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Probiotics in Aquaculture

Support health, performance and growth of aquatic species

Probiotics for farmed fish and shrimp are beneficial bacteria that are commonly added to aquaculture systems in order to help support health, performance and growth.  

Decades of research on the application of probiotics in aquaculture have been primarily driven by the need to reduce or eliminate antibiotics from production systems and improve sustainability.  

The important role of probiotics in aquaculture is increasing. This is primarily due to disease, which represents the biggest constraint in aquaculture, and is a huge challenge for future growth and expansion.  

In order to effectively manage disease, three factors must be considered:  

  1. Host
  2. Pathogen
  3. Environment


In order to effectively manage disease, three factors must be considered: Host, Pathogen, Environment
3 factors must be considered in how probiotics in aquaculture can help manage heath and avoid disease
Due to the enormous natural diversity of bacteria, it is possible to use different types of probiotics in aquaculture, to target each of these bottlenecks.

Probiotics to improve the environment 

Several probiotic bacteria species are able to improve the environment of aquaculture systems. Aquatic pathogens are able to grow and proliferate in the environment, as they benefit from high organic matter loading, which is primarily derived from feed, feces and phytoplankton. Further, as the organic matter decomposes, nitrogen wastes (ammonia, nitrite and nitrate), are formed as part of the nitrogen cycle.  

Nitrification and Denitrification (adapted from Hagenbuch, 2007)
Nitrification and denitrification (adapted from Hagenbuch, 2007) are processes that can be influenced by probiotics in aquaculture
Source: BIOMIN

Although this is a natural process, the artificial amount of organic matter in aquaculture production systems is often too high for such a reliance on this existing removal system. Since water is constantly being ingested by all aquatic animals, improving water quality (bioremediation) in aquaculture, is an important requirement for both shrimp and fish farming.  

Often overlooked, is the quality of aquaculture sediments, especially important for bottom dwelling species, such as shrimp. Organic material can accumulate, and as it degrades, it will consume oxygen and generate toxic metabolites, including nitrogen wastes and hydrogen sulfide. These conditions can lead to huge mortalities, so bioremediation bacteria are equally important as soil probiotics in aquaculture.  

Probiotics can produce substances that inhibit pathogen growth or kill pathogens.

Probiotics to reduce pathogens 

Picture of petri dish demonstrating the bactericidal or bacteriostatic effects of probiotics in aquaculture on pathogens
Probiotics in aquaculture can have bactericidal or bacteriostatic effects on pathogens.

Evolution has allowed certain bacterial strains to develop defense mechanisms, in order to gain competitive advantage. This means that some probiotic species are capable of producing a wide range of chemical substances that have bactericidal or bacteriostatic effects on pathogens.  

Compounds produced by beneficial bacteria that restrict pathogens include:  

  • Antibiotics
  • Bacteriocins
  • Siderophores
  • Lysozymes
  • Proteases
  • Hydrogen peroxide
  • Organic acids
  • Ammonia
  • Diacetyl

Vibrio control 

The use of probiotics in aquaculture to improve pond environment and control Vibrio populations has been one of the most common strategies used by farmers to fight EMS outbreaks. 

It is not necessary to kill a pathogen in order to control its abundance and prevent its infection. Recently, it was discovered that certain pathogens are able to communicate, termed quorum sensing, in order to increase their virulence, survival and form biofilms.  

Some probiotics, as well as some plant extracts (e.g. cinnamaldehyde from cinnamon) have quorum quenching properties, which refers to the breaking of this communication. Ultimately, this means that although the pathogen may still be present, it has lower virulence and may be easier to control via other mechanisms or pathways. The presence of probiotic-produced inhibitory substances is thought to aid the barrier function against opportunistic pathogens. 

Probiotics for host growth performance and health 

An effective aquaculture probiotic which can colonize the gut has two benefits:  

  • Competitive exclusion of pathogens 
  • Immune support  

Competitive exclusion 

If a probiotic bacteria is able to colonize the intestine, at least temporarily, by adhering and growing within the intestinal mucus and mucosa, it can reduce the available receptor sites for pathogens and stimulate their removal from infected regions. This mechanism is called competitive exclusion.  

Scientists have suggested that this mechanism may be more beneficial when probiotics are administered to juvenile or first feeding aquatic animals, or to older animals immediately after antibiotic treatment. The period of attachment can be vary greatly, and depends on the probiotic and host species, time and dosage of probiotic supplementation and environmental conditions.  

Immune support

By attaching to different receptors, probiotics are able to interact with the host immune system. Many studies have investigated the effect of probiotics on the immune system in fish and shrimp, focusing on both the innate and adaptive immune response as well as the localized (i.e. intestine) and systemic (whole organism) response.  

At the systemic level, probiotics have commonly been reported to improve hematological and immunological profiles, while at the localized level, they can improve barrier function and modulate gene expression pathways. Since aquatic animals are mostly reliant on their innate immune system, this mechanism may provide broad-spectrum disease resistance against multiple pathogenic threats.  

The gut is home to a large number of commensal microorganisms. It is important that these are protected by the host as they provide important functions in intestinal development, nutrition and immunity. Anti-inflammatory cytokines are part of a tolerance mechanism which acts to de-sensitize the host, thus it does not initiate an immune response to attack ‘good’ bacteria. Furthermore, they act to balance out the pro-inflammatory cytokines, thus maintaining an equilibrium within the mucosal immune system.  

In vivo trials using tilapia, demonstrates that the gene expression of two anti-inflammatory genes, IL-10 and TGFβ, can also be increased by the addition of AquaStar® Growout. This result tells us two things; firstly, that the host does not see the probiotics as a threat and secondly that the probiotics can help to promote and maintain mucosal tolerance. 

Modulation of intestinal immunity through TLR signaling
Modulation of intestinal immunity through TLR signaling. Pathogens (and probiotics) bind to TLR. Upon activation, adaptor proteins such as myeloid differentiation primary response protein 88 (MYD88) are recruited. When this happens, IkB (inhibitor of nuclear factor kappa B (NFkB)) is phosphorylated (P) and degraded by the cell. This allows NFkB to pass from the cytoplasm into the nucleus of the cell where initiates the cytokine transcription. Source: adapted from Cerf-Bensussan & Gaboriau-Routhiau, 2010.

Digestion and feed efficiency  

Probiotic effects on nutrient utilization, digestion and growth are the most widely researched, likely due to its simplicity to collect such data, and its commercial relevance. A couple of mechanisms can explain improvements in these parameters. Firstly, Bacillus spp. are well known for their capacity to produce extracellular enzymes. When used in aquafeed, these enzymes can improve the digestibility and reduce FCR. Ultimately, improving FCR in aqua feeds has economic benefits since feed can be the largest cost fraction for a producer, and can also improve water quality as less waste is released.  

Gut structure and function  

Other aqua probiotics use alternative mechanisms. For example, there are numerous reports on lactic acid bacteria improving intestinal morphology, through greater villi length, more numerous villi and/ or greater microvilli density. All these observations increase the surface area of the gut, allowing more nutrients to be absorbed by the host.  

Strengthening the barrier: microvilli density 

Beneath the mucus layer, lies the epithelia, primarily consisting of enterocytes. These cells are lined with microvilli. Using electron microscopy, it was shown that the probiotic significantly increases microvilli density in the gut. The benefit of this increase is two-fold. First more numerous microvilli will increase the surface area so the host can acquire more nutrients from the feed. Second, any gaps between microvilli present an opportunity for pathogens to translocate the epithelia and infect the fish. Thus a higher microvilli density, caused by the probiotic, contributes to a more efficient barrier between the inside of the gut and the outside, blocking pathogens. 

Electron micrographs showing microvilli from fish fed a control diet (a) and probiotic supplemented diet (b).
Electron micrographs showing microvilli from fish fed a control diet (a) and probiotic supplemented diet (b). Gaps between microvilli (MV), as seen in micrograph a, provide an entry point for opportunistic pathogens.
Compared to micrograph b, the microvilli provide an impenetrable barrier, blocking pathogen entry.
Source: BIOMIN

Weighing the benefits 

It should also be noted that not all investigations report increased growth performance, however it should be noted that growth performance similar to the control treatments is not necessarily a bad result, if the probiotic can manifest other benefits (e.g. immune function, disease resistance) are observed, which likely requires energy and resources.  

Main categories of probiotics for aquaculture 
Main categories of probiotics for aquaculture 

Choosing the right probiotic

  • Probiotics in aquaculture are an established management tool for improving gut health and environmental quality. There are many different probiotics for aquaculture products. Major categories in commercial formulations include Bacillus spp., lactic acid bacteria (LAB), yeast, and nitrifying/ denitrifying bacteria.  

  • Theoretically, a probiotic bacteria needs just a single mode of action. However, given the complexity of aquaculture systems, it is argued that formulations using multiple species, or better, multiple genera, may provide complementary modes of action, and therefore conferring multiple benefits to the animal, producer and ultimately the sector as a whole. This should be a key consideration when choosing aquaculture probiotics suppliers.