Bonamia in oysters: non-invasive and sensitive fecal tests

The European flat oyster, Ostrea edulis, a key native species in Europe’s coastal ecosystems, has seen its populations drastically decline over the past two centuries due to overfishing, habitat loss, and diseases. Currently, they are 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 although it is harmless to humans.

Timely detection of this pathogen before moving animals to disease-free areas or new farms is a fundamental challenge. Until now, detecting the parasite’s presence involved dissecting a sample of oysters, an approach that is not only destructive but also impractical for monitoring rare or restoration-targeted populations. Faced with this problem, a scientist from Heriot-Watt has worked with colleagues from the Roslin Institute at the University of Edinburgh to develop an innovative method that allows the detection of this deadly parasite without harming the mollusks. This breakthrough offers hope for aquaculture and conservation efforts.

Detecting the parasite without sacrificing the oyster

The innovative approach presented is based on the ability to detect the DNA of the parasite Bonamia ostreae in the material produced by oysters during their normal metabolic activity. The team from Heriot-Watt and the Roslin Institute has pioneered this new method that uses oyster feces to search for the parasite’s DNA. By analyzing the waste material left after keeping oysters overnight in aerated seawater, scientists can determine if any oysters are infected, without harming a single animal.

Dr. Tim Bean, lead author of the study and a member of the Roslin Institute at the University of Edinburgh, explains the logic behind this technique, noting that “oyster feces contain traces of Bonamia DNA if they are infected.” He adds, “By sampling this material, we can screen a large number of oysters at once without needing to sacrifice them.”

What does the non-invasive methodology consist of?

The method involves the following steps:

• Quarantine and collection: Oysters are kept in quarantine overnight in aerated artificial seawater. During this period, the animals produce feces and pseudofeces (sediment particles and mucus that have not been ingested).
• Sampling: The next day, these sedimented feces and pseudofeces are carefully collected from the bottom of the containers.
• DNA extraction and analysis: DNA is extracted from this biological material and analyzed by specific qPCR to detect the presence of Bonamia ostreae DNA.

Researchers highlight that both intra- and extracellular forms of the parasite are present in oyster feces and pseudofeces. It is believed that infected hemocytes (the oyster’s immune cells) regularly migrate across the epithelium, releasing parasites into the intestinal lumen or onto external surfaces, which are then excreted. This could explain why feces prove to be such a potent indicator of infection.

Promising results: sensitivity and method validation

This non-invasive approach has proven to be not only a viable alternative but, in some respects, superior to existing techniques. The team tested the method at several sites in the UK, including waters with confirmed Bonamia presence in Essex and West Loch Tarbert in Scotland (Argyll).

Greater sensitivity than eDNA in water

In comparative studies, pathogen detection from feces/pseudofeces samples was more sensitive than environmental DNA (eDNA) sampling directly from tank water. For example, in the study conducted in Mersea (England), Bonamia DNA was detected more frequently in DNA extracted from sediment (3 out of 7 buckets) than in DNA extracted from water (2 out of 7 buckets).

Sensitivity comparable to traditional destructive methods

Crucially, when compared with results from conventional histology and qPCR from tissue extracted from oysters (“gold standard” methods), the new non-invasive method demonstrated comparable levels of sensitivity. In fact, the team found that 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. Sensitivity assays indicated that the method can detect as few as 30 copies of the Bonamia ostreae 18S rRNA gene in a 250 mg sediment sample, underscoring its high detection capability. If Bonamia is present in the sample, it is very likely to be detected.

Field validation and control

The method’s efficacy was tested in various scenarios:

• Sites positive for Bonamia: Oysters were collected from Mersea (England) and West Loch Tarbert (Scotland), known for the parasite’s presence.
• Sites negative for Bonamia: As a control, oysters from Loch Craignish and Loch Melfort (Scotland), sites reported as Bonamia-free, were used. In these control sites, all sediment samples tested negative for Bonamia ostreae and positive for Ostrea edulis DNA, confirming the test’s specificity and correct DNA extraction, with no false positives detected.

Implications for aquaculture and flat oyster restoration

The development of this non-invasive method, described as “excellent news for oyster restoration across Europe” by Professor Bill Sanderson of Heriot-Watt University, who leads several oyster restoration projects in Scotland, has significant advantages and practical applications. The native flat oyster, once widespread along European coasts, has become a conservation priority due to its ecological importance: oyster reefs provide vital habitat, filter water, and stabilize marine sediments. However, efforts to restore wild oyster populations and expand sustainable aquaculture have been repeatedly thwarted by Bonamia ostreae.

Professor Sanderson emphasizes: “Oyster restoration involves breeding and then moving thousands of oysters from one site to another. We must not take parasites or diseases with us, especially ones as deadly as Bonamia ostreae.” He adds, “This new tool gives us a way to quickly and cheaply monitor for infection while protecting valuable oyster stocks. There are now more than 50 restoration sites throughout Europe, and this test could be a lifesaver for all of them.”

The advantages include:

• Improved biosecurity: Allows for more thorough and frequent monitoring of animals before transfer, minimizing the risk of spreading the disease to parasite-free areas.
• Scalability and cost-effectiveness: Sampling feces/pseudofeces is simple, can be done on a large scale (e.g., in repurposed depuration units), and is economical, especially compared to sacrificing animals for analysis. This reduces costs for producers and allows for sampling a larger number of individuals, increasing sensitivity at the population level.
• Conservation of populations: Being non-destructive, it is ideal for monitoring small or endangered wild populations where sacrificing individuals for diagnosis would be counterproductive.
• Facilitates proactive testing: Its ease of use and low cost can encourage producers to conduct more regular testing, rather than waiting for clinical signs or mortalities to appear.

Furthermore, the method has been validated in field and laboratory settings and is portable enough to be used on-site with mobile DNA analysis kits. Unlike other DNA-based detection methods, which often rely on complex laboratory setups, this new approach uses a field-ready extraction and PCR system.

Conclusion and future perspectives

The non-invasive detection method for Bonamia ostreae from Ostrea edulis feces and pseudofeces represents a significant advancement for aquaculture health and the conservation of this emblematic species. It offers a scalable, cost-effective, and sensitive tool that overcomes many of the limitations of traditional diagnostic methods.

According to Dr. Bean, “it’s 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 are trying to protect.”

Scientists are now working on further refining the process and exploring whether similar techniques could be used to detect other diseases or even invasive species. The integration of technologies such as LAMP (Loop-mediated isothermal amplification) assays, which allow for rapid field analysis, could further enhance the applicability and utility of this technique.

The findings were published in the journal Aquaculture and were ed by the UK Seafood Innovation Fund and the Sustainable Aquaculture Innovation Centre, with additional funding from the Dornoch Environmental Enhancement Project, ed by The Glenmorangie Company. This development contributes to the long-term protection and sustainability of European flat oyster populations.

Tim P. Bean
The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus, 
The University of Edinburgh
Midlothian EH25 9RG, UK
Email: [email protected]

Reference (open access)
Regan, T., Vythalingam, L., Nascimento-Schulze, J., Paisley, O., Karmitz, A., Hanley, N. M., Sanderson, W. G., & Bean, T. P. (2025). Non-invasive detection method for Bonamia ostreae infected Ostrea edulis. Aquaculture, 599, 742153. https://doi.org/10.1016/j.aquaculture.2025.742153