Anabiomics

Anabiomics: A Substrate-Led Approach to the Microbiome

Anabiomics starts with a simple idea: microbial communities are shaped not only by which organisms are present, but by the nutritional environment surrounding them. That means looking upstream at digestion, nutrient availability and the substrate reaching the microbiome.

Science explainer

Content type

Science explainer

Focus

Nutrient availability, microbial substrate and microbiome function

The big question

Much of microbiome science begins by asking which microorganisms are present.

Anabiomics begins one step earlier.

It asks:

What nutritional environment are those microorganisms living in?

Every microbial community depends on the compounds available to it.

In the gut, those compounds are shaped by diet, digestion, absorption and the material that continues further downstream.

That means microbial activity is influenced not only by the organisms themselves, but by the substrate they encounter.

Anabiomics is therefore a way of looking at the microbiome through the relationship between digestion, nutrient availability and microbial function.

How do scientists study it?

A substrate-led approach brings together several areas of digestive and microbiome science.

The first is diet.

Food determines which nutrients enter the digestive system.

The second is digestion.

Mechanical and enzymatic processes break nutrients down, allowing some components to be absorbed earlier in the gastrointestinal tract.

The third is substrate availability.

Material that is not absorbed continues downstream, where it becomes available to microbial communities.

The fourth is microbial activity.

Microorganisms use available substrate, producing a wide range of metabolites and fermentation products.

By studying these stages together, researchers can explore how changes upstream may be associated with changes in the microbial environment downstream.

What can we measure?

A substrate-led approach can involve several different measurements.

Digestibility

How much of a nutrient is digested and absorbed before reaching the lower gastrointestinal tract?

Substrate availability

Which nutrients and compounds remain available further downstream?

Microbial composition

Which microorganisms are present within the microbial community?

Microbial function

Which metabolic pathways appear to be active?

Metabolites

Which compounds are produced, transformed or consumed within the gut environment?

By combining these measurements, researchers can investigate the pathway from food entering the digestive system to microbial activity further along the gut.

What have we learned?

One of the clearest principles emerging from nutritional microbiome research is that microorganisms respond to the environment around them.

Change the available substrate, and microbial activity can change.

That does not necessarily mean the microbial community will transform completely.

Different microorganisms can sometimes perform similar metabolic functions, and microbial communities can show a degree of functional redundancy.

This is why anabiomics places emphasis on both the nutritional environment and what the microbiome is doing, rather than focusing only on the abundance of individual bacterial groups.

The central idea is simple:

Microbial composition matters, but substrate and function matter too.

Why does this matter?

Anabiomics provides a useful framework for thinking about the gut as one connected system.

Instead of viewing digestion and the microbiome as separate subjects, it links them together:

Diet → Digestion → Substrate → Microbiome → Metabolites

Each stage can influence the next.

This means one way to think about the microbiome is not simply to ask how to change which microorganisms are present.

We can also ask how to influence the environment in which those microorganisms live.

That shift — from microbes alone to microbes within their nutritional environment — is the central idea behind a substrate-led approach to microbiome science.

What should we keep in mind?

A substrate-led model is a useful framework, but the gut is more complex than a simple linear pathway.

Microorganisms can interact with one another, compete for nutrients and produce compounds that become substrates for other microbes.

The host also influences the gut environment through secretions, absorption, immune activity and gastrointestinal transit.

Microbial activity can therefore influence the environment just as the environment influences microbial activity.

It is also difficult to measure exactly which substrates are available to specific microbial populations at a particular point in time.

For that reason, anabiomics should be understood as a way of organising and investigating these relationships rather than as a complete description of everything happening within the gut.

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.

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.

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.

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