New test uses oyster faeces to detect deadly parasite Bonamia

A team of scientists from two Scottish universities has developed a groundbreaking method to detect a deadly oyster parasite without harming the shellfish.

Numbers of the European flat oyster (Ostrea edulis) have plummeted over the past two centuries due to overfishing, habitat loss and disease. They are now rare and protected in the wild. 

Among the most persistent threats is Bonamia ostreae, a microscopic parasite that causes a condition known as bonamiosis, which can devastate oyster populations but is harmless to humans. 

Until now, detecting the presence of the parasite has involved dissecting a sample of oysters, an approach that is impractical for monitoring rare or restoration-targeted populations.

But researchers from the University of Edinburgh’s Roslin Institute and Heriot-Watt University have pioneered a new method that uses oyster faeces to screen for the parasite’s DNA. By analysing the waste material left after holding oysters overnight in aerated seawater, scientists can determine whether any oysters are infected, without harming a single mollusc.

Test sites in Essex and Argyll 

Lead author Dr Tim Bean from Roslin Institute said the technique is a step forward for oyster conservation and aquaculture biosecurity.

“Oysters' poo contains traces of Bonamia DNA if they’re infected. By sampling this material, we can screen large numbers of oysters at once without the need to sacrifice them," said Bean.

The team tested the method at several sites across the UK, including Bonamia-positive waters in Essex and West Loch Tarbert in Scotland.

They found the non-invasive method was at least as sensitive as traditional tissue sampling and histology, and often more effective than water-based environmental DNA techniques.

Protecting the future 

Once widespread across Europe’s coasts, the native flat oyster has become a conservation priority due to its ecological importance. Oyster reefs provide habitat, filter water, and stabilise marine sediments.

But efforts to restore wild oyster populations and expand sustainable farming have been repeatedly thwarted by Bonamia ostreae. The parasite invades oyster immune cells, spreads unnoticed, and can wipe out populations.

Professor Bill Sanderson from Heriot-Watt University, who leads several oyster restoration projects across Scotland, said: “This is excellent news for oyster restoration across Europe. 

“Oyster restoration involves growing and then moving thousands of oysters from one site to another. We mustn’t take parasites or diseases with us, especially ones as deadly as Bonamia ostreae. 

“This new tool gives us a way to quickly and cheaply monitor for infection while protecting precious oyster stocks.

“There are more than 50 restoration sites throughout Europe now, and this test could be a lifesaver for all those.” 

The method has already been validated in field and lab settings and is portable enough to be used on-site with mobile DNA testing kits. It also proved highly accurate in negative control sites, with no false positives detected.

Scalable, cheap, and field-friendly

Unlike other DNA-based detection methods, which often rely on complex lab setups, the new approach uses a field-ready extraction and PCR system. 

According to the research team, it is scalable, cost-effective, and adaptable to other marine pathogens.

Bean said: “This is about giving restoration teams, oyster farmers, and regulators the tools they need to respond quickly and effectively to disease threats - without compromising the very species they’re trying to protect.”

The scientists are now working on refining the process further and exploring whether similar techniques could be used to detect other diseases or even invasive species.

Their findings were published in the journal Aquaculture and supported by the UK government's UK Seafood Innovation Fund and the Scottish Government's Sustainable Aquaculture Innovation Centre (SAIC), with additional funding from the Dornoch Environmental Enhancement Project, supported by The Glenmorangie Company.