Beyond Who Is There: What Is the Gut Microbiome Actually Doing?

For years, microbiome research has focused on one main question: which bacteria are present?

But knowing who is there does not necessarily tell us what they are doing.

A major study published in Cell Metabolism, led by Prof. Tiannan Guo and colleagues, analyzed the microbial proteins actually being produced in 1,967 stool samples from 1,399 middle-aged and older adults. The researchers identified more than 92,000 microbial proteins and connected microbial functions with ageing, metabolic diseases and medication use.

From composition to function

Ageing was associated with changes in microbial pathways involved in carbon metabolism and energy production.

Across metabolic diseases, the researchers also observed reductions in bacterial proteins involved in carbohydrate, energy and amino acid metabolism, as well as short-chain fatty acid production.

One bacterium was particularly interesting: Megasphaera elsdenii.

It emerged as a hub species in type 2 diabetes. Experimental work suggested that antidiabetic drugs may promote this bacterium and that it could influence glucose regulation through butyrate production.

This raises a simple but important question:

Should we stop asking only “Which microbes are there?” and start asking “What are they actually doing?”

Metagenomics tells us what microorganisms could do. Metaproteomics brings us closer to what they are actually doing.

This shift from microbial composition to microbial function could open new perspectives for biomarkers, healthy ageing and microbiome-based therapies.

 

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