Digestion

Digestion Before the Microbiome: Why Upstream Matters

The microbiome does not receive food exactly as it was eaten. What reaches microbial communities further along the gut has already been shaped by digestion, absorption and transit through the digestive system — helping determine the nutritional environment those microbes encounter.

Science explainer

Digestion Before the Microbiome: Why Upstream Matters

Content type

Science explainer

Focus

Digestion, nutrient availability and microbial substrate

The big question

When we talk about feeding the gut microbiome, it is easy to imagine that microorganisms simply encounter the food placed in a dog's bowl.

In reality, they do not.

Food undergoes a series of mechanical and chemical processes as it travels through the digestive system. Nutrients are broken down, absorbed and transformed along the way.

By the time material reaches microbial communities further downstream, it can be very different from what was originally eaten.

This leads to an important question:

If digestion changes what reaches the microbiome, can we really understand the microbiome without also understanding what happens upstream?

How do scientists study it?

Digestion begins before food ever reaches the large intestine.

Food is physically broken down and mixed with digestive secretions. Enzymes then help break larger nutrients into smaller components that can be absorbed.

Proteins can be broken down into peptides and amino acids.

Fats are digested into smaller lipid components.

Digestible carbohydrates can be broken into sugars that are available for absorption.

Not everything is digested or absorbed to the same extent.

The material that remains continues through the gastrointestinal tract, where it becomes part of the nutritional environment encountered by microbial communities.

This means the amount and type of substrate reaching the microbiome depend partly on what happened earlier during digestion.

What can we measure?

There are several ways of looking at this relationship.

Digestibility

Researchers can estimate how much of a nutrient disappears from the digestive tract rather than being recovered later in faeces.

Microbial composition

DNA-based methods can show which microbial groups are present and whether their relative abundance changes.

Fermentation products

Microorganisms transform available substrates into other compounds. These can include short-chain fatty acids and many other metabolites.

Metabolomics

Metabolomic techniques allow researchers to examine a broad range of small molecules and can provide additional information about activity within the gut ecosystem.

Looking at digestion and microbial activity together can therefore help connect what happens earlier in the digestive tract with what happens later.

What have we learned?

One of the clearest lessons from nutritional microbiome research is that microbial communities respond to the material available to them.

Changing a diet can alter both the amount and the type of substrate reaching the lower digestive tract.

For example, changes in dietary protein, fat and carbohydrate can be associated with changes in microbial composition and fermentation products.

Different dogs can also process food differently.

Body size, diet composition, transit time, nutrient digestibility and other physiological factors can influence the gastrointestinal environment.

The microbiome is therefore not simply responding to an ingredient list.

It is responding to what remains available after digestion has already taken place.

Why does this matter?

It gives us a different way to think about the gut.

Microbiome strategies often begin with the microorganisms themselves.

But there is another place to start:

What are we asking those microorganisms to live on?

The nutritional environment reaching the microbiome is partly the result of everything that has already happened upstream.

That creates a connected pathway:

Diet → Digestion → Substrate → Microbiome

This does not mean digestion determines the microbiome on its own. The gut is far more complex than that.

But it does mean digestion and the microbiome should not always be considered as separate subjects.

Changing what is digested earlier has the potential to change what becomes available later.

That relationship between digestion and microbial substrate is an important area of nutritional science — and one of the ideas underlying our approach to the canine gut.

The next stage of the process is covered in our guide to bioavailability and nutrient absorption.

Our practical guide to supporting dog gut health translates this upstream relationship into everyday feeding choices and observations owners can make at home.

What should we keep in mind?

The relationship between digestion and the microbiome is not a simple one-way pathway.

Microorganisms themselves contribute to digestion and metabolism, particularly within the large intestine.

Two diets with apparently similar nutrient compositions may also behave differently because of ingredient selection, processing, digestibility and physical structure.

Individual dogs differ too.

Age, breed, body size, environment, existing microbial communities and gastrointestinal transit can all influence what happens inside the gut.

And a change in microbial composition does not automatically mean that the change is beneficial or harmful.

For those reasons, researchers increasingly look beyond individual bacterial groups and consider nutrient availability, microbial function and metabolites alongside composition.

Sources and further reading

References

Further reading:

Wernimont SM, Radosevich J, Jackson MI, et al. The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease. Frontiers in Microbiology. 2020;11:1266.

Pilla R, Suchodolski JS. The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease. Frontiers in Veterinary Science. 2020;6:498.

Hooda S, Minamoto Y, Suchodolski JS, Swanson KS. Current state of knowledge: the canine gastrointestinal microbiome. Animal Health Research Reviews. 2012;13(1):78–88.

Deng P, Swanson KS. Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges. British Journal of Nutrition. 2015;113:S6–S17.

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