A microscopic view of Staphylococcus aureus cells (round, black) residing in their biofilm (PSMα1 functional amyloid filaments and extracellular polysaccharides, blue). Photography courtesy of Ümit Akbey and Kasper Hansen.
By Phoebe Ingraham Renda
Understanding the structure of biofilms—the sticky and tenacious settlements that bacteria build—is crucial for breaking the cycle of reinfection and developing new ways to fight biofilm-associated bacterial infections, which often complicate common implant surgeries, such as knee and hip replacements.
Two consecutive studies by University of Pittsburgh researchers have revealed dynamic biofilm blueprints for two highly pathogenic bacteria: Pseudomonas aeruginosa and Staphylococcus aureus.
Now, the researchers say, “Let the demolition begin!”
Design Reveal
Just seven of the 1,513 known pathogenic bacterial species—nicknamed ESKAPEE pathogens for their ability to “escape” antibiotics and antimicrobial therapies—are responsible for approximately 60–80% of microbial infections, because they all produce biofilms.
Biofilms are bacteria’s natural way of forming communities but, in the case of pathogenic infections, these communities live in a bunker. As these communities form, bacterial residents are encased in a dense scaffold that makes them untouchable to outside interference, including the host’s immune system and antibiotics.
It would take up to 1,000 times the standard dose of antibiotics to penetrate biofilms, but a dose that high would be toxic to patients. As a result, antibiotic treatments only kill bacteria living outside the biofilm. After antibiotic therapies end, the bacteria protected within the biofilm begin to divide and reignite the infection. As extended and frequent antibiotic treatments are given to manage these stubborn infections, the bacteria often gain antibiotic resistance.
Biofilm-forming bacterial species make and assemble functional amyloids (proteins that aggregate to create stable filament structures), which give biofilms their structure and rigidity. These bacterial amyloids are structurally akin to disease amyloids implicated in Alzheimer’s and other brain diseases, which are caused by misfolding of normal proteins. However, unlike those harmful amyloids, bacteria assemble their amyloids on purpose to build biofilms.
“There is no effective drug at the moment that targets these structures to disrupt the biofilms and help antibiotics to kill,” says Ümit Akbey, assistant professor of structural biology, School of Medicine, and corresponding author on both research studies.
Additionally, to further complicate matters, each bacterial species builds and assembles functional amyloids slightly differently, meaning no single drug will be universally effective against all biofilm-forming bacteria.
“The problem is that we don’t know the architectures of biofilms at high enough resolution to target them, so the infections go on forever,” says Akbey. “But, if you know the structures, we can design drugs based on that structure and knowing the mechanism of its formation. That is where we come into play!”
This high-resolution structural insight is what Pitt researchers Akbey; Mert Gur, associate professor of computational and systems biology; Kasper Holst Hansen, doctoral student; Chang Hyeock Byeon, research technician; Abdulkadir Tunç, research technician; and James Conway, professor and chair of structural biology, achieved for P. aeruginosa and S. aureus biofilms with collaborators Maria Andresen and Thomas Boesen from Aarhus University in Denmark. Both publications provide first-time, highly detailed looks at how Pseudomonas and Streptococcus bacteria build their biofilm structures from the “ground up.”
From left: Abdulkadir Tunç, James Conway, Ümit Akbey, Mert Golcuk, Chang Hyeock Byeon and Mert Gur—all contributors to one or both structural biology studies published in PNAS and Science Advances, which offer unprecedented insights into how P. aeruginosa and S. aureus form biofilms using their critical functional amyloids FapC and PSMα1, respectively. Photography by Rayni Shiring/University of Pittsburgh.
Both bacteria are categorized as high priority on the 2024 World Health Organization’s Bacterial Priority Pathogen List, which comprises antibiotic-resistant bacteria that are hard to treat, cause serious illness, are becoming more drug resistant, spread easily, are difficult to prevent and have few treatment options in development.
In a Science Advances manuscript, published Sept. 24, 2025, the research team used an integrative structural biology approach to provide the first complete, high-resolution structural view of FapC biogenesis. FapC is the major biofilm-forming functional amyloid that is essential to the structural integrity of Pseudomonas biofilms. Their integrative research approach combined structural biology techniques, nuclear magnetic resonance, cryo-electron microscopy and all-atom molecular dynamics simulations.
“The molecular dynamics part is particularly distinctive,” says Gur, who is a corresponding author for the publication with Akbey. “You rarely see combinations of computational and experimental methods that span protein folding and aggregation in the biofilm forming pathway. In this study, you have experimental structural biologists, computational biologists, different departments and different techniques coming together for an amazing story.”
This finding follows research, published August 2024 in PNAS, that provided the first-ever, high-resolution structural insights into the functional amyloid structure of PSMα1 from S. aureus and details how the amyloids assemble to build the bacteria’s biofilm structure. This work was also the first cross-b biofilm-forming functional amyloid structure ever determined, and the first amyloid structure resolved using the three-dimensional structure determination software package CryoSPARC.
Atomic top and side views of the functional amyloid structures of PSMα1 from Staphylococcus aureus (left, blue) and FapC from Pseudomonas aeruginosa (right, red) biofilms. Photography courtesy of Ümit Akbey and Kasper Hansen.
Tear Down
These structural breakthroughs mark an important step toward new antibiofilm strategies. By revealing the structures of FapC and PSMa1, research studies can now work to design structure-based drug possibilities to combat these biofilms directly. Antibiofilm strategies may range from novel drugs, such as small molecules that break existing biofilms apart and disrupt assembly, to coatings for medical devices that resist microbial colonization by preventing biofilms from forming.
“Our findings don’t just tell us how bacteria protect themselves,” says Gur. “They give us a starting point for dismantling those defenses and restoring the power of antibiotics against infections that currently seem unstoppable.”
Media contact: HSNews@pitt.edu