Understanding the role of the shrimp gut microbiome in health and disease.

Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment.

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

The microbiome actually deals with micro-organisms that are associated with indigenous body parts and the entire gut system in all animals, including human beings. These microbes are linked with roles involving hereditary traits, defence against diseases and strengthening overall immunity, which determines the health status of an organism. Considerable efforts have been made to find out the microbiome diversity and their taxonomic identification in finfish and shellfish and its importance has been correlated with various physiological functions and activities. In recent past due to the availability of advanced molecular tools, some efforts have also been made on DNA sequencing of these microbes to understand the environmental impact and other stress factors on their genomic structural profile. There are reports on the use of next-generation sequencing (NGS) technology, including amplicon and shot-gun approaches, and associated bioinformatics tools to count and classify commensal microbiome at the species level. The microbiome present in the whole body, particularly in the gut systems of finfish and shellfish, not only contributes to digestion but also has an impact on nutrition, growth, reproduction, immune system and vulnerability of the host fish to diseases. Therefore, the study of such microbial communities is highly relevant for the development of new and innovative bio-products which will be a vital source to build bio and pharmaceutical industries, including aquaculture. In recent years, attempts have been made to discover the chemical ingredients present in these microbes in the form of biomolecules/bioactive compounds with their functions and usefulness for various health benefits, particularly for the treatment of different types of disorders in animals. Therefore, it has been speculated that microbiomes hold great promise not only as a cure for ailments but also as a preventive measure for the number of infectious diseases. This kind of exploration of new breeds of microbes with their miraculous ingredients will definitely help to accelerate the development of the drugs, pharmaceutical and other biological related industries. Probiotic research and bioinformatics skills will further escalate these opportunities in the sector. In the present review, efforts have been made to collect comprehensive information on the finfish and shellfish microbiome, their diversity and functional properties, relationship with diseases, health status, data on species-specific metagenomics, probiotic research and bioinformatics skills. Further, emphasis has also been made to carry out microbiome research on priority basis not only to keep healthy environment of the fish farming sector but also for the sustainable growth of biological related industries, including aquaculture.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/jpn.13619

Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview.

Phosphorus and nitrogen removal by a novel phosphate-accumulating organism, Arthrobacter sp. HHEP5 capable of heterotrophic nitrification-aerobic denitrification: Safety assessment, removal characterization, mechanism exploration and wastewater treatment.

Microorganisms play crucial roles in nutrient cycling, water quality maintenance, and farmed animal health. Increasing evidences have revealed a close association between unstable microbial environments and disease occurrences in aquaculture. Thereupon, we used high-throughput sequencing technology to comprehensively compare the bacterial communities of water, sediment, and intestine in mariculture ponds at the middle and late stages of Litopenaeus vannamei farming and analyzed whether changes of their microbiota assemblages were associated with environmental factors and shrimp physiological health. Results showed that bacterial community structures were significantly distinct among water, sediment, and intestine; meanwhile, the relative abundances of intestinal dominant taxa were significantly changed between different rearing stages. Compared with intestine and water, shrimp intestine and sediment had a similar profile of the dominant bacterial genera by cluster analysis, and the observed species, diversity indexes, and shared OTUs of bacterial communities in intestine and sediment were simultaneously increased after shrimp were farmed for 90 days. These results reflected a closer relationship between microbiotas in sediment and intestine, which was further proved by nonmetric multidimensional scaling analysis. However, bacterial communities in water, sediment, and intestine responded differently to environmental variables by redundancy and correlation analysis. More importantly, shrimp physiological parameters were closely associated with bacterial variations in the gut and/or ambient, especially the gut microbiota owning significantly high levels of predicted functional pathways involved in disease emergence. These findings may greatly add to our understanding of the microbiota characteristics of the shrimp pond ecosystem and the complex interactions among shrimp, ambient microflora, and environmental variables.

Microbiota assemblages of water, sediment, and intestine and their associations with environmental factors and shrimp physiological health

Aims The present study aimed to reveal microbial relationship between shrimp intestine and ambient in higher place shrimp ponds from the aspects of composition and function. Methods and results Metagenome and 16S rRNA gene sequencing were used to compare microbial compositions and functions of water, effluent and shrimp intestine in higher place Litopenaeus vannamei ponds. Although the three groups had similar dominant phyla, such as Proteobacteria, Bacteroidetes and Tenericutes, their bacterial compositions at the genus level were obviously different. Compared to effluent and intestine, the relative abundance of Vibrio as common opportunistic pathogen for shrimp was significantly higher in water. However, cluster analysis showed that intestinal microbial composition was more similar to that of effluent than water. Metagenomic data showed that the predominant microbial functions in the three groups were mostly related to energy production and biosynthesis, while carbohydrate metabolism was relatively enriched in intestinal microbiota. More importantly, Proteobacteria played a critical role in carbon metabolism and biosynthesis of amino acids in the three habitats, and Vibrio had the most functions related to bacterial virulence and infection. Conclusions Shrimp intestinal microbiota had a close correlation with the ambient microbiota in both structure and function. As the most dominant phylum, Proteobacteria was very important for microbiota communication and nutrient cycling in higher place shrimp ponds. Moreover, due to the pathogenicity, it was necessary to monitor the abundant changes of Vibrio in water to decrease the risk of shrimp disease outbreaks. Significance and impact of the study These above results may be helpful to comprehensively understand the characteristics and functions of microbiota in higher place shrimp ponds, thereby providing basic information for developing the management strategies of entire microbiota to sustain shrimp health.

Metagenomic comparison of structure and function of microbial community between water, effluent and shrimp intestine of higher place Litopenaeus vannamei ponds

Microbial fermentation is an efficient, economical and eco-friendly approach to overcome the limitations in soybean meal replacement of fish meal in aquaculture. However, little research focused on the development of shrimp-derived strains for fermentation of SBM. In this study, Bacillus sanfensis (SQVG18) and Bacillus stratosphericus (SQVG22) were screened from shrimp intestine for fermentation according to the activities of protease, cellulase and phytase. The optimized fermentation conditions of SQVG18 and SQVG22 were as follow: fermentation temperature (40°C vs 35°C), fermentation time (48h both), inoculation amount [4% both (v/m)], solid-liquid ratio [1:1.2 vs 1:1 (g/ml)]. After 48 h fermentation, SQVG18 and SQVG22 increased crude protein content by 6.93% and 5.95%, respectively; degraded most of macromolecular proteins to micromolecular proteins (< 20 kDa); improved amino acids profiles, like lysine and methionine in particular; significantly decreased the anti-nutritional factors such as trypsin inhibitor, glycinin and β-conglycinin (P < 0.05). In addition, both strains were observed no hemolytic activity, less antibiotic resistance genes and definite inhibition to common shrimp pathogens of Vibrio alginolyticus sp. and Vibrio parahaemolyticus sp. These results indicated that both strains could improve nutrition values of soybean meal effectively and have potential applications in shrimp culture.

Screening of bacterial strains from the gut of Pacific White Shrimp (Litopenaeus vannamei) and their efficiencies in improving the fermentation of soybean meal

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Microbiota assemblages of water, sediment, and intestine and their associations with environmental factors and shrimp physiological health

Metagenomic comparison of structure and function of microbial community between water, effluent and shrimp intestine of higher place Litopenaeus vannamei ponds

Screening of bacterial strains from the gut of Pacific White Shrimp (Litopenaeus vannamei) and their efficiencies in improving the fermentation of soybean meal