Beyond Killing Pathogens: Building a Healthier Microbiome for Fish and Shrimp

A 2026 scientific review highlights how probiotics, prebiotics and synbiotics are shaping a new approach to aquaculture health: not only controlling pathogens, but also actively building a healthier gut microbiome to support digestion, immunity and resilience in farmed animals.

As aquaculture becomes more intensive, fish and shrimp are increasingly exposed to high stocking densities, environmental fluctuations, stress and disease risks. For many years, antibiotics and chemicals have been used to control pathogens. However, overuse can increase residue risks, affect the environment and accelerate the development of antimicrobial resistance.

A 2026 review published in Frontiers in Marine Science shows that scientific attention is shifting from simply “killing pathogens” towards managing beneficial gut microorganisms. The three main approaches receiving growing interest are probiotics, prebiotics and synbiotics.

Feed is an important delivery route

Probiotics and prebiotics are often incorporated into diets to influence the gut environment of farmed fish and shrimp.

Prebiotics: “food” for beneficial bacteria

The simplest way to understand prebiotics is as substrates that help beneficial gut bacteria grow and function more effectively.

Probiotics: adding beneficial microorganisms

Probiotics are beneficial microorganisms such as Bacillus, Lactobacillus, Enterococcus and certain yeasts. When appropriately added through feed or the culture environment, they may compete with harmful bacteria, help stabilise the gut microbiome and stimulate immune responses. Some strains may also increase digestive enzyme activity, helping animals use nutrients more efficiently.

Prebiotics: a nutrient source for beneficial bacteria

Prebiotics are not living microorganisms. They are substrates such as FOS, GOS, MOS, inulin and β-glucan that are not fully digested by the host but can be utilised by beneficial gut bacteria. In simple terms: if probiotics are the “beneficial bacteria”, prebiotics are the “food source” that helps those bacteria grow and function.

When fermented in the gut, prebiotics may generate short-chain fatty acids that support intestinal cells, help regulate inflammatory responses and improve the digestive environment. Studies included in the review report potential benefits for growth, survival, immune function and stress tolerance.

Synbiotics: when the two approaches work together

Synbiotics combine probiotics with prebiotics. The aim is not simply to add two ingredients together, but to select a suitable prebiotic that helps the probiotic survive and perform more effectively in the gut. Many studies suggest that this combination may support intestinal structure, digestive enzymes, nutrient absorption, immunity and resistance to pathogens.

Helping animals cope with stress

In intensive farming systems, stress caused by temperature, stocking density, water quality or disease pressure can increase oxidative stress. Probiotics and synbiotics have been reported to support antioxidant enzyme systems such as superoxide dismutase and catalase, potentially helping animals cope better with challenging conditions.

There is no single formula for every farm

Effectiveness depends on the microbial strain, type of prebiotic, dosage, species and life stage, duration of use, delivery method and environmental conditions. Therefore, the principle of “the more, the better” is not scientifically sound.