Indigenous bacterial flora play a critical role in the lives of their vertebrate hosts. In human and mouse models it is increasingly clear that innate and adaptive immunity develop in close consort with the commensal microbiome. Furthermore several aspects of digestion and nutrient metabolism are governed by intestinal microflora. Research on teleosts has responded relatively slowly to the revolution in microbiomics. Nonetheless, progress has been made in biotic and gnotobiotic zebrafish models, defining a core microbiome and describing its role in development. However, microbiome research in other teleost species, especially those important from an aquaculture perspective, has been relatively slow. In this review, we examine progress in teleost microbiome research to date. We discuss teleost microbiomes in health and disease, microbiome ontogeny, prospects for successful microbiome manipulation (especially in an aquaculture setting) and attempt to identify important future research themes. We predict an explosion in research in this sector in line with the increasing global demand for fish protein, and the need to find sustainable approaches to improve aquaculture yield. The reduced cost and increasing ease of next generation sequencing technologies provides the technological backing, and the next 10 years will be an exciting time for teleost microbiome research.

Along with the intensification of culture systems to meet the increasing global demands, there was an elevated risk for diseases outbreak and substantial loss for farmers. In view of several drawbacks caused by prophylactic administration of antibiotics, strict regulations have been established to ban or minimize their application in aquaculture. As an alternative to antibiotics, dietary administration of feed additives has received increasing attention during the past three decades. Probiotics, prebiotics, synbiotics and medicinal plants were among the most promising feed supplements for control or treatments of bacterial, viral and parasitic diseases of fish and shellfish. The present review summarizes and discusses the topic of potential application of probiotics as a means of disease control with comprehensive look at the available literature. The possible mode of action of probiotics (Strengthening immune response, competition for binding sites, production of antibacterial substances, and competition for nutrients) in providing protection against diseases is described. Besides, we have classified different pathogens and separately described the effects of probiotics as protective strategy. Furthermore, we have addressed the gaps of existing knowledge as well as the topics that merit further investigations. Overall, the present review paper revealed potential of different probiont to be used as protective agent against various pathogens.

In fish, like other organisms, the lack of balance between the production of reactive oxygen species (ROS) and antioxidant defense system (so-called oxidative stress) can cause DNA hydroxylation, protein denaturation, lipid peroxidation, apoptosis, and ultimately cell damage. To improve the antioxidant defense capability, different approaches such as the administration of synthetic antioxidants were practiced. During the past years, dietary approaches have been suggested as a promising way of increasing the antioxidant defense activity in different fish and shellfish species. Among them, microbial feed additives (including pre-, pro-, and synbiotics) showed promising effects in terms of affecting antioxidant enzymes activities. Their mechanism of action in influencing the antioxidant system is not fully understood. The present review briefly discussed the antioxidant defense activity in fish, influencing factors with special focus on dietary approaches and microbial feed additives. In addition, the proposed mechanism of action of microbial feed additives on the antioxidant system has been discussed.

A complex and dynamic community of microorganisms, play important roles within the fish gastrointestinal (GI) tract. Of the bacteria colonizing the GI tract, are lactic acid bacteria (LAB) generally considered as favorable microorganism due to their abilities to stimulating host GI development, digestive function, mucosal tolerance, stimulating immune response, and improved disease resistance. In early finfish studies, were culture-dependent methods used to enumerate bacterial population levels within the GI tract. However, due to limitations by using culture methods, culture-independent techniques have been used during the last decade. These investigations have revealed the presence of Lactobacillus, Lactococcus, Leuconostoc, Enterococcus, Streptococcus, Carnobacterium, Weissella, and Pediococcus as indigenous species. Numerous strains of LAB isolated from finfish are able to produce antibacterial substances toward different potential fish pathogenic bacteria as well as human pathogens. LAB are revealed be the most promising bacterial genera as probiotic in aquaculture. During the decade numerous investigations are performed on evaluation of probiotic properties of different genus and species of LAB. Except limited contradictory reports, most of administered strains displayed beneficial effects on both, growth—and reproductive performance, immune responses and disease resistance of finfish. This eventually led to industrial scale up and introduction LAB-based commercial probiotics. Pathogenic LAB belonging to the genera Streptococcus, Enterococcus, Lactobacillus, Carnobacterium, and Lactococcus have been detected from ascites, kidney, liver, heart, and spleen of several finfish species. These pathogenic bacteria will be addressed in present review which includes their impacts on finfish aquaculture, possible routes for treatment. Finfish share many common structures and functions of the immune system with warm-blooded animals, although apparent differences exist. This similarity in the immune system may result in many shared LAB effects between finfish and land animals. LAB-fed fish show an increase in innate immune activities leading to disease resistances: neutrophil activity, lysozyme secretion, phagocytosis, and production of pro-inflammatory cytokines (IL-1β, IL-6, IL-8, and TNF-α). However, some LAB strains preferentially induces IL-10 instead, a potent anti-inflammatory cytokine. These results indicate that LAB may vary in their immunological effects depending on the species and hosts. So far, the immunological studies using LAB have been focused on their effects on innate immunity. However, these studies need to be further extended by investigating their involvement in the modulation of adaptive immunity. The present review paper focuses on recent findings in the field of isolation and detection of LAB, their administration as probiotic in aquaculture and their interaction with fish immune responses. Furthermore, the mode of action of probiotics on finfish are discussed.

Species of Bacillus are spore-forming bacteria that are resistant to aggressive physical and chemical conditions, with various species showing unusual physiological features enabling them to survive in various environmental conditions including fresh waters, marine sediments, desert sands, hot springs, Arctic soils, and the gastrointestinal tract of finfish and shellfish. They are able to rapidly replicate and tolerate a multitude of environmental conditions, giving a wide range of beneficial effects in the aquaculture sector. Application of Bacillus spp. as probiotics in feed or for bioremediation of aquaculture rearing water has great potential for sustainable aquaculture. Species of Bacillus may play a desirable role in removing waste products from aquaculture environments, maintaining optimum water quality, and reducing stress, which can lead to an improved immuno-physiological balance, better growth and enhanced survival in target aquatic animals. Application of probiotic Bacillus spp. can enhance growth and immune function of aquatic organisms. Probiotic Bacillus can also assist in maintaining a higher density of beneficial bacteria and a lower load of pathogenic agents in aquaculture ponds. Much is still unknown, however, about how the probiotic efficacy of specific Bacillus species is affected by different aquatic animal species, age and growth condition, water quality, and diet. Also, the details of mode of actions of Bacillus spp. on the immune-physiological functions of aquatic organisms as well as their functions as bioremediators of water quality need further studies. This review addresses the presence of Bacillus spp. in the gastrointestinal tract of finfish and shellfish, their ability to produce enzymes and antibacterial compounds, and their efficacy and potency as probiotics in aquaculture.