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Targeting mucosal biofilms in patients

with gastrointestinal disorders

WWTF project number: LS18-053

Inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS) are chronic gastrointestinal disorders that affect 10–15% of the Western population. These disorders reduce quality of life and result in substantial socioeconomic costs. The underlying disease mechanisms are poorly understood and there is no effective treatment other than symptomatic relief.


Recently, we have observed bacterial biofilms in the gastrointestinal tract of IBD and IBS patients, but their disease relevance, function and composition are unknown. This project aims to (i) use proteomic, metagenomic, and transcriptomic biofilm, normal mucosa and stool sample profiles to identify disease-specific biomarkers, (ii) characterise the bacterial biofilms through culture, functional assays and next-generation sequencing techniques, and (iii) develop gut-specific biofilm modulators to explore novel therapeutic strategies.


This project brings together experts in gastroenterology, microbiology, proteomics and therapeutic lead discovery to improve treatment for IBD and IBS patients. Innovative aspects include: (i) biomarker discovery, (ii) using gut-stable antimicrobial peptides for safer treatment options, and (iii) antibiotic and dietary screens for rapid translation into the clinic. Expected outcomes include (i) novel information on biofilm composition, growth, formation and disease association, (ii) biomarkers to aid diagnosis and treatment, and (iii) novel therapeutic avenues for IBD and IBS patients.

Biofilm microscopy 03.jpg

Figure. (A) Colonoscopic image of a colonic biofilm, a dense layer sticking to the mucosal wall. (B) Fluorescence in situ hybridization with Eub338 (green) to detect all bacteria (white arrows) residing in the biofilm of a patient with ulcerative colitis. DAPI (blue) was used to visualize DNA; the border of the epithelium is marked by a dotted line.

Research team

A/Prof. Markus Muttenthaler

Medicinal Chemist

Prof. Christoph Gasche


Prof. Athanasios Makristathis


Team members

Dr. Michaela Lang

Dr. Vineeta Khare

Dr. Wolfgang Barousch

DI. Maximilian Baumgartner

DI. Bernhard Jandl

MSc Anton Klotz

BA Marion

Fabian Hof


Prof. David Berry (University of Vienna)

Prof. Pedro Gois (University of Lissabon)

A/Prof. Mark Blaskovich (The University of Queensland) 

Dr. Selma Tobudic (Medical University of Vienna)

Dr. Jovana Mihajlovic

Dr. Manuel Kussmann

What is it all about?

Key Results

Baumgartner M, Lang M, Holley H, Crepaz D, Hausmann B, Pjevac P, Moser D, Hof F, Beer A, Orgler E, Frick A, Khare V, Evstatiev R, Strohmaier S, Primas C, Dolak W, Köcher T, Kristaps K, Rath T, Neurath MF, Berry D, Makristathis A, Muttenthaler M, Gasche C.

Mucosal biofilms are an endoscopic feature of irritable bowel syndrome and ulcerative colitis. 

Gastroenterology, 2021, DOI: 10.1053/j.gastro.2021.06.024. (IF=33.9, Top 5% of Category). 

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