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

Preliminary investigation on the effect of Vibrio splendidus stimulation on the intestinal flora of Strongylocentrotus intermedius

To better understand the effect of Vibrio splendidus infection on Strongylocentrotus intermedius, 16S rRNA sequencing was carried out to investigate the intestinal flora of S. intermedius stimulated by 0 CFU/mL (Con), 1.5 × 107 CFU/mL (Vib1) and 1.5 × 108 CFU/mL (Vib2) concentrations of V. splendidus. The results showed that there was significant difference in intestinal flora diversity between Con group and Vib1 group, but no significant difference between Con group and Vib2 group. However, there were significant differences in the composition of intestinal flora among all groups. Bacteroidota, Proteobacteria and Firmicutes were the dominant phylum in the Con group. The abundance of Bacteroidota and Firmicutes decreased and Proteobacteria increased in Vib1 and Vib2 groups. The relative abundance of the potential probiotic bacteria Muribaculaceae and Alloprevotella was significantly lower in the Vib1 and Vib2 groups. In addition, the opportunistic pathogen Desulfovibrio was found in Vib1 and Vib2 groups. It is evident that V. splendidus infection not only alters the composition of the microbial community in the intestinal tract of S. intermedius, but may also lead to the production of opportunistic pathogens, which could be potentially harmful to the health of S. intermedius. The results of this study provide a foundation for exploring the diseases caused by V. splendidus stimulation leading to an imbalance in the intestinal flora of S. intermedius, and contribute to our further understanding of the role of Vibrio on the health of S. intermedius.

Effects of antibacterial peptides from Brevibacillus texasporus on growth performance, meat quality and gut health of cultured largemouth bass (Micropterus salmoides)

The aim of this study was to investigate the effects of antibacterial peptides from Brevibacillus texasporus (BT) on the growth performance, meat quality and gut health of cultured largemouth bass (Micropterus salmoides). Largemouth bass (36.17 ± 1.52 g) were divided into 2 groups and each group was fed with diets supplemented with or without 200 ppm of BT peptides for 130 days. The results showed that BT peptides had no significant influences on growth performance and body indexes, but significantly enhanced total antioxidant capacity and lysozyme content in the serum. Moreover, digestive enzymes activities and intestinal villous height were also prominently increased. From meat quality aspect, no significant differences were found in nutritional components, amino acid composition, fatty acid composition and texture property, except the values of hardness, gumminess and γ-linolenic acid (C18:3n6) were remarkably increased after BT peptides intervention. Finally, the results of gut microbiota and short chain fatty acids revealed that BT peptides significantly decreased the relative abundances of harmful bacteria such as genus Acinetobacter and Pseudomonas, and increased the production of short chain fatty acids. In conclusion, this study confirmed that BT peptides could be used to improve the health of largemouth bass, which provided novel insights into the application of antimicrobial peptides in aquacultures.

Effects of essential amino acids supplementation in a low-protein diet on growth performance, intestinal health and microbiota of juvenile blotched snakehead (Channa maculata)

Developing a low-protein feed is important for the sustainable advancement of aquaculture. The aim of this study was to investigate the effects of essential amino acid (EAA) supplementation in a low-protein diet on the growth, intestinal health, and microbiota of the juvenile blotched snakehead, Channa maculata in an 8-week trial conducted in a recirculating aquaculture system. Three isoenergetic diets were formulated to include a control group (48.66 % crude protein (CP), HP), a low protein group (42.54 % CP, LP), and a low protein supplementation EAA group (44.44 % CP, LP-AA). The results showed that significantly lower weight gain (WG), specific growth rate (SGR), protein efficiency ratio (PER), and feed efficiency ratio (FER) were observed in fish that were fed LP than in the HP and LP-AA groups (P < 0.05). The HP and LP-AA groups exhibited a significant increase in intestinal villus length, villus width, and muscular thickness compared to the LP group (P < 0.05). Additionally, the HP and LP-AA groups demonstrated significantly higher levels of intestinal total antioxidant capacity (T-AOC), catalase (CAT), and superoxide dismutase (SOD) and lower levels of malondialdehyde (MDA) compared to the LP group (P < 0.05). The apoptosis rate of intestinal cells in the LP group was significantly higher than those in the LP and HP groups (P < 0.05). The mRNA expression levels of superoxide dismutase (sod), nuclear factor kappa B p65 subunit (nfκb-p65), heat shock protein 70 (hsp70), and inhibitor of NF-κBα (iκba) in the intestine were significantly higher in the LP group than those in the HP and LP-AA groups (P < 0.05). The 16s RNA analysis indicated that EAA supplementation significantly increased the growth of Desulfovibrio and altered the intestinal microflora. The relative abundances of Firmicutes and Cyanobacteria were positively correlated with antioxidant parameters (CAT and T-AOC), whereas Desulfobacterota was negatively correlated with sod and T-AOC. The genera Bacillus, Bacteroides, and Rothia were associated with the favorable maintenance of gut health. In conclusion, dietary supplementation with EAAs to achieve a balanced amino acid profile could potentially reduce the dietary protein levels from 48.66 % to 44.44 % without adversely affecting the growth and intestinal health of juvenile blotched snakeheads.

A comprehensive review on the utilization of probiotics in aquaculture towards sustainable shrimp farming

Probiotics in shrimp aquaculture have gained considerable attention as a potential solution to enhance production efficiency, disease management, and overall sustainability. Probiotics, beneficial microorganisms, have shown promising effects when administered to shrimp as dietary supplements or water additives. Their inclusion has been linked to improved gut health, nutrient absorption, and disease resistance in shrimp. Probiotics also play a crucial role in maintaining a balanced microbial community within the shrimp pond environment, enhancing water quality and reducing pathogen prevalence. This article briefly summarizes the many ways that probiotics are used in shrimp farming and the advantages that come with them. Despite the promising results, challenges such as strain selection, dosage optimization, and environmental conditions are carefully addressed for successful probiotic integration in shrimp aquaculture. The potential of probiotics as a sustainable and ecologically friendly method of promoting shrimp development and health while advancing environmentally friendly shrimp farming techniques is highlighted in this analysis. Further research is required to fully exploit probiotics' benefits and develop practical guidelines for their effective implementation in shrimp aquaculture.

Exploring the Efficacy of Pellitorine as an Antiparasitic Agent Against Argulus: Impacts on Antioxidant Levels and Immune Responses in Goldfish (Carassius auratus)

INTRODUCTION

Argulus spp. infestation is a significant challenge for aquaculture, currently, there are no approved medications available to efficiently manage this parasite. Consequently, mechanical removal of parasites using forceps and natural substances like herbs are being explored as alternative treatment methods. Pellitorine (PLE) is a naturally occurring compound found in several plant species. It is classified as an alkaloid and belongs to the class of compounds known as amides.

MATERIALS AND METHODS

This study aimed to evaluate the effectiveness of PLE in preventing Argulus spp. infestations in goldfish (Carassius auratus) and to determine the optimal dosage of PLE for the detachment of Argulus spp.

RESULTS

The findings of this study revealed that PLE enhanced the immune response of goldfish by promoting superoxide dismutase (SOD) and catalase (CAT) in Argulus-infected goldfish. Additionally, PLE induces reactive oxygen species (ROS) generation and cellular damage in the Argulus. PLE at a dosage of 5 mg/mL was able to detach 80% of the argulus from goldfish within 12 h. Therapeutic index was found to be 5.99, suggesting that PLE is the safest drug.

CONCLUSIONS

Therefore, our findings suggest that PLE can be a suitable and effective treatment option for preventing Argulus infestations in goldfish. The results of this study can guide the use of PLE at an optimal dosage to control Argulus infestation in goldfish.

Polystyrene microplastics interaction and influence on the growth kinetics and metabolism of tilapia gut probiotic Bacillus tropicus ACS1

Gut probiotic bacteria play a significant role in the host health, immunity, and survival. In aquaculture, changes in the gut microbiome of fishes affect the overall productivity and product quality. In the scenario of growing plastic pollution and associated microplastic prevalence, the current study was designed to investigate the interactions and impact of prepared polystyrene microplastics (PS-MPs) of irregular surface morphology on a probiotic bacteria Bacillus tropicus ACS1, isolated from the gut of Oreochromis mossambicus (commonly called as Tilapia). The cell viability was significantly increased along with changes in bacterial growth kinetics upon exposure to varying concentrations of PS-MPs. The microplastic exposure also increased the production of exopolysaccharides (EPS) and induced slight changes in the IR spectra of the EPS. A peak representing a carbonyl linkage that could be attributed to the glycosidic linkages between sugars disappeared following exposure to higher concentrations of PS-MPs. The interaction between the bacteria and the microplastics was visualized using scanning electron microscopy (SEM) and the colonization of the bacteria with active biofilm formation was observed. The investigation of PS-MP induced oxidative stress in the bacteria revealed the generation of reactive oxygen species (ROS) and increase in anti-oxidant enzyme concentrations, superoxide dismutase (SOD), and catalase. The study provides new insights into the effect of microplastics on gut probiotics of an economically significant aquaculture species.

Impacts of pyraclostrobin on intestinal health and the intestinal microbiota in common carp (Cyprinus carpio L.)

Pyraclostrobin (PYR) is a strobilurin fungicide that is commonly used in agriculture, and its use in agriculture may lead to an increase in its residue in the aquatic environment and may have a deleterious influence on the intestinal health of aquatic creatures. Here, common carp were chronically exposed to PYR (0, 0.5, or 5.0 μg/L) for 30 d to determine its effect on the physical and immunological barrier and intestinal microbiota in the intestine. PYR exposure caused significant histological changes; altered the mRNA expression levels of occludin, claudin-2, and zonula occludens-1 (ZO-1); induced oxidative stress in the common carp intestine; and increased the serum D-lactate and diamine oxidase (DAO) levels. Moreover, PYR significantly increased the protein expression levels of tumour necrosis factor alpha (TNF-α), interleukin 1 beta (IL-1β), and IL-6 while decreasing the level of transforming growth factor beta (TGF-β). Further studies revealed that PYR significantly reduced lysozyme (LZM) and acid phosphatase (ACP) activities as well as complement 3 (C3) and immunoglobulin M (IgM) levels. Furthermore, PYR decreased gut microbial diversity while increasing the abundance of pathogenic bacteria such as Aeromonas and Shewanella, causing an intestinal microbial disturbances in common carp. These results imply that PYR has a negative impact on fish intestinal health and may pose serious health risks to fish by disrupting the intestinal microbiota, physical barrier, and immunological barrier in common carp.

Impaired intestinal immunity and microbial diversity in common carp exposed to cadmium

Waterborne cadmium (Cd) accumulates in the fish intestine and causes irreversible toxicity by disrupting intestinal immunity and microbial diversity. To explore the toxicity of environmentally available high Cd concentration on intestinal immunity and microbial diversity of fish, we selected the widely used bioindicator model species, Common carp (Cyprinus carpio). Literature review and Cd pollution data supported sequential doses of 0.2, 0.4, 0.8, 1.6, 3.2, and 6.4 mg/L Cd for 30 days. Based on intestinal tissue Cd accumulation, previous studies, and environmentally available Cd data, 0.4 and 1.6 mg/L Cd were selected for further studies. Intestinal Cd bioaccumulation increased significantly to ~100 times in fish exposed to 1.6 mg/L Cd. We observed villous atrophy, increased goblet cells with mucus production, muscularis erosion, and thickened lamina propria due to intense inflammatory cell infiltration in the intestine at this Cd concentration. Cd-induced immunosuppression occurred with increased lysozyme, alkaline phosphate (AKP), and acid phosphate (ACP). High levels of catalase (CAT), total antioxidant capacity (T-AOC), malondialdehyde (MDA), and hydrogen peroxide (H2O2) suggested induced oxidative stress and poor metabolism by α-amylase and lipase suppression for Cd toxicity. Proteobacteria (41.2 %), Firmicutes (21.8 %), and Bacteroidetes (17.5 %) were the dominant bacterial phyla in the common carp intestine. Additionally, potential pathogenic Cyanobacteria increased in Cd-treated fish. The decrease of beneficiary bacteria like Aeromonas, and Cetobacterium indicated Cd toxicity. Overall, these findings indicate harmful consequences of high Cd concentration in the intestinal homeostasis and health status of fish.

Seaweed and Seaweed-Based Functional Metabolites as Potential Modulators of Growth, Immune and Antioxidant Responses, and Gut Microbiota in Fish

Seaweed, also known as macroalgae, represents a vast resource that can be categorized into three taxonomic groups: Rhodophyta (red), Chlorophyta (green), and Phaeophyceae (brown). They are a good source of essential nutrients such as proteins, minerals, vitamins, and omega-3 fatty acids. Seaweed also contains a wide range of functional metabolites, including polyphenols, polysaccharides, and pigments. This study comprehensively discusses seaweed and seaweed-derived metabolites and their potential as a functional feed ingredient in aquafeed for aquaculture production. Past research has discussed the nutritional role of seaweed in promoting the growth performance of fish, but their effects on immune response and gut health in fish have received considerably less attention in the published literature. Existing research, however, has demonstrated that dietary seaweed and seaweed-based metabolite supplementation positively impact the antioxidant status, disease resistance, and stress response in fish. Additionally, seaweed supplementation can promote the growth of beneficial bacteria and inhibit the proliferation of harmful bacteria, thereby improving gut health and nutrient absorption in fish. Nevertheless, an important balance remains between dietary seaweed inclusion level and the resultant metabolic alteration in fish. This review highlights the current state of knowledge and the associated importance of continued research endeavors regarding seaweed and seaweed-based functional metabolites as potential modulators of growth, immune and antioxidant response, and gut microbiota composition in fish.

Dietary Bacillus cereus LS2 protects juvenile sea cucumber Apostichopus japonicus against Vibrio splendidus infection

This study aimed to investigate the effects of Bacillus cereus LS2 on the growth performance, innate immunity, intestinal microbiota, and disease resistance of sea cucumber Apostichopus japonicus. After feeding with LS2 for 30 days, results showed that dietary with LS2 had a significant improvement in the growth rate and immune parameters (including total coelomocytes counts, phagocytosis, respiratory burst, and immune-related enzymes) of juvenile sea cucumbers. Subsequently, transcriptome sequencing and qRT-PCR verification were performed to analyze the potential mechanism of LS2 diet and thus improve the immune response of A. japonicus. GO and KEGG pathway analysis indicated that LS2 can primarily activate the "Lectins" and "complement and coagulation cascades" pathways to modulate the innate immunity of the sea cucumbers. Furthermore, 16S rRNA sequencing was used to analyze the intestinal microbial composition of sea cucumbers after dietary with LS2. Results showed that Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the most prevalent phyla in A. japonicus intestinal microbiota. The abundance of Actinobacteria (46.20%) and Bacteroidetes (12.80%) were significantly higher in the LS2 group, whereas the relative abundance of Proteobacteria (49.98%) and Firmicutes (14.97%) were higher in the control group. The LDA scores of Nocardiaceae and Rhodococcus were also the highest taxa after the dietary administration of LS2, indicating that Actinobacteria phylum played a pivotal role in the intestinal microbial function of A. japonicus. Overall, these results suggested that feeding with Bacillus LS2 may be beneficial for A. japonicus farming.

Effects of plant-derived protein and rapeseed oil on growth performance and gut microbiomes in rainbow trout

BACKGROUND

Rainbow trout (Oncorhynchus mykiss) is becoming popular with the increased demand for fish protein. However, the limited resources and expense of fish meal and oil have become restrictive factors for the development of the rainbow trout related industry. To solve this problem, plant-derived proteins and vegetable oils have been developed as alternative resources. The present study focuses on evaluating the effects of two experimental diets, FMR (fish meal replaced with plant-derived protein) and FOR (fish oil replaced with rapeseed oil), through the alteration of the gut microbiota in triploid rainbow trout. The commercial diet was used in the control group (FOM).

RESULTS

Amplicon sequencing of the 16S and 18S rRNA genes was used to assess the changes in gut bacteria and fungi. Our analysis suggested that the α-diversity of both bacteria and fungi decreased significantly in the FMR and FOR groups, and β-diversity was distinct between FOM/FMR and FOM/FOR based on principal coordinate analysis (PCoA). The abundance of the Planctomycetota phylum increased significantly in the FMR group, while that of Firmicutes and Bacteroidetes decreased. We also found that the fungal phylum Ascomycota was significantly increased in the FMR and FOR groups. At the genus level, we found that the abundance of Citrobacter was the lowest and that of pathogenic Schlesneria, Brevundimonas, and Mycoplasma was highest in the FMR and FOR groups. Meanwhile, the pathogenic fungal genera Verticillium and Aspergillus were highest in the FMR and FOR groups. Furthermore, canonical correspondence analysis (CCA) and network analysis suggested that the relatively low-abundance genera, including the beneficial bacteria Methylobacterium, Enterococcus, Clostridium, Exiguobacterium, Sphingomonas and Bacteroides and the fungi Papiliotrema, Preussia, and Stachybotrys, were positively correlated with plant protein or rapeseed oil. There were more modules that had the above beneficial genera as the hub nodes in the FMR and FOR groups.

CONCLUSIONS

Our study suggested that the FMR and FOR diets could affect the gut microbiome in rainbow trout, which might offset the effects of the dominant and pathogenic microbial genera. This could be the underlying mechanism of explaining why no significant difference was observed in body weight between the different groups.

The impact of microplastics on bivalve mollusks: A bibliometric and scientific review

Bivalves are important members of the ecosystem and their populations are declining globally, making them a concern for their role in ecosystem services and the fishing industry. Bivalves are excellent bioindicators of MPs pollution due to their widespread distribution, filtering capabilities, and close association with human health. Microplastics (MPs) have direct and indirect impacts on bivalves, affecting their physiology, habitat structure, food sources, and persistence of organic pollutants. This review provides an extensive overview of the impact of MPs on bivalves, covering various aspects such as their economic significance, ecological roles, and importance in biomonitoring environmental quality. The article presents the current state of knowledge on the sources and pathways of MPs in aquatic environments and their effects on bivalves. The mechanisms underlying the effects of MPs on bivalves, including ingestion, filtration activity, feeding inhibition, accumulation, bioaccumulation, and reproduction, are also discussed. Additionally, a bibliometric analysis of research on MPs in bivalves is presented, highlighting the number of papers, geographical distribution, and keyword clusters relating to MPs. Finally, the review emphasizes the importance of ongoing research and the development of mitigation strategies to reduce the negative effects of MPs pollution on bivalves and their habitats in oceans and coastal waters.

One Health and Global Health View of Antimicrobial Susceptibility through the "Eye" of Aeromonas: Systematic Review and Meta-Analysis

Antimicrobial resistance (AMR) is one of the most pressing public health concerns; therefore, it is imperative to advance our understanding of the factors influencing AMR from Global and One Health perspectives. To address this, Aeromonas populations were identified using 16S rRNA gene libraries among human, agriculture, aquaculture, drinking water, surface water, and wastewater samples, supporting its use as indicator bacteria to study AMR. A systematic review and meta-analysis was then performed from Global and One Health perspectives, including data from 221 articles describing 15 891 isolates from 57 countries. The interconnectedness of different environments was evident as minimal differences were identified between sectors among 21 different antimicrobials. However, resistance to critically important antibiotics (aztreonam and cefepime) was significantly higher among wastewater populations compared with clinical isolates. Additionally, isolates from untreated wastewater typically exhibited increased AMR compared with those from treated wastewater. Furthermore, aquaculture was associated with increased AMR to ciprofloxacin and tetracycline compared with wild-caught seafood. Using the World Health Organization AWaRe classifications, countries with lower consumption of "Access" compared to "Watch" drugs from 2000 to 2015 demonstrated higher AMR levels. The current analysis revealed negative correlations between AMR and anthropogenic factors, such as environmental performance indices and socioeconomic standing. Environmental health and sanitation were two of the environmental factors most strongly correlated with AMR. The current analysis highlights the negative impacts of "Watch" drug overconsumption, anthropogenic activity, absence of wastewater infrastructure, and aquaculture on AMR, thus stressing the need for proper infrastructure and global regulations to combat this growing problem.

Microplastics in feed cause sublethal changes in the intestinal microbiota and a non-specific immune response indicator of the freshwater crayfish Procambarus clarkii (Decapoda: Cambaridae)

Microplastics (MP) are a hazardous pollutant of global concern that threatens aquatic ecosystems and public health. We used the invasive, cosmopolitan, and environmentally versatile red swamp crayfish Procambarus clarkii as a model to study the effects of MP on the intestinal microbiome. Crayfish collected from the environment were compared with specimens exposed to recycled Polyethylene terephthalate (rPET) MP in feed (30%) for 96 h in the laboratory and a control group. We analyzed the 16S rRNA of the intestinal bacteria by PCR-DGGE and high-throughput sequencing. MP exposure caused dysbiosis of the intestinal microbiota, with an increase in Alphaproteobacteria and Actinobacteria. We detected higher abundance of opportunistic genera such as Klebsiella, Acinetobacter, Hydromonas, Pseudomonas, Gemmobacter, and Enterobacter on MP fed organisms. Moreover, MP exposure reduced the abundance of Clostridia and Bateroidetes, which are important for immune system development and pathogen prevention. Furthermore, MP exposure decreased the phenoloxidase (PO) immune response in crayfish. There was a significant difference in the richness of intestinal bacterial communities after consumption of food contaminated with MP, likely increasing the abundance of opportunistic bacteria in the intestinal microbiota. Our results suggest that MP alter the gut microbial composition and impair the health of P. clarkii.

Microbiomes in the context of developing sustainable intensified aquaculture

With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in "closed" aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture.

The Gut Microbiota of Farmed and Wild Brook Trout (Salvelinus fontinalis): Evaluation of Feed-Related Differences Using 16S rRNA Gene Metabarcoding

The gut microbiota has become a topic of increasing importance in various fields, including aquaculture. Several fish species have been the subject of investigations concerning the intestinal microbiota, which have compared different variables, including the intestinal portions, the environment, and diet. In this study, the microbiota of farmed and wild brook trout (Salvelinus fontinalis) were analyzed, in which the wall and content of the medial portion of the intestine were considered separately. A total of 66 fish (age class 2+) were sampled, of which 46 were wild and 20 were farmed brook trout, in two different years. Microbiota data were obtained using a 16S metabarcoding approach by analyzing the V3-V4 hypervariable regions of the corresponding 16S rRNA. The data showed that the core microbiota of these species consist of Proteobacteria (Alpha- and Gammaproteobacteria), Actinobacteria, Firmicutes (Bacilli and Clostridia), and, only for farmed animals, Fusobacteria. The latter taxon's presence is likely related to the fishmeal-based diet administered to farmed brook trout. Indeed, alpha and beta diversity analysis showed differences between wild and farmed fish. Finally, statistically significant differences in the microbiota composition were observed between the intestinal walls and contents of wild fish, while no differences were detected in reared animals. Our work represents the first study on the intestinal microbiota of brook trout with respect to both farmed and wild specimens. Future studies might focus on the comparison of our data with those pertaining to other fish species and on the study of other portions of the brook trout intestine.

Dietary administration of a postbiotic, heat-killed Pediococcus pentosaceus PP4012 enhances growth performance, immune response and modulates intestinal microbiota of white shrimp, Penaeus vannamei

The efficacy of postbiotics on the immune-related gene expression and gut microbiota of white shrimp (Penaeus vannamei) remains unexplored. A commercial heat-killed postbiotic Pediococcus pentosaceus PP4012 was used to evaluate the growth performance, intestinal morphology, immunological status, and microbial community of white shrimp after dietary administration in this study. White shrimp (0.040 ± 0.003 g) were divided into three treatments; a control, inanimate P. pentosaceus (10⁵ CFU g feed^-1) at low concentration (IPL) and inanimate P. pentosaceus (10⁶ CFU g feed^-1) at high concentrations (IPH). The diets of IPL and IPH significantly increased final weight, specific growth rate and production compared to the control group. Shrimp fed with IPL and IPH significantly utilized feed more efficiently than those fed the control diet. The IPH treatment significantly lowered the cumulative mortality rate compared to the control and IPL diet following Vibrio parahaemolyticus infection. No significant difference was observed for Vibrio-like and lactic acid bacteria in intestine of shrimp fed with the control diet and the experimental diets. Adding inanimate P. pentosaceus significantly improved immune responses such as lysozyme and phagocytic activity compared to the control group. However, the total hemocyte count, phenoloxidase activity, respiratory burst, and superoxide dismutase were not significantly different among treatments. The immune-related genes alf, pen3a, and pen4 expression were significantly higher in shrimp fed IPL diet compared with control and IPH. Taxonomic identification of bacterial genera in all dietary groups belonged to two predominant phyla, Proteobacteria and Bacteroidota. An abundance of Photobacterium, Motilimonas, Litorilituus, and Firmicutes bacterium ZOR0006 were identified in the intestine of shrimp fed postbiotic diets. Unique microbes such as Cohaesibacter was discovered in the shrimp fed IPL while Candidatus Campbellbacteria, uncultured Verrucomicrobium DEV114 and Paenalcaligenes were discovered in the intestines of shrimp fed IPH diet. Collectively, these data suggest that including heat-killed P. pentosaceus, particularly IPH, can enhance growth performance, promote microbial diversity, elevate immune responses, and increase shrimp's resistance to V. parahaemolyticus.

Sustainable Fish Feeds with Insects and Probiotics Positively Affect Freshwater and Marine Fish Gut Microbiota

Aquaculture is the fastest-growing agricultural industry in the world. Fishmeal is an essential component of commercial fish diets, but its long-term sustainability is a concern. Therefore, it is important to find alternatives to fishmeal that have a similar nutritional value and, at the same time, are affordable and readily available. The search for high-quality alternatives to fishmeal and fish oil has interested researchers worldwide. Over the past 20 years, different insect meals have been studied as a potential alternate source of fishmeal in aquafeeds. On the other hand, probiotics-live microbial strains-are being used as dietary supplements and showing beneficial effects on fish growth and health status. Fish gut microbiota plays a significant role in nutrition metabolism, which affects a number of other physiological functions, including fish growth and development, immune regulation, and pathogen resistance. One of the key reasons for studying fish gut microbiota is the possibility to modify microbial communities that inhabit the intestine to benefit host growth and health. The development of DNA sequencing technologies and advanced bioinformatics tools has made metagenomic analysis a feasible method for researching gut microbes. In this review, we analyze and summarize the current knowledge provided by studies of our research group on using insect meal and probiotic supplements in aquafeed formulations and their effects on different fish gut microbiota. We also highlight future research directions to make insect meals a key source of proteins for sustainable aquaculture and explore the challenges associated with the use of probiotics. Insect meals and probiotics will undoubtedly have a positive effect on the long-term sustainability and profitability of aquaculture.

Relationship of environmental factors in pond water and dynamic changes of gut microbes of sea bass Lateolabrax japonicus

The effect of structure of gut microbes on the health of host has attracted increasing attention. Sea bass Lateolabrax japonicus is an important farmed fish in China. The relationship of the dynamic changes of intestinal bacterial communities in L. japonicus and the cultural water environment is very important for healthy culture. Here, the diversity and abundance of the gut microbial communities of L. japonicus were evaluated during the culture using 16S rRNA Illumina sequencing. Both the opportunistic pathogens Aeromonas (1.68%), Vibrio (1.59%), and Acinetobacter (1.22%); and the potential probiotics Lactobacillus (2.27%), Bacillus (1.16%), and Lactococcus (0.37%) were distributed in the gut of L. japonicus. The increasing concentration of nitrogen of water environments with the increase of culture time significantly correlated with shifts in the microbial community structure: 40.04% of gut microbial changes due to nitrogen concentration. Higher concentrations of nitrogen showed a significantly negative correlation with intestinal probiotics in L. japonicus. The results indicate that the abundance of intestinal bacteria of L. japonicus is mainly driven by the changes of environmental factors (e.g., nitrogen), and it’s very important that the linking environmental parameters with bacterial data of guts could be used as an early warning indicator in L. japonicus heath culture.

Host-microbiome interaction in fish and shellfish: An overview

The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.

Effects of Dietary Supplementation with Bacillus amyloliquefaciens US573 on Intestinal Morphology and Gut Microbiota of European Sea Bass

Probiotics or direct-fed microbials (DFM) have proven strong potential for improving aquaculture sustainability. This study aims to evaluate the effects of dietary supplementation with the DFM Bacillus amyloliquefaciens US573 on growth performance, intestinal morphology, and gut microbiota (GM) of European sea bass. For this purpose, healthy fish were divided into two feeding trials in triplicate of 25 fish in each tank. The fish were fed with a control basal diet or a DFM-supplemented diet for 42 days. Results showed that, while no significant effects on growth performance were observed, the length and abundance of villi were higher in the DFM-fed group. The benefic effects of DFM supplementation included also the absence of cysts formation and the increase in number of goblet cells playing essential role in immune response. Through DNA metabarcoding analysis of GM, 5 phyla and 14 major genera were identified. At day 42, the main microbiome changes in response to B. amyloliquefaciens US573 addition included the significant decrease in abundance of Actinobacteria phylum that perfectly correlates with a decrease in Nocardia genus representatives which represent serious threat in marine and freshwater fish. On the contrary, an obvious dominance of Betaproteobacteria associated with the abundance in Variovorax genus members, known for their ability to metabolize numerous substrates, was recorded. Interestingly, Firmicutes, particularly species affiliated to the genus Sporosarcina with recent promising probiotic potential, were identified as the most abundant. These results suggest that B. amyloliquefaciens US573 can be effectively recommended as health-promoting DFM in European sea bass farming.

Molluscs-A ticking microbial bomb

Bivalve shellfish consumption (ark shells, clams, cockles, and oysters) has increased over the last decades. Following this trend, infectious disease outbreaks associated with their consumption have been reported more frequently. Molluscs are a diverse group of organisms found wild and farmed. They are common on our tables, but unfortunately, despite their great taste, they can also pose a threat as a potential vector for numerous species of pathogenic microorganisms. Clams, in particular, might be filled with pathogens because of their filter-feeding diet. This specific way of feeding favors the accumulation of excessive amounts of pathogenic microorganisms like Vibrio spp., including Vibrio cholerae and V. parahaemolyticus, Pseudomonas aeruginosa, Escherichia coli, Arcobacter spp., and fecal coliforms, and intestinal enterococci. The problems of pathogen dissemination and disease outbreaks caused by exogenous bacteria in many geographical regions quickly became an unwanted effect of globalized food supply chains, global climate change, and natural pathogen transmission dynamics. Moreover, some pathogens like Shewanella spp., with high zoonotic potential, are spreading worldwide along with food transport. These bacteria, contained in food, are also responsible for the potential transmission of antibiotic-resistance genes to species belonging to the human microbiota. Finally, they end up in wastewater, thus colonizing new areas, which enables them to introduce new antibiotic-resistance genes (ARG) into the environment and extend the existing spectrum of ARGs already present in local biomes. Foodborne pathogens require modern methods of detection. Similarly, detecting ARGs is necessary to prevent resistance dissemination in new environments, thus preventing future outbreaks, which could threaten associated consumers and workers in the food processing industry.

Exploring the interactions between the gut microbiome and the shifting surrounding aquatic environment in fisheries and aquaculture: A review

The rise of "new" sequencing technologies and the development of sophisticated bioinformatics tools have dramatically increased the study of the aquaculture microbiome. Microbial communities exist in complex and dynamic communities that play a vital role in the stability of healthy ecosystems. The gut microbiome contributes to multiple aspects of the host's physiological health status, ranging from nutritional regulation to immune modulation. Although studies of the gut microbiome in aquaculture are growing rapidly, the interrelationships between the aquaculture microbiome and its aquatic environment have not been discussed and summarized. In particular, few reviews have focused on the potential mechanisms driving the alteration of the gut microbiome by surrounding aquatic environmental factors. Here, we review current knowledge on the host gut microbiome and its interrelationship with the microbiome of the surrounding environment, mainly including the main methods for characterizing the gut microbiome, the composition and function of microbial communities, the dynamics of microbial interactions, and the relationship between the gut microbiome and the surrounding water/sediment microbiome. Our review highlights two potential mechanisms for how surrounding aquatic environmental factors drive the gut microbiome. This may deepen the understanding of the interactions between the microbiome and environmental factors. Lastly, we also briefly describe the research gaps in current knowledge and prospects for the future orientation of research. This review provides a framework for studying the complex relationship between the host gut microbiome and environmental stresses to better facilitate the widespread application of microbiome technologies in fisheries and aquaculture.

Composition and distribution of bacterial communities and antibiotic resistance genes in fish of four mariculture systems

Fish-related antibiotic resistance genes (ARGs) have attracted attention for their potentially harmful effects on food safety and human health through the food chain transfer. However, the potential factors affecting these ARGs have not been fully explored. In this study, ARGs and bacterial communities in the fish gut, mucosal skin, and gill filaments in fish were comprehensively evaluated in four different mariculture systems formed by hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), Gracilaria bailinae, and Litopenaeus vannamei using different combinations. The results showed that 9 ARGs were detected in the gut and mucosal skin and 6 ARGs in the gill filaments. The detection rate of aphA1 was the highest, and the abundance was 1.91 × 10^-3 - 6.30 × 10^-2 copies per 16 S rRNA gene. Transposase gene (tnpA-04) was detected in all samples with the abundance of 3.57 × 10^-3 - 3.59 × 10^-2 copies per 16 S rRNA gene, and was strongly correlated with multiple ARGs (e.g., aphA1, tet(34), mphA-02). Proteobacteria, Deinococcus-Thermus, Firmicutes, and Bacteroidetes were the dominant phyla in the four mariculture systems, accounting for 65.1%-96.2% of the total bacterial community. Notably, the high relative abundance of Stenotrophomonas, a potential human pathogen, was elevated by 20.5% in the hybrid grouper gut in the monoculture system. In addition, variation partitioning analysis (VPA) showed that the difference in bacterial communities between mariculture systems was the main driving factor of ARGs distribution differences in hybrid groupers. This study provides a new comprehensive understanding of the characterization of fish-related ARGs contamination in different mariculture systems and facilitates the assessment of potential risks of ARGs and pathogen taxa to human health.

Characterization of Gut Microbiome in the Mud Snail Cipangopaludina cathayensis in Response to High-Temperature Stress

Simple Summary

This study investigated the effects of high-temperature stress on the intestinal microbiome of Cipangopaludina cathayensis. High-temperature exposure significantly changed the intestinal microbiota structure of C. cathayensis. The relative abundance of putatively beneficial bacteria decreased, whereas the relative abundance of putatively pathogenic bacteria increased after thermal stress. Consistent with the trends of change in the intestinal microbiota, the high-temperature treatment inhibited some carbohydrate metabolism pathways and induced certain disease-related pathways. Thermal stress disrupts the homeostasis of gut microbiota, which may lead to disease outbreak in C. cathayensis.

Abstract

The mud snail Cipangopaludina cathayensis is a widely distributed species in China. Particularly in Guangxi province, mud snail farming contributes significantly to the economic development. However, global warming in recent decades poses a serious threat to global aquaculture production. The rising water temperature is harmful to aquatic animals. The present study explored the effects of high temperature on the intestinal microbiota of C. cathayensis. Snail intestinal samples were collected from the control and high-temperature groups on days 3 and 7 to determine the gut microbiota composition and diversity. Gut bacterial community composition was investigated using high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA genes. Our results suggested that thermal stress altered the gut microbiome structure of C. cathayensis. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes were dominant in C. cathayensis gut microbiota. The T2 treatment (32 ± 1 °C, day 7) significantly decreased the relative abundance of Firmicutes, Actinobacteria, and Deinococcus-Thermus. In T2, the abundance of several genera of putatively beneficial bacteria (Pseudomonas, Aeromonas, Rhodobacter, and Bacteroides) decreased, whereas the abundance of Halomonas—a pathogenic bacterial genus—increased. The functional prediction results indicated that T2 treatment inhibited some carbohydrate metabolism pathways and induced certain disease-related pathways (e.g., those related to systemic lupus erythematosus, Vibrio cholerae infection, hypertrophic cardiomyopathy, and shigellosis). Thus, high temperature profoundly affected the community structure and function of C. cathayensis gut microbiota. The results provide insights into the mechanisms associated with response of C. cathayensis intestinal microbiota to global warming.

Effects of cadmium exposure on intestinal microflora of Cipangopaludina cathayensis

As one of the most environmentally toxic heavy metals, cadmium (Cd) has attracted the attention of researchers globally. In particular, Guangxi, a province in southwestern China, has been subjected to severe Cd pollution due to geogenic processes and anthropogenic activities. Cd can be accumulated in aquatic animals and transferred to the human body through the food chain, with potential health risks. The aim of the present study was to explore the effects of waterborne Cd exposure (0.5 mg/L and 1.5 mg/L) on the intestinal microbiota of mudsnail, Cipangopaludina cathayensis, which is favored by farmers and consumers in Guangxi. Gut bacterial community composition was investigated using high-throughput sequencing of the V3–V4 segment of the bacterial 16S rRNA gene. Our results indicated that C. cathayensis could tolerate low Cd (0.5 mg/L) stress, while Cd exposure at high doses (1.5 mg/L) exerted considerable effects on microbiota composition. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in the mudsnail gut microbiota. The relative abundances of Bacteroidetes increased significantly under high Cd exposure (H14) (p < 0.01), with no significant change in the low Cd exposure (L14) treatment. The dominant genera with significant differences in relative abundance were Pseudomonas, Cloacibacterium, Acinetobacter, Dechloromonas, and Rhodobacter. In addition, Cd exposure could significantly alter the pathways associated with metabolism, cellular processes, environmental information processing, genetic information processing, human diseases, and organismal systems. Notably, compared to the L14 treatment, some disease-related pathways were enriched, while some xenobiotic and organic compound biodegradation and metabolism pathways were significantly inhibited in the H14 group. Overall, Cd exposure profoundly influenced community structure and function of gut microbiota, which may in turn influence C. cathayensis gut homeostasis and health.