The role of the microbiome in IBD

By Rob Clancy, staff writer

Researchers are taking a new approach to a debilitating illness by looking for a microbiome-based cause of Inflammatory Bowel Disease (IBD).

Dr Gemma D'Adamo and A/Prof Sam Forster examine a cell culture as part of their research into the role of the microbiome in inflammatory bowel disease (IBD).
L-R: Gemma D’Adamo, Associate Professor Sam Forster

CSL Centenary Fellow, Associate Professor Sam Forster leads a team at Hudson Institute of Medical Research studying the role of the microbiome in IBD. They have discovered a key group of bacteria connected to the disease, which are now being developed to be used in new IBD treatments.

“One of the keys to our research is that we’ve developed new, more precise methods to understand the interactions between the microbiome and disease,” said A/Prof Forster.

“Taking biopsies directly from the site of disease and also from healthy parts of the same patient allows the team to analyse the differences in the local microbiome – previous research typically relies on faecal samples, which collect microbiome from both.

“Faecal sampling is like using a bulldozer and trying to work out what a forest looks like from the debris that you capture,” A/Prof Forster said. “Biopsy-based sampling is equivalent to finding an individual ant and knowing it lives only on the leaves of a particular type of tree.”

PhD student Gemma D’Adamo added: “Our team also uses a technique called clade-based analysis: rather than using existing species classifications we have used a new analysis that identifies the group of bacteria which share a particular function, such as those driving a disease.”

“We use this for bacteria to find the specific groups that have the ability to impact disease outcome,” she said.

Identifying live biotherapeutics

Consultant Paediatric Gastroenterologist at Monash Children's Hospital, Dr Edward Giles works with Dr Gemma D'Adamo and A/Prof Sam Forster, researching the role of the microbiome in inflammatory bowel disease (IBD).
Dr Edward Giles

The good news for the almost 75,000 Australians with IBD is that this work is identifying key candidates for development as live biotherapeutics.

“Our research identifies key bacteria that may play a role in exacerbating symptoms of inflammatory bowel disease – this provides hope of better managed symptoms for IBD patients,” said Dr Edward Giles, the lead clinical researcher from Hudson Institute of Medical Research and Monash Health.

A/Prof Forster’s team is also working closely with the Adelaide-based biotechnology company Biomebank, whose mission is to treat and prevent disease by restoring gut microbial ecology.

Their latest research is published this week in the journal Cell Reports Medicine.


  • Inflammatory bowel disease affects one in 250 people aged between 5 and 40 in Australia, including up to 10,000 children
  • Approximately 25% of patients present before the age of 20, yet there is no cure and they will suffer their entire adult lives
  • The gut microbiome is thought to play a key role in disease yet direct understanding of key bacterial groups that drive disease remains elusive.

Collaborators | Biomebank, Monash Health, Monash Uni

Funders | CSL, NHMRC, ARC

Journal information | Gemma D’Adamo et al, (2023) Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease, Cell Reports Medicine.  DOI:

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