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Beneficial microorganisms maintain the ecosystems, plants, animals and humans working in healthy conditions. In nature, around 95% of all microorganisms produce beneficial effects by increasing nutrients digestion and assimilation, preventing pathogens development and by improving environmental parameters. However, increase in human population and indiscriminate uses of antibiotics have been exerting a great pressure on agriculture, livestock, aquaculture, and also to the environment. This pressure has induced the decomposition of environmental parameters and the development of pathogenic strains resistant to most antibiotics. Therefore, all antibiotics have been restricted by corresponding authorities; hence, new and healthy alternatives to prevent or eliminate these pathogens need to be identified. Thus, probiotic bacteria utilization in aquaculture systems has emerged as a solution to prevent pathogens development, to enhance nutrients assimilation and to improve environmental parameters. In this sense, B. subtilis is an ideal multifunctional probiotic bacterium, with the capacity to solve these problems and also to increase aquaculture profitability.

Aquaculture contributes more than one-third of the animal protein from marine sources worldwide. A significant proportion of aquaculture products are derived from marine protostomes that are commonly referred to as ‘marine invertebrates’. Among them, penaeid shrimp (Ecdysozosoa, Arthropoda) and bivalve molluscs (Lophotrochozoa, Mollusca) are economically important. Mass rearing of arthropods and molluscs causes problems with pathogens in aquatic ecosystems that are exploited by humans. Remarkably, species of corals (Cnidaria) living in non-exploited ecosystems also suffer from devastating infectious diseases that display intriguing similarities with those affecting farmed animals. Infectious diseases affecting wild and farmed animals that are present in marine environments are predicted to increase in the future. This paper summarizes the role of the main pathogens and their interaction with host immunity, with a specific focus on antimicrobial peptides (AMPs) and pathogen resistance against AMPs. We provide a detailed review of penaeid shrimp AMPs and their role at the interface between the host and its resident/pathogenic microbiota. We also briefly describe the relevance of marine invertebrate AMPs in an applied context. This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.

Biofloc (BF) stands out as a promising system for sustainable shrimp farming. Optimizing various culture conditions, such as stocking density, carbohydrate source, and feeding management, is crucial for the widespread adoption of the BF system. This study compares the growth performance of white-leg shrimp ( Litopenaeus vannamei ) in culture ponds at low density (LD) with 50 organisms/m 2 and high density (HD) with 200 organisms/m 2 . Post-larvae of white-leg shrimp were stocked for 16 weeks in both LD and HD groups. The LD group exhibited a superior survival rate, growth rate, and feed consumption compared to the HD group. The BF from the LD system recorded a significantly higher protein content (16.63 ± 0.21%) than the HD group (15.21 ± 0.34%). Heterotrophic bacterial counts in water did not significantly differ with stocking density. However, Vibrio count in water samples was higher in the HD group (3.59 ± 0.35 log CFU/mL) compared to the LD group (2.45 ± 0.43 log CFU/mL). The whole shrimp body analysis revealed significantly higher protein and lipid content in the LD group. In contrast, the total aerobic bacterial count in shrimp from the HD group was high, with the identification of Salmonella enterica ssp. arizonae . Additionally, Vibrio counts in shrimp samples were significantly higher in the HD group (4.63 ± 0.32 log CFU/g) compared to the LD group (3.57 ± 0.22 log CFU/g). The expression levels of immune-associated genes, including prophenoloxidase, transglutaminase, penaiedin 3, superoxide dismutase, lysozyme, serine proteinase, and the growth-related gene ras-related protein ( rap-2a ), were significantly enhanced in the LD group. Conversely, stress-related gene expression increased significantly in the HD group. Hepatopancreases amylase, lipase, and protease were higher in the LD group, while trypsin activity did not differ significantly. Antioxidant enzyme activity (catalase, glutathione, glutathione peroxidase, and superoxide dismutase) significantly increased in the LD group. The histological structure of hepatopancreas, musculature, and female gonads remained similar in both densities. However, negative effects were observed in the gills' histology of the HD group. These results suggest that increasing stocking density is associated with significantly negative biological, microbial, and physiological effects on white-leg shrimp under the BF system.

Increasing evidence has revealed a close association between intestinal bacterial communities and human health. However, given that host phylogeny shapes the composition of intestinal microbiota, it is unclear whether changes in intestinal microbiota structure in relation to shrimp health status. In this study, we collected shrimp and seawater samples from ponds with healthy and diseased shrimps to understand variations in bacterial communities among habitats (water and intestine) and/or health status. The bacterial communities were clustered according to the original habitat and health status. Habitat and health status constrained 14.6 and 7.7 % of the variation in bacterial communities, respectively. Changes in shrimp intestinal bacterial communities occurred in parallel with changes in disease severity, reflecting the transition from a healthy to a diseased state. This pattern was further evidenced by 38 bacterial families that were significantly different in abundance between healthy and diseased shrimps; moderate changes were observed in shrimps with sub-optimal health. In addition, within a given bacterial family, the patterns of enrichment or decrease were consistent with the known functions of those bacteria. Furthermore, the identified 119 indicator taxa exhibited a discriminative pattern similar to the variation in the community as a whole. Overall, this study suggests that changes in intestinal bacterial communities are closely associated with the severity of shrimp disease and that indicator taxa can be used to evaluate shrimp health status.

Penaeus monodon is a major marine aquaculture species; however, production intensification has increased water-quality deterioration and disease pressure. Copper-loaded montmorillonite (Cu-MMT) is a functional clay additive with adsorption and antimicrobial properties, yet the optimal application mode remains unclear. We compared a control (KZ), water application (PZ), and dietary inclusion (BZ) of Cu-MMT in P. monodon. BZ was associated with higher survival and a numerically higher specific growth rate, whereas final body weight did not differ among treatments. Antioxidant status improved in BZ, with higher catalase (CAT) and total superoxide dismutase (T-SOD) activities (both p < 0.05). Hepatopancreas RNA-seq identified 949 differentially expressed genes (DEGs) for KZ vs. PZ and 814 DEGs for KZ vs. BZ. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that PZ was enriched for redox processes, transporter activity, and amino-acid biosynthesis—indicative of a stress-defense state—whereas BZ was enriched for proteolysis, endoplasmic-reticulum protein processing, and proteasome pathways, consistent with an anabolic, protein-quality-control–oriented mode. Intestinal 16S rRNA profiling indicated higher diversity and reduced putative pathogens in BZ. Overall, dietary Cu-MMT is the preferred application, shifting shrimp from an energy-consuming stress response to efficient anabolism and thereby improving performance and survival.

Invertebrates rely on innate immunity, including humoral and cellular immunity, to resist pathogenic infection. Previous studies showed that forkhead box transcription factor O (FOXO) participates in mucosal immune responses of mammals and the gut humoral immune regulation of invertebrates. However, whether FOXO is involved in systemic and cellular immunity regulation in invertebrates remains unknown. In the present study, we identified a FOXO from shrimp ( Marsupenaeus japonicus) and found that it was expressed at relatively basal levels in normal shrimp, but was upregulated significantly in shrimp challenged by Vibrio anguillarum . FOXO played a critical role in maintaining hemolymph and intestinal microbiota homeostasis by promoting the expression of Relish , the transcription factor of the immune deficiency (IMD) pathway for expression of antimicrobial peptides (AMPs) in shrimp. We also found that pathogen infection activated FOXO and induced its nuclear translocation by reducing serine/threonine kinase AKT activity. In the nucleus, activated FOXO directly regulated the expression of its target Amp and Relish genes against bacterial infection. Furthermore, FOXO was identified as being involved in cellular immunity by promoting the phagocytosis of hemocytes through upregulating the expression of the phagocytotic receptor scavenger receptor C ( Src ), and two small GTPases, Rab5 and Rab7 , which are related to phagosome trafficking to the lysosome in the cytoplasm. Taken together, our results indicated that FOXO exerts its effects on homeostasis of hemolymph and the enteric microbiota by activating the IMD pathway in normal shrimp, and directly or indirectly promoting AMP expression and enhancing phagocytosis of hemocytes against pathogens in bacteria-infected shrimp. This study revealed the different functions of FOXO in the mucosal (local) and systemic antibacterial immunity of invertebrates.

Vitamin E (tocopherols, VE) is a lipid-soluble antioxidant involved in neutralizing reactive oxygen species and maintaining immune function in animals. This study aimed to determine the optimum dietary VE requirement of juvenile Pacific white shrimp ( Penaeus vannamei ) for growth, feed utilization, immune responses, antioxidative capacity, diet digestibility, intestinal histomorphology and disease resistance against Vibrio parahaemolyticus . Eight experimental diets were formulated to contain graded levels of VE (0, 20, 40, 60, 80, 100, 120 and 240 mg/kg; designated as VE0, VE20, VE40, VE60, VE80, VE100, VE120 and VE240). Four replicate groups, each containing 30 shrimp (0.20 ± 0.04 g), were fed one of the diets six times daily for 56 days. Shrimp fed VE80 diet exhibited significantly increased growth performance compared to shrimp fed VE0, VE20 and VE240 diets. Non-specific immune responses were significantly enhanced in shrimp fed VE60-VE80 diets. Hepatopancreatic lipid peroxidation in VE80 group was significantly lower compared to the VE0 group. The expression of Crustin , C-MnSOD and GPx genes in the hepatopancreas was significantly upregulated in VE80 group. Graded dietary VE levels significantly linearly increased hemolymph and hepatopancreas VE concentrations. Intestinal villi height and width were significantly improved with dietary VE supplementation. The digestibility of protein, lipid and dry matter was significantly higher in shrimp fed VE80 diet compared to those fed VE0 diet. The resistance against V. parahaemolyticus was significantly higher in shrimp fed VE80, VE100 and VE120 diets compared to those fed VE0 and VE20 diets. The optimal dietary VE level for Pacific white shrimp was estimated to be 72.17 mg/kg for weight gain and 72.21 mg/kg specific growth rate, based on broken-line analysis. In conclusion, optimal dietary VE supplementation enhances shrimp growth, immunity, antioxidative defense and disease resistance against V. parahaemolyticus , thereby reducing the risk of early mortality syndrome caused by acute hepatopancreatic necrosis disease.

Increasing evidence indicates that dysbiosis in the gut microbiota contributes to disease pathogenesis. However, whether certain taxa are universally indicative of diverse shrimp diseases is unclear thus far. We conducted a meta-analysis to explore the divergences in gut microbiota between healthy and diseased shrimp. The gut bacterial communities of healthy shrimp varied significantly (P < 0.05 in each comparison) over ontogenetic stages, and were distinct from the corresponding diseased cohorts at each life stage. Both phylogenetic-based mean nearest taxon distance analysis and multivariate dispersion testing revealed that shrimp disease weakened the relative importance of deterministic processes in governing the gut microbiota. Partitioning beta diversity analysis indicated that temporal turnover governed the gut microbiota as healthy shrimp aged, whereas this trend was retarded in disease cohorts, concurrent with an increased nestedness. After ruling out the age-discriminatory and disease-specific orders, a high diagnosed accuracy (85.9%) of shrimp health status was achieved by using the profiles of the 11 universal disease-discriminatory orders as independent variables. These findings improve current understanding of how disease alters the ecological processes that govern the shrimp gut microbiota assembly, and exemplifies the potential application of universal bacterial signatures to diagnose the incidence of diverse shrimp diseases, irrespective of causal pathogens.

Background Recently, increasing evidence supports that some complex diseases are not attributed to a given pathogen, but dysbiosis in the host intestinal microbiota (IM). The full intestinal ecosystem alterations, rather than a single pathogen, are associated with white feces syndrome (WFS), a globally severe non-infectious shrimp disease, while no experimental evidence to explore the causality. Herein, we conducted comprehensive metagenomic and metabolomic analysis, and intestinal microbiota transplantation (IMT) to investigate the causal relationship between IM dysbiosis and WFS. Results Compared to the Control shrimp, we found dramatically decreased microbial richness and diversity in WFS shrimp. Ten genera, such as Vibrio , Candidatus Bacilloplasma, Photobacterium , and Aeromonas , were overrepresented in WFS, whereas 11 genera, including Shewanella , Chitinibacter , and Rhodobacter were enriched in control. The divergent changes in these populations might contribute the observation that a decline of pathways conferring lipoic acid metabolism and mineral absorption in WFS. Meanwhile, some sorts of metabolites, especially lipids and organic acids, were found to be related to the IM alteration in WFS. Integrated with multiomics and IMT, we demonstrated that significant alterations in the community composition, functional potentials, and metabolites of IM were closely linked to shrimp WFS. The distinguished metabolites which were attributed to the IM dysbiosis were validated by feed-supplementary challenge. Both homogenous selection and heterogeneous selection process were less pronounced in WFS microbial community assembly. Notably, IMT shrimp from WFS donors eventually developed WFS clinical signs, while the dysbiotic IM can be recharacterized in recipient shrimp. Conclusions Collectively, our findings offer solid evidence of the causality between IM dysbiosis and shrimp WFS, which exemplify the ‘microecological Koch’s postulates’ (an intestinal microbiota dysbiosis, a disease) in disease etiology, and inspire our cogitation on etiology from an ecological perspective. FQ9SoidJJGxv1orPr3YvZs Video abstract

Increasing evidence has revealed a close interplay between the gut bacterial communities and host growth performance. However, until recently, studies generally ignored the contribution of eukaryotes, endobiotic organisms. To fill this gap, we used Illumina sequencing technology on eukaryotic 18S rRNA gene to compare the structures of gut eukaryotic communities among cohabitating retarded, overgrown, and normal shrimp obtained from identically managed ponds. Results showed that a significant difference between gut eukaryotic communities differed significantly between water and intestine and among three shrimp categories. Structural equation modeling revealed that changes in the gut eukaryotic community were positively related to digestive enzyme activities, which in turn influenced shrimp growth performance ( λ  = 0.97, P  < 0.001). Overgrown shrimp exhibited a more complex and cooperative gut eukaryotic interspecies interaction than retarded and normal shrimp, which may facilitate their nutrient acquisition efficiency. Notably, the distribution of dominant eukaryotic genera and shifts in keystone species were closely concordant with shrimp growth performance. In summary, this study provides an integrated overview on direct roles of gut eukaryotic communities in shrimp growth performance instead of well-studied bacterial assembly.