Meet the microscopic community helping to keep us healthy

What is the gut microbiome?

The gut microbiome is the community of microorganisms living in our digestive system. It includes bacteria, viruses and fungi, and the substances they produce. 

"Each microbiome is unique," says Dr Cao.

"Our microbiome changes throughout life and is influenced by factors such as diet, age, environment, medication and overall health."

Each person's microbiome is unique, creating a highly dynamic ecosystem inside the body.

How does the microbiome work?

Many gut microbes help break down components of food that our own digestive enzymes cannot process, particularly certain types of fibre.

"When gut microbes break down fibre, they produce compounds that help nourish the intestinal lining and support important bodily functions," Dr Cao says.

"These compounds can influence metabolism, inflammation and immune activity."

Gut microbes also help produce some vitamins and prevent harmful organisms from taking over the gut. Scientists have linked changes in the microbiome to conditions including inflammatory bowel disease, obesity and allergies, although the relationship is complex.

"The microbiome and human health influence each other in both directions," Dr Cao says.

"Microbes may contribute to disease, but illness, medication and diet can also reshape the microbiome."

Keeping the ecosystem healthy

There is no single "perfect" microbiome.

"A healthy microbiome is not about having a specific list of microbes," Dr Cao says.

"It's about having a stable community that can perform important functions and recover after disruption."

Diet is one of the most important factors people can influence. Vegetables, fruit, legumes and whole grains provide a variety of fibres that support a healthy microbiome.

Sleep, exercise, stress levels and medication use can also affect the health of the gut ecosystem.

What about pre and probiotics?

Prebiotics are substances, often forms of fibre, that feed beneficial microbes already living in the gut. Probiotics introduce live microorganisms through fermented foods or supplements.

"Probiotics can be helpful in some situations, but they're not one-size-fits-all," Dr Cao says.

"Their effectiveness depends on the strain, the dose and the individual."

For most healthy people, he says a varied, fibre-rich diet remains the best place to start.

Where microbes meet immunity

The gut lining faces a difficult task. It must absorb nutrients while coexisting with trillions of microbes and preventing harmful organisms from entering the body.

"The intestinal lining acts like a carefully managed border," Dr Cao says.

"It constantly decides what should be tolerated and what requires an immune response."

Researchers at UQ's Frazer Institute recently uncovered how specialised microfold cells help organise immune defences within the intestine.

The findings showed these cells act as local control centres, coordinating nearby immune cells that produce protective signals and helping maintain a healthy intestinal lining.

"This ongoing communication helps the body live alongside beneficial microbes while remaining ready to respond to harmful ones," Dr Cao says.

"When this balance breaks down, the effects can extend far beyond the gut."

What’s next?

Researchers are continuing to investigate the complex relationship between the microbiome, the intestinal lining and the immune system.

"The microbiome, intestinal lining and immune system are constantly exchanging chemical signals," Dr Cao says.

"By understanding these conversations, we may be able to develop more precise diets, probiotics and treatments tailored to individual needs."

Rather than searching for a single "good microbiome", researchers are increasingly focused on identifying which microbial functions have been disrupted and how best to restore them for each person.

Read the study, featured on the cover of Nature Immunology.