Microbes to revolutionize the sustainability of invertebrate aquaculture

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By Milthon Lujan

Full scale experimental design to identify beneficial bacteria for microbial education. Source: Dantan et al., (2024). Rev Aquac.
Full scale experimental design to identify beneficial bacteria for microbial education. Source: Dantan et al., (2024). Rev Aquac.

Aquaculture, the farming of aquatic organisms, has become the fastest-growing food production sector worldwide. However, this success is threatened by an increasing number of diseases affecting cultivated invertebrates such as oysters, shrimp, and abalone.

These diseases are often caused by viruses, bacteria, or parasites, but a new understanding of the role of the microbiome (the community of microorganisms living inside and around these animals) is shedding light on potential solutions.

A team of scientists from IFREMER, Univ Montpellier, and Univ Bretagne published a scientific review informing the crustacean and mollusk aquaculture industry about potential breeding practices to mitigate diseases and economic losses.

This article delves into the complexities of marine invertebrate diseases, highlighting their impact on production and exploring possible solutions based on harnessing the power of beneficial microbes.

The Scope of the Problem

Aquaculture now surpasses wild fishing as the primary source of seafood, with production reaching 86.4 million tons in 2020. However, disease outbreaks pose a significant risk, causing billions of dollars in losses and threatening the livelihoods of many people.

Invertebrates such as oysters, shrimp, and abalone are particularly vulnerable and suffer from viral, bacterial, and parasitic infections. White Spot Syndrome Virus (WSSV) in shrimp can cause 100% mortality in a matter of days, while Pacific Oyster Mortality Syndrome (POMS) has significantly impacted global oyster production. These diseases not only cause massive die-offs but also result in substantial economic losses for the industry.

For years, we have focused on fish, mollusks, and crustaceans as individuals. But research now reveals that these creatures are holobionts, ecosystems intertwined with their resident microbes. Understanding and influencing this microbial community opens up exciting possibilities for sustainable and resilient aquaculture.

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The Role of the Microbiota

Traditionally, disease control focused on identifying and eliminating harmful pathogens. However, the article introduces the concept of multifactorial and polymicrobial diseases, where disruptions in the delicate balance of the microbiome play a crucial role. Environmental stressors, such as temperature changes or pollution, can trigger dysbiosis, leading to the proliferation of opportunistic pathogens and increased susceptibility to diseases.

As detailed in the study, many diseases involve complex interactions between the environment, pathogens, and the host’s microbiome. In this regard, alterations in natural microbial communities within aquaculture farm animals can pave the way for opportunistic pathogens, leading to multifactorial and polymicrobial diseases.

White Feces Syndrome (WFS) in shrimp and Pacific Oyster Mortality Syndrome (POMS) are examples of such multifactorial diseases.

A Shift towards Microbiome Management

Traditional approaches often rely on antagonistic methods such as water sterilization and antibiotics, raising concerns about resistance and sustainability.

However, a new wave of research explores how to harness the power of beneficial microbes for a more sustainable approach. Probiotics, mutualistic symbionts, and bacteriophages are being investigated for their potential to directly combat pathogens through antimicrobial compounds, competition, or predation.

The article proposes a shift away from traditional antagonistic approaches like water sterilization and antibiotics towards harnessing the power of the microbiome itself. This involves:

  • Probiotics: Introducing beneficial microorganisms that compete with pathogens, produce antimicrobials, or even directly attack them.
  • Mutualistic symbionts: Using beneficial bacteria that live in symbiosis with the host, providing protection and other benefits.
  • Bacteriophages: Utilizing viruses that specifically attack and eliminate harmful bacteria.

Unraveling the Hidden Power of the Microbiome

The scientific review explores the crucial role of the microbiome in various mollusk and crustacean diseases. When this microscopic balance is disrupted (dysbiosis), pathogens can take hold and cause devastating outbreaks and economic losses. Examples include:

  • Pacific Oyster Mortality Syndrome (POMS), where a herpes-like virus triggers dysbiosis, leaving oysters vulnerable to bacterial attack.
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The Probiotic Revolution

Instead of directly fighting pathogens, the holobiont approach promotes cultivating a healthy and balanced microbiome. Probiotics, beneficial bacteria, show promise in restoring balance and preventing diseases. Imagine introducing helpful “microbial tenants” to displace harmful ones, bolstering the host’s natural defenses.

The scientific review goes beyond probiotics and proposes two innovative strategies:

  • Identification of “good neighbor” microbes: Researchers aim to identify bacterial communities associated with robust health in different species. By understanding these beneficial actors, we can encourage their presence in aquaculture environments.
  • Microbial education during early life: This fascinating concept involves introducing beneficial microbes during larval stages, shaping the developing immune system for long-term resilience against stress and diseases.

Benefits Beyond Health

By promoting holobiont health, we can achieve more than just disease prevention. A balanced microbiome can potentially:

  • Enhance the growth and development of cultivated species.
  • Improve resistance to environmental stressors such as temperature fluctuations and pollution.
  • Reduce dependence on antibiotics and other harmful treatments.

The Future: “Microbial Education”

The article emphasizes the crucial role of the microbiome during early development in shaping the host’s immune system. Studies show that early exposure to specific beneficial microbes can “educate” the immune system, leading to lasting protection against diseases in the future. This opens up exciting possibilities for using these “next-generation probiotics” in larval rearing stages, which could result in healthier and more resilient aquaculture animals.

Emerging evidence suggests the fundamental role of the microbiome in early life stages in shaping the host’s immune system throughout its life.

Scientists are exploring the possibility of using this knowledge to identify and harness “health-promoting bacteria” during larval rearing.

By shaping the microbiome from the start, these “next-generation probiotics” could offer long-term benefits for disease resistance and overall health.


This review aims to equip the aquaculture industry with knowledge about holobiont theory and its potential applications. By adopting microbial management strategies, we can move towards a future of sustainable, healthy, and resilient aquaculture, ensuring food security for future generations.

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The article presents a compelling case for moving beyond traditional disease control methods and harnessing the potential of the microbiome in aquaculture. By understanding and manipulating the complex interactions between the host, pathogens, and beneficial microbes, we can develop innovative strategies to ensure the sustainability and resilience of this vital food production sector.

Thus, investing in research on “microbial education” and harnessing beneficial microbes has the potential to revolutionize how we approach disease prevention and promote the long-term health of farmed aquatic animals.

Céline Cosseau
IHPE UMR 5244, Université de Perpignan Via Domitia
58 Avenue Paul Alduy Bât R, F-66860 Perpignan Cedex, France.
Email: celine.cosseau@univ-perp.fr

Reference (open access)
Dantan L, Toulza E, Petton B, et al. Microbial education for marine invertebrate disease prevention in aquaculture. Rev Aquac. 2024; 1-15. doi:10.1111/raq.12893