog's microbial community was from another dog's.

Host and environmental factors

Microbiome variation was compared with:

age

body weight

sex and neuter status

diet

and geographic region

Individual bacterial species

The researchers also examined which species were more strongly associated with particular diets, body sizes or ages.

04

What was observed?

The study produced several useful findings.

Twenty-three species formed a core microbiome

Researchers identified 23 bacterial species that appeared consistently across the healthy reference population.

Together, those species represented approximately 75% of the faecal microbiome on average.

Examples included:

Peptacetobacter hiranonis

Megamonas funiformis

Prevotella copri

Turicibacter sanguinis

Collinsella intestinalis

and Blautia hansenii

Healthy dogs still differed substantially from one another

Although a common core could be identified, there was considerable variation between individuals.

No single host factor explained most of the microbiome.

Diet was the strongest measured predictor

Of the factors examined, diet explained the largest proportion of variation in overall microbiome composition.

Even then, it accounted for only around 5% of the observed variation.

Geographic region accounted for approximately 2.2%, body weight 1.8%, sex and neuter status 1.1%, and age 1.1%.

Body size mattered

Dogs of intermediate body weight had the highest microbiome diversity in some analyses.

Sixteen bacterial species were significantly more abundant as dog body weight increased.

Age was associated with specific bacterial changes

Several species, including Prevotella copri and Bacteroides coprocola, declined with age.

Escherichia coli showed the opposite relationship.

Diet changed which species were relatively abundant

Raw-fed dogs and kibble-fed dogs showed different species profiles.

For example, raw-fed dogs had greater relative abundance of several species including Bacteroides vulgatus and Enterococcus faecium.

Kibble-fed dogs had greater relative abundance of species including Collinsella intestinalis, Megamonas funiformis and Prevotella copri.

Importantly, these differences do not establish that one dietary pattern produced a healthier microbiome than another.

05

What does this study tell us?

This study shows that there may be a recognisable core canine microbiome, but there is no single microbial profile that every healthy dog must match.

That is an important distinction.

Healthy dogs shared a substantial group of bacterial species, yet individual microbiomes still varied according to multiple influences.

A useful way to think about this is:

Core microbiome + Diet + Age + Body size + Environment + Individual biology = Individual microbial profile

The relatively small effect size of each individual factor is particularly important.

Even diet, the strongest factor examined, explained only a small proportion of total microbiome variation.

This suggests that interpreting a canine microbiome from one bacterial measurement alone can be misleading.

It also supports the idea that microbial composition should be considered alongside:

metabolites

digestive function

diet

host characteristics

and

observable outcomes

rather than treating the presence or absence of an individual bacterial species as a complete measure of gut health.

06

What doesn't this study tell us?

Several limitations are important.

Cross-sectional study

Each dog was essentially sampled at one point in time.

The study therefore cannot show how stable the identified core microbiome is within the same dog over months or years.

Most dogs were presumed healthy rather than clinically verified

Only 56 of the 286 dogs underwent the more stringent health verification used for the stool-donor population.

The remainder were classified using owner-reported information and study exclusion criteria.

North American population

All dogs lived in North America.

Microbiomes in dogs living in other regions, diets and environments may differ.

Uneven body-size distribution

Most dogs were medium or large.

Very small and very large dogs were represented by smaller numbers.

Diet categories were broad

Labels such as kibble, raw and cooked food encompass many different formulations and nutrient profiles.

The study cannot identify which specific dietary components produced the observed differences.

16S sequencing measures composition rather than complete function

Full-length 16S provides improved species-level resolution, but it does not directly measure microbial metabolites or every functional gene.

Commercial involvement

All authors were employees of AnimalBiome.

The company funded the study and was involved in study design, data collection, analysis, interpretation and manuscript preparation.

That does not invalidate the findings, but it is relevant context when evaluating the evidence.

Original research

Study details

Study
Species-level characterization of the core microbiome in healthy dogs using full-length 16S rRNA gene sequencing
Authors
Connie A. Rojas
Brian Park
Elisa Scarsella
Guillaume Jospin
Zhandra Entrolezo
Jessica K. Jarett
Alex Martin
Holly H. Ganz
Institutions
AnimalBiome, Oakland, California, USA
Reference
Rojas CA, Park B, Scarsella E, Jospin G, Entrolezo Z, Jarett JK, Martin A, Ganz HH. Species-level characterization of the core microbiome in healthy dogs using full-length 16S rRNA gene sequencing. Frontiers in Veterinary Science. 2024;11:1405470.

The study analysed faecal microbiomes from 286 healthy or presumed-healthy companion dogs living in North America using full-length 16S rRNA sequencing.

DOI: 10.3389/fvets.2024.1405470
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