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The Microbiome

Independent Research: Probiotic Use Explained Less Than 0.5% of Microbiome Variation

A 2024 peer-reviewed study compared 86 healthy dogs receiving bacterial probiotics with 286 similar dogs not receiving them. Probiotic use was not associated with significant differences in core bacterial species or overall microbiome diversity and explained only around 0.3–0.4% of variation in microbial community composition. The findings highlight an important distinction between consuming live bacteria and substantially restructuring an established gut microbiome.

Peer reviewed Open access
Independent Research: Probiotic Use Explained Less Than 0.5% of Microbiome Variation
Year
2024
Study type
Peer-reviewed cross-sectional microbiome study
Sample
372 healthy or presumed-healthy companion dogs: 286 not receiving bacterial probiotics and 86 receiving bacterial probiotics
Measured
Core bacterial species, microbial richness, diversity and overall community composition in dogs receiving or not receiving bacterial probiotics
01

The research question

If probiotics are intended to influence the gut microbiome, how large a microbiome difference can actually be detected in dogs already receiving them?

Rojas and colleagues had an unusually useful dataset for exploring this question.

Their healthy reference population contained 286 dogs that were not receiving bacterial probiotics.

A further 86 dogs met the same general health criteria but were receiving bacterial probiotic products.

Rather than asking whether one specific probiotic strain could produce a biological effect under highly controlled conditions, this analysis asked a broader real-world question:

How much of the natural variation between healthy canine microbiomes was associated with probiotic use?

02

What did the researchers do?

Faecal samples were collected from companion dogs living in homes across North America.

The main healthy reference population included 286 dogs.

To qualify for that reference group, dogs had to meet criteria including:

no reported clinical signs

no relevant physical conditions

no current medications

no antibiotics within the previous 12 months

and no bacterial probiotic use

The researchers then identified 86 additional dogs that met the same general health criteria except that they were receiving bacterial probiotics.

This produced two comparison groups:

No bacterial probiotics: 286 dogs

Receiving bacterial probiotics: 86 dogs

Faecal samples were analysed using full-length 16S ribosomal RNA sequencing.

The researchers compared:

the number of core bacterial species

the proportion of the microbiome represented by those core species

microbial richness

overall microbial diversity

and differences in microbial community composition.

03

What did they measure?

The analysis focused on several common measures of microbiome structure.

Core bacterial species

Researchers examined whether dogs receiving probiotics had a different number or proportion of the bacterial species identified as part of the healthy canine core microbiome.

Microbial richness

This assessed how many different bacterial groups were detected.

Alpha diversity

Measures including Shannon and Gini-Simpson diversity were used to assess the structure and evenness of the microbial community within individual dogs.

Beta diversity

This assessed how different the overall microbiome composition was between probiotic users and non-users.

Two different approaches were used to compare community-level variation.

The key question was whether probiotic use was associated with a broad and measurable restructuring of the faecal bacterial ecosystem.

04

What was observed?

The result was surprisingly limited.

Core bacterial species were not significantly different

Dogs receiving bacterial probiotics did not have a significantly different number of core bacterial species.

The overall proportion of the microbiome represented by those core species was also not significantly different.

Microbial richness did not differ

There was no significant difference in Chao1 richness between probiotic users and non-users.

Overall diversity did not differ

Shannon diversity and Gini-Simpson diversity were also not significantly different.

Community composition differed only marginally

Using one measure of community difference, the comparison between probiotic and non-probiotic dogs was not statistically significant.

Using another, the result approached conventional statistical significance but remained marginal.

The effect size was extremely small

Most importantly, probiotic status explained only around:

0.3–0.4% of total microbiome variation

That means almost all of the differences between individual dogs' microbiomes were associated with factors other than whether or not they were receiving a bacterial probiotic.

This is a useful reminder that probiotic intake does not necessarily correspond with a large or easily detectable restructuring of the faecal microbiome.

05

What does this study tell us?

This analysis challenges a very simple assumption:

taking live bacteria does not necessarily mean that the existing gut microbiome will be substantially reorganised.

Among these otherwise healthy dogs, probiotic users did not have:

more core bacterial species

greater microbial richness

greater overall diversity

or a clearly distinct microbial community

compared with non-users.

And probiotic status explained less than half of one percent of total microbiome variation.

That does not mean probiotics cannot have biological effects.

A probiotic organism could potentially:

pass temporarily through the gastrointestinal tract

produce metabolites

interact with resident microorganisms

or influence the host

without becoming a major or persistent part of the faecal microbiome.

But the study does show that:

probiotic consumption ≠ major microbiome restructuring

at least in this cross-sectional population.

This distinction is important when comparing different approaches to gut modulation.

A probiotic attempts to influence the ecosystem by adding microorganisms.

A fibre or prebiotic intervention changes what substrates are available to the microbial community.

An upstream nutritional approach may instead alter digestive processing before material reaches the lower gut.

These are biologically different strategies and should not be expected to produce identical microbiome outcomes.

06

What doesn't this study tell us?

This result should be interpreted carefully.

This was not a randomised probiotic trial

Dogs were already receiving probiotics as part of their normal routine.

The researchers did not allocate dogs to treatment.

The probiotic products were not standardised

Different dogs may have been receiving different:

species

strains

formulations

doses

and frequencies

This is a major limitation.

The study cannot determine whether one particular probiotic product was effective or ineffective.

Duration of probiotic use was not controlled

Dogs may have been receiving probiotics for very different lengths of time.

Only faecal bacterial composition was examined

The study did not comprehensively measure the metabolome or other functional outcomes.

A probiotic could potentially alter microbial activity without causing a large shift in bacterial composition.

Cross-sectional design

Dogs were compared with one another rather than being measured before and after starting a probiotic.

Individual baseline differences therefore remain important.

Healthy dogs

The results should not automatically be applied to dogs with gastrointestinal disease or other clinical conditions.

Small effect does not mean no effect

An intervention could produce a biologically meaningful change in a narrow pathway without explaining much of the total variation in the entire microbiome.

Commercial involvement

The study was funded by AnimalBiome, and all authors were employees of the company.

That does not invalidate the findings, but it is relevant context when interpreting the study.

The correct conclusion is therefore not:

probiotics do nothing

It is:

probiotic use was associated with very little of the overall variation in faecal microbiome structure in this population of healthy dogs.

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.

Published 2 September 2024.

As part of the study, faecal microbiomes from 286 healthy or presumed-healthy dogs not receiving bacterial probiotics were compared with 86 otherwise eligible dogs receiving bacterial probiotics.

No significant differences were detected in core microbiome measures or alpha diversity, while differences in beta diversity were marginal and probiotic status explained only around 0.3–0.4% of total microbiome variation.

DOI: 10.3389/fvets.2024.1405470
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