As the most diverse vertebrate group and a major component of a growing global aquaculture industry, teleosts continue to attract significant scientific attention. The growth in global aquaculture, driven by declines in wild stocks, has provided additional empirical demand, and thus opportunities, to explore teleost diversity. Among key developments is the recent growth in microbiome exploration, facilitated by advances in high-throughput sequencing technologies. Here, we consider studies on teleost gut microbiomes in the context of sustainable aquaculture, which we have discussed in four themes: diet, immunity, artificial selection and closed-loop systems. We demonstrate the influence aquaculture has had on gut microbiome research, while also providing a road map for the main deterministic forces that influence the gut microbiome, with topical applications to aquaculture. Functional significance is considered within an aquaculture context with reference to impacts on nutrition and immunity. Finally, we identify key knowledge gaps, both methodological and conceptual, and propose promising applications of gut microbiome manipulation to aquaculture, and future priorities in microbiome research. These include insect-based feeds, vaccination, mechanism of pro- and prebiotics, artificial selection on the hologenome, in-water bacteriophages in recirculating aquaculture systems (RAS), physiochemical properties of water and dysbiosis as a biomarker.

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The role of the gut microbiome in sustainable teleost aquaculture.

Microorganisms play a crucial and unique role in fish and fish product safety. The presence of human pathogens and the formation of histamine caused by spoilage bacteria make the control of both pathogenic and spoilage microorganisms critical for fish product safety. To provide a comprehensive and updated overview of the involvement of microorganisms in fish and fish product safety, this paper reviewed outbreak and recall surveillance data obtained from government agencies from 1998 to 2018 and identified major safety concerns associated with both domestic and imported fish products. The review also summarized all available literature about the prevalence of major and emerging microbial safety concerns, including Salmonella spp., Listeria monocytogenes, and Aeromonas hydrophila, in different fish and fish products and the survival of these pathogens under different storage conditions. The prevalence of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs), two emerging food safety concerns, is also reviewed. Pathogenic and spoilage microorganisms as well as ARB and ARGs can be introduced into fish and fish products in both preharvest and postharvest stages. Many novel intervention strategies have been proposed and tested for the control of different microorganisms on fish and fish products. One key question that needs to be considered when developing and implementing novel control measures is how to ensure that the measures are cost and environment friendly as well as sustainable. Over the years, regulations have been established to provide guidance documents for good farming and processing practices. To be more prepared for the globalization of the food chain, harmonization of regulations is still needed.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/1541-4337.12671

The microbial safety of fish and fish products: Recent advances in understanding its significance, contamination sources, and control strategies.

Probiotics for Preventing Ventilator-Associated Pneumonia

Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.

Antimicrobial Peptides: An Update on Classifications and Databases

The microbiome of the host and its surroundings play a vital role in its health and well-being Unlike the terrestrial organisms that maternally acquire its microbiome, the aquatic species mainly get colonized by the microorganisms in its aquatic surrounding and are exposed to a wide variety of microbial community based on the type of aquatic environment the host inhabits This review is focused on the aquaculture and shrimp microbiome and factors that influence its microbiome such as prebiotics, probiotics, synbiotics, diet, stress conditions, frequency and type of antibiotics used, host physiological conditions and developmental stages This review also casts light on the role of the microbiome in enhancing the shrimp health, immune response, microbial colonization, and the effects of the biofloc system on shrimp and aquaculture microbiome Moreover, beneficial microbes can be a safer alternative to harmful antibiotics used in aquaculture, which can thereby prevent the emergence of superbugs and also enhance the production rate A proper understanding of the interactions between the host and its microbiome can help us to modulate and manipulate the aquaculture microbiome to enhance the health of aquatic organisms, which ensures the growth of the aquaculture industry Therefore, the treatment strategies should be targeted towards the modulation of shrimp and aquaculture microbiome, which acts as beneficial partners to overcome the challenges confronted by the aquaculture sector

Healthy microbiome: a key to successful and sustainable shrimp aquaculture

Fish gut microbiome confers various effects to the host fish; this includes overall size, metabolism, feeding behaviour and immune response in the fish. The emergence of antimicrobial-resistant (AMR) bacteria and hard to cure fish diseases warrant the possible utilization of gut microbes that exhibits a positive effect on the fish and thus lead to the usage of these microbes as probiotics. The widespread and systematic use of antibiotics has led to severe biological and ecological problems, especially the development of antibiotic resistance that affects the gut microbiota of aquatic organisms. Probiotics are proposed as an effective and environmentally friendly alternative to antibiotics, known as beneficial microbes. At the same time, prebiotics are considered beneficial to the host's health and growth by decreasing the prevalence of intestinal pathogens and/or changing the development of bacterial metabolites related to health. Uprise of sequencing technology and the development of intricate bioinformatics tools has provided a way to study these gut microbes through metagenomic analysis. From various metagenomic studies, ample of information was obtained; such information includes the effect of the gut microbiome on the physiology of fish, gut microbe composition of different fish, factors affecting the gut microbial composition of the fish and the immunological effect of gut microbes in fish; such this information related to the fish gut microbiome, their function and their importance in aquaculture is discussed in this review.

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Gut microbiota metagenomics in aquaculture: factors influencing gut microbiome and its physiological role in fish

Antimicrobial peptides (AMPs) are short molecules produced by almost all organisms. Fish AMPs contain innate immune components as their primary immune molecules. The fish AMPs include piscidins, hepcidins, defensins, cathelicidins and histone-derived peptides. Piscidin is potent and broad-spectrum; this peptide was conserved among Acanthopterygii superorder and is therapeutically important among other AMPs. It was present mainly in the tissues of gills, muscle, head-kidney, skin and intestine of teleost. Piscidin AMP family includes piscidin, moronecidin, pleurocidin, epinecidin, gaduscidin, misgurin, dicentracin, chrysophsin and myxinidin. This review reports the structural properties of various piscidin and their mode of action as it is important to know their mechanism how the peptide involved in antimicrobial activity. In addition, the gene expression of piscidin which influenced the immune responses, their pharmaceutical importance and biological applications were described. Overall, the review explains a broad spectrum of knowledge on piscidin, its classes and types, structure, cytotoxicity, membrane permeabilization, properties and therapeutical implications.

Praveen Kumar

Papers

Gut microbiota metagenomics in aquaculture: factors influencing gut microbiome and its physiological role in fish

Piscidin, Fish Antimicrobial Peptide: Structure, Classification, Properties, Mechanism, Gene Regulation and Therapeutical Importance