The Microbiome

Microbiome Composition vs Function: What’s the Difference?

Knowing which microorganisms are present in the gut is useful, but it is only part of the picture. Scientists increasingly look at what those microbes are doing, what compounds they produce, and how microbial activity relates to the wider nutritional environment.

Science explainer

Microbiome Composition vs Function: What’s the Difference?

Content type

Science explainer

Focus

Microbial composition, function and metabolites

The big question

Microbiome studies often tell us which microorganisms are present in a sample.

That is useful information, but it does not automatically tell us what those microorganisms are doing.

Two microbial communities can look different in terms of the bacteria they contain while still carrying out some of the same functions.

Equally, communities that appear broadly similar in composition may behave differently if the nutritional environment around them changes.

This leads to an important distinction in microbiome science:

Composition asks who is there. Function asks what they are doing.

How do scientists study it?

Scientists use different tools to investigate different layers of the microbiome.

DNA sequencing can be used to identify microbial groups and compare their relative abundance.

This helps describe composition.

Other approaches look more directly at microbial potential or activity.

Metagenomics can provide information about genes present within a microbial community.

Metatranscriptomics can examine which genes are being actively expressed.

Metabolomics measures small molecules found within biological samples and can provide clues about microbial and host activity.

Researchers may also measure specific fermentation products, such as short-chain fatty acids.

Together, these techniques can help move from simply describing which microorganisms are present towards understanding what is happening within the gut ecosystem.

What can we measure?

There are several distinct layers scientists can examine.

Composition

Which microorganisms are present, and in what relative proportions?

Genetic potential

Which genes and metabolic pathways are carried by the microbial community?

Activity

Which biological processes appear to be active at a particular time?

Metabolites

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

Nutritional environment

Which nutrients and substrates are available to microbial communities?

Each of these measurements provides different information.

Looking at them together can give a more complete picture than relying on microbial composition alone.

What have we learned?

One of the major lessons from modern microbiome science is that microbial identity and microbial function are related, but they are not the same thing.

Different microbial species can sometimes perform similar metabolic roles.

The same microbial species may also behave differently depending on the nutrients available to it and the wider environment within the gut.

This means that an increase or decrease in a particular bacterial group does not always translate directly into a predictable biological effect.

For that reason, researchers increasingly combine microbiome profiling with measurements of metabolites and other markers of microbial activity.

The question is shifting from simply:

“Which bacteria are there?”

towards:

“What is this microbial community doing?”

Why does this matter?

Thinking about function changes the way we look at the microbiome.

A microbial ecosystem is not simply a list of organisms.

It is an active community continuously interacting with nutrients, digestive products and compounds produced by both the host and other microorganisms.

That means the nutritional environment matters.

Microbes require substrate to carry out metabolic activity, and changing the compounds available to them can influence what they do.

This creates a useful framework:

Composition → who is there

Environment → what reaches them

Function → what they do

Looking across all three can provide a richer understanding of the gut than composition alone.

Our guide to 16S microbiome analysis explains one way researchers describe which bacterial groups are present.

What should we keep in mind?

Measuring microbial function is challenging.

Many metabolites can be produced by more than one microbial species, and some can also be produced or modified by the animal itself.

A faecal sample represents only one point in a complex digestive system and does not capture every process occurring elsewhere in the gastrointestinal tract.

Metabolite concentrations can also be influenced by diet, absorption, transit time and sample handling.

Even advanced techniques therefore provide only part of the picture.

For this reason, microbiome composition, microbial function and the nutritional environment are best interpreted together rather than treated as completely separate measurements.

Sources and further reading

References

Further reading:

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.

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.

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.

Suchodolski JS. Diagnosis and interpretation of intestinal dysbiosis in dogs and cats. The Veterinary Journal. 2016;215:30–37.

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