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

Unveiling the Characteristics of Microbiota in Different Mucosal Layers of Leopard Coral Grouper (Plectropomus leopardus)

Mucosal microbiomes play an important role in digestion, nutrition, and resistance to pathogens and toxins in fish; thus, characterizing the mucosal microbiomes of economically important fish species is paramount. In this study, mucosal microbiomes of healthy leopard coral grouper (Plectropomus leopardus), which is of economic importance worldwide, were systematically analyzed and compared by using 16S rRNA amplicon sequencing. The analysis of alpha-diversity and beta-diversity revealed significant differences in the structure and composition of the microbial community between different mucosal layers of P. leopardus. The skin microbiota showed the lowest microbial diversity among the three tissues, and the highest interindividual variability within gill groups was observed. Proteobacteria is the dominant phylum of the gut, skin, and gill microbiomes. Microbial biomarkers of the three mucosal tissues were identified, with the genera Parvibaculum, Aminobacter, Sphingobium, and Ralstonia for skin; Mesoflavibacter, Winogradskyella, Malaciobacter, Nautella, and Marinobacterium for gills; and Cetobacterium, Photobacterium, and Vibrio for gut. These genera were also the core microorganisms in each tissue. A large number of identical pathways of the three mucosal surfaces microbiome (e.g., pathways related to metabolism, human diseases, genetic/environmental information processing) and some specifically enriched pathways in each tissue were identified. Co-occurrence network analysis revealed that there were more ecological communities and higher functional diversity in the gill microbiota, and the interactions between gut microbiota are closer and more stable. Our study provides a new perspective for a comprehensive understanding of the mucosal microbiota of P. leopardus, contributing to an in-depth exploration of the interaction between fish and microorganisms, and may help to predict potential disease outbreaks, thus promoting the development of the fish farming industry.

Harnessing the fish gut microbiome and immune system to enhance disease resistance in aquaculture

The increasing global reliance on aquaculture is challenged by disease outbreaks, exacerbated by antibiotic resistance, and environmental stressors. Traditional strategies, such as antibiotic treatments and chemical interventions, are becoming less effective, necessitating a shift toward microbiota-based disease control. The fish gut microbiome is a key determinant of immune homeostasis and pathogen resistance. However, previous reviews lack integration of microbiome engineering, machine learning, and next-generation sequencing in fish health strategies. This review encompasses recent advancements in microbiome research, including dietary strategies such as prebiotics, probiotics, synbiotics, and phytogenic feed additives. It synthesizes the latest metagenomic insights, microbiota modulation techniques, and AI-driven disease prediction models. It presents a novel conceptual framework for disease control using microbiome-based approaches in aquaculture. Additionally, we explore emerging methodologies, including microbiota transplantation and synthetic probiotics, to develop precision microbiome interventions. By bridging existing knowledge gaps, this review provides actionable insights into sustainable aquaculture practices through microbiome-driven disease resistance.

The influence of dietary maize starch levels on growth, immunity, liver health, and intestinal microbiota of juvenile Asian red-tailed catfish (Hemibagrus wyckioides)

The effects of starch on fish are species-dependent. The present study aimed to explore effects of dietary maize starch on growth, hepatopancreas health, and intestinal microbiota in juvenile Asian red-tailed catfish, Hemibagrus wyckioides. A total of 450 catfish with an average initial weight of approximately 23.97 ± 0.04 g were randomly assigned to five dietary treatments named as CK (0 %), C8 (8 %), C16 (16 %), C24 (24 %), and C32 (32 %), containing corresponding levels of maize starch. Weight gain, serum acid phosphatase and alkaline phosphatase activities, as well as the levels of complement components 3, components 4, and immunoglobulin M, increased linearly with rising dietary starch levels (P < 0.05), reaching the highest values in the C32 group. A linear increase in hepatosomatic index was observed with increasing dietary starch levels (P < 0.05). Hepatocellular vacuolation and elevated lipid droplet accumulation were evident in the C32 group. Serum concentrations of triglycerides, cholesterol, alanine aminotransferase, and aspartate aminotransferase were significantly elevated in the C24 and C32 compared to CK and C8 groups, and exhibited a positive linear relationship with dietary starch levels (P < 0.05). Compared with the CK group, dietary starch supplementation in the C16 and C32 groups significantly altered gut microbial composition. The C16 and C32 diets increased the relative abundances of Cetobacterium and Lactococcus, shifted microbial metabolism toward carbohydrate and nucleotide pathways, and reduced microbial diversity and network complexity, while enhancing competitive interactions within the community. In contrast, The CK diet favored amino acid and nitrogen metabolism. Collectively, a 32 % starch level supported optimal growth and improved immune responses in H. wyckioides, the risk of hepatic lipid accumulation highlights the need for longer-term studies to assess potential health implications.

Effects of Short-Term Feeding with Diets Containing Insect Meal on the Gut Microbiota of African Catfish Hybrids

The impact of short-term feeding of three distinct diets containing insect meals on the intestinal microbiota of African catfish hybrid (Clarias gariepinus × Heterobranchus longifilis) juveniles was examined. The animals received experimental diets containing 30% insect meals derived from black soldier-fly larvae (BSL) (Hermetia illucens), yellow mealworm (Tenebrio molitor) or blue bottle-fly larvae (Calliphora vicina) for 18 days. The relative abundance of the Bacillaceae, the Planococcaceae and other bacteria significantly increased (p < 0.05) in the intestinal microbiota of the BSL group and also in the pooled group of the three catfish groups that received insect meals. Several strains of the Bacillales cultured from BSL feed had higher (p < 0.05) abundance in the intestinal microbiota of the BSL group compared to those of the control group. Among these Bacillales strains, a single fosB antibiotic resistance gene was identified. In the gut resistomes of both the BSL and the control catfish groups, the tetA(P), tetB(P) and lnu(C) antibiotic-resistance determinants were detected, while fosB was detected only in the BSL group. Overall, the study showed that a short-term shift to diets containing insect meals can induce significant (q < 0.05) changes in the gut microbiota of the African catfish without the development of reduced α-diversity and without the overgrowth of bacteria pathogenic to fish.

Interactions of erythromycin and an antibiotic mixture with the gut microbiome of juvenile rainbow trout

Erythromycin (ERY) is a commonly used antibiotic found in wastewater effluents and the environment globally. Due to the bioactivity by which they kill and prevent bacterial growth, ERY and other antibiotics may have significant unwanted impacts on the gut microbiome of fishes. The overall objective of this project was to assess effects on the gut microbiome in response to exposure to ERY alone or in a mixture with other common antibiotics, which was accomplished in two experiments. The objectives of experiment 1 as a pilot study were to understand uptake and depuration of ERY in juvenile rainbow trout (RBT) over a 7-d exposure to three concentrations of ERY followed by a 7-d depuration period. Furthermore, throughout the study changes in gut microbiome were assessed. In experiment 2, an identical experimental design was used to assess the effects of a mixture of antibiotics containing, in addition to ERY, 100 μg/g each of ampicillin, metronidazole, and ciprofloxacin. In that study, three matrices were analyzed, with gut collected for 16S rRNA metabarcoding, blood plasma for non-targeted metabolomics, and brain tissue for mRNA-seq analysis. ERY was relatively quickly depurated from fish and gut microbiome dysbiosis was observed at 7 d after exposure, with a slight recovery after the 7-d depuration period. A greater number of plasma metabolites was dysregulated at 14 d compared to 7 d revealing distinct temporal dynamics compared to gut microbiome dysbiosis. Furthermore, several transformation products of antibiotics and biomarker metabolites were observed in plasma due to antibiotic exposure. The transcriptome of the brain was only slightly altered due to antibiotic exposure. Results of these studies will help inform aquaculture practitioners and risk assessors when assessing the potential impacts of antibiotics present in fish feed and the environment, with implications for host health.

Amplicon sequencing reveals growth-associated microbial communities in black tiger shrimp (Penaeus monodon)

Recent evidence has underscored the significance of intestinal microbes in host growth performance, shedding light on the complex relationship between gut microbiota and host physiology. Even though Penaeus monodon exhibits notable size variations attributed to rapid growth and larger body mass, the specific association of the microbial community with body size remains unexplored. In this study, we employed a 16S rRNA amplicon sequencing approach to investigate the composition, diversity, and functional potential of gut microbiota in two populations of adult P. monodon (fast-growing and slow-growing). Significant variations in microbial architecture were found between the study groups based on alpha and beta diversity analyses. Differential abundance analysis identified the enrichment of specific genera, including Desulfovibrio, Ferrimonas, and Fusibacter, in the fast-growing P. monodon. These genera have been previously implicated in female shrimp growth. Functional prediction of the observed microbiota composition highlighted the predominance of growth-associated pathways, such as iron and sulfur metabolism, in the fast-growing population. Overall, our comprehensive analysis revealed discernible differences in gut microbiota between fast-growing and slow-growing populations of P. monodon, possibly indicating dynamic changes associated with host growth and development. The variations observed in the abundance of growth-related microbial taxa between these populations may provide insights into the underlying mechanisms influencing shrimp growth and development.

Variable phylosymbiosis and cophylogeny patterns in wild fish gut microbiota of a large subtropical river

The persistence and specificity of fish host-microbial interaction during evolution is an important part of exploring the host-microbial symbiosis mechanism. However, it remains unclear how the environmental and host factors shape fish host-microbe symbiotic relationships in subtropical rivers with complex natural environments. Freshwater fish are important consumers in rivers and lakes and are considered keystone species in maintaining the stability of food webs there. In this study, patterns and mechanisms shaping gut microbiota community in 42 fish species from the Pearl River, in the subtropical zone of China, were investigated. The results showed that fish host specificity is a key driver of gut microbiota evolution and diversification. Different taxonomic levels of the host showed different degrees of contribution to gut microbiota variation. Geographical location and habitat type were the next most important factors in shaping gut microbiota across the 42 fishes, followed by diet and gut trait. Our results emphasized the contribution of stochastic processes (drift and homogenizing dispersal) in the gut microbial community assembly of freshwater fishes in the middle and lower reaches of the Pearl River. Phylosymbiosis is evident at both global and local levels, which are jointly shaped by complex factors including ecological or host physiological filtration and evolutionary processes. The core microbiota showed co-evolutionary relationships of varying degrees with different taxonomic groups. We speculate that host genetic isolation or habitat variation facilitates the heterogeneous selection (deterministic process), which occurs and results in different host-core bacterium specificity.

IMPORTANCE

Freshwater fish are regarded as the dominant consumers in rivers and lakes. Due to their diverse feeding modes, fish significantly enhance the trophic link and nutrient recycling/retention in aquatic habitats. For this, they are often considered keystone species in maintaining the stability of food webs in rivers and lakes. A significant part of fish nutrition is essentially mediated by their gut microbiota, which can enhance fish tolerance to fluctuations in external resources and improve the efficiency of nutrients extracted from various food sources. As gut bacterial symbionts have a profound impact on the nutrition and development of their hosts, as well as their overall fitness, it is critical to answer the question of how hosts maintain these benefits by procuring or inheriting these vital symbionts, which is still largely unanswered, especially for freshwater fish. Our study provides new insights into the co-evolutionary relationship between wild fish and their symbiotic microbiome, the hidden diversity of gut microbiome, and the ecological adaptation potential of wild freshwater fish.

Integrative RNA-Seq analysis of host-parasite interactions and microbiota shifts in the gills of two fish species infected with monogeneans

Monogenean infections represent a significant threat to aquaculture by compromising fish health. These parasites can cause severe histological damage and increase mortality rates. The white snook (Centropomus viridis) and the gilthead seabream (Sparus aurata) are two commercially important fish species that become susceptible to diseases when infected with monogeneans. Understanding the molecular mechanisms underlying host responses to infection is essential for developing effective disease management strategies. In this study, we performed an integrative RNA-Seq analysis using transcriptomic datasets from C. viridis and S. aurata infected with the monogeneans Rhabdosynochus viridisi and Sparicotyle chrysophrii, respectively. These datasets originate from three studies, allowing us to investigate host gene expression changes, monogenean gene activation, and microbiota shifts associated with infection. Our analysis of the gill microbiota revealed significant alterations in bacterial composition between infected and uninfected fish. In the microbiota of both C. viridis and S. aurata, eight bacterial families were more abundant in infected fish, whereas eleven and four families, respectively, were more abundant in uninfected fish. In monogeneans, the molecular mechanisms shared across all Bioprojects included extracellular matrix organization, proteolysis, and gluconeogenesis, processes that may be involved in parasite colonization and survival within the host. In fish, our analysis identified shared molecular mechanisms between S. aurata and C. viridis, including oxygen carrier activity, cytokine regulation, bacterial response, and cadherin-mediated adhesion, highlighting a complex interplay between the host immune system, microbiota, and parasite. These findings enhance our understanding of fish-microbiome-parasite interactions and offer valuable perspectives for improving disease control strategies in aquaculture.

The association of seasonal dietary shift with fecal metabolome and microbiota in the captive Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis)

The gut microbiota can act as a buffer against changes in energy and food availability and adapt plastically to fluctuations in the host's diet. However, it is unknown how changes in the gut microbiome with the seasons impact microbial metabolism and the accessibility of nutrients to hosts. The study utilized 16S rRNA and UHPLC-MS/MS approaches to examine seasonal fecal metabolome variations in the captive Yangtze finless porpoises (YFPs) to determine if these variations are linked to nutrient intake or gut microbiome composition changes. The YFPs were mostly fed a frozen and live fish diet, with different food intakes yearly. We found that gut microbial diversity remained constant, but community structure varied seasonally. Firmicutes and Cyanobacteria were higher in winter, Actinobacteria in spring and fall, and proteobacteria in summer. The genus Paeniclostridium was significantly higher in the spring season, Romboutsia and Clostridium_sensu_stricto_13 were significantly higher in the summer, while Terrisporobacter and Macrococcus were significantly higher in the fall group. The study reported that seasonal dietary variation significantly impacted the fecal metabolome by affecting the metabolism, including energy, amino acid, carbohydrate, and nucleotide metabolism of the captive YFP. Moreover, significant correlations between metabolome and microbiome were found, and these correlations may indicate that the captive YFP has adapted to cope with dietary variations and enhance energy acquisition. These findings improve our knowledge of the link between microbiota, diet, metabolites, and the physiology of the host and suggest that gut microbial populations may adapt continuously to changes in diet.

Destruction of the intestinal microbiota and gut-liver axis homeostasis by microcystin-LR-induced inflammation in the common carp (Cyprinus carpio)

Water eutrophication leads to the frequent occurrence of cyanobacterial blooms, which pose a serious threat to the health and survival of fish, the top consumer in freshwater ecosystems. The hepatotoxicity induced by microcystin-LR (MC-LR) has been well studied; however, its impact on the intestinal flora and the gut-liver axis has rarely been reported. This study aimed to investigate the harmful effects of acute oral (303.89 µg/kg.bw) and intraperitoneal (i.p., 101.3 µg/kg.bw) exposure to MC-LR on the intestine and liver and the gut-liver axis of common carp. The results showed that the transaminase activity and levels of proinflammatory factors increased significantly, and histological abnormalities were observed, indicating that MC-LR induced a hepatoenteric inflammatory response. The levels of gram-negative bacteria increased, but the expression levels of bile acid (BA)-related genes (cyp7a1, cyp8b1, cyp27a1, and fxr) and the short-chain fatty acid (SCFA) content decreased as the LPS level increased. These results suggest that MC-LR exposure induces liver inflammation and impairs BA synthesis, weakening intestinal defences and promoting LPS-related hepatic inflammation. Additionally, increased intestinal permeability and reduced SCFA synthesis can further compromise intestinal epithelium protection. The inflammation induced by MC-LR was significantly more severe in the liver than in the intestine, and the recovery of the liver was slower. This study enhances the understanding of the environmental risks posed by cyanobacteria.

Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing

The burgeoning field of aquaculture has become a pivotal contributor to global food security and economic growth, presently surpassing capture fisheries in aquatic animal production as evidenced by recent statistics. However, the dense fish populations inherent in aquaculture systems exacerbate abiotic stressors and promote pathogenic spread, posing a risk to sustainability and yield. This study delves into the transformative potential of metagenomics, a method that directly retrieves genetic material from environmental samples, in elucidating microbial dynamics within aquaculture ecosystems. Our findings affirm that metagenomics, bolstered by tools in big data analytics, bioinformatics, and machine learning, can significantly enhance the precision of microbial assessment and pathogen detection. Furthermore, we explore quantum computing's emergent role, which promises unparalleled efficiency in data processing and model construction, poised to address the limitations of conventional computational techniques. Distinct from metabarcoding, metagenomics offers an expansive, unbiased profile of microbial biodiversity, revolutionizing our capacity to monitor, predict, and manage aquaculture systems with high accuracy and adaptability. Despite the challenges of computational demands and variability in data standardization, this study advocates for continued technological integration, thereby fostering resilient and sustainable aquaculture practices in a climate of escalating global food requirements.

Effect of green propolis crude extract on the modulation of intestinal microbiota and on the productive performance of juvenile Nile tilapia

The study aimed to investigate the impact of dietary supplementation with green propolis crude extract on juvenile tilapia's growth and intestinal microbiota. The experiment was conducted in raceway tanks with a volume of 19m3, comprising two treatments with three replicates each. Fish were assigned to either a control diet or a diet supplemented with 0.67% green propolis crude extract. Each experimental unit consisted of 30 fish, initially averaging 22.38 g ± 0.32 in weight, and which were fed ad libitum for 60 days. Results demonstrated that dietary supplementation with green propolis crude extract significantly improved the growth of juvenile tilapia compared to the control group. Firmicutes, Proteobacteria, Verrucomicrobia, Bacteroidetes, and Cyanobacteria were identified as the predominant bacterial phyla in the intestinal microbiota of both groups. The genera Candidatus xiphinematobacter (Verrucomicrobia) and Somerae (Firmicutes) were consistently abundant across treatments, with Somerae and Dispar as the most prevalent species. Significant differences in alpha diversity were observed between treatments at the genus and species levels according to the Chao 1 index. However, no significant differences were detected in Shannon index diversity between the control and green propolis crude extract groups. Beta diversity analysis revealed distinct clustering between treatments. Linear discriminant analysis Effect Size (LEfSe) highlighted significant differences in bacterial abundance between the control and green propolis crude extract groups. In conclusion, dietary supplementation with green propolis crude extract improved growth. It also modulated the intestinal microbiota of juvenile Thai tilapia.

Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments

Fish gut microbial communities are important for the breakdown and energy harvesting of the host diet. Microbes within the fish gut are selected by environmental and evolutionary factors. To understand how fish gut microbial communities are shaped by diet, three tropical fish species (hawkfish, Paracirrhites arcatus; yellow tang, Zebrasoma flavescens; and triggerfish, Rhinecanthus aculeatus) were fed piscivorous (fish meal pellets), herbivorous (seaweed), and invertivorous (shrimp) diets, respectively. From fecal samples, a total of 43 metagenome assembled genomes (MAGs) were recovered from all fish diet treatments. Each host-diet treatment harbored distinct microbial communities based on taxonomy, with Proteobacteria, Bacteroidota, and Firmicutes being the most represented. Based on their metagenomes, MAGs from all three host-diet treatments demonstrated a baseline ability to degrade proteinaceous, fatty acid, and simple carbohydrate inputs and carry out central carbon metabolism, lactate and formate fermentation, acetogenesis, nitrate respiration, and B vitamin synthesis. The herbivorous yellow tang harbored more functionally diverse MAGs with some complex polysaccharide degradation specialists, while the piscivorous hawkfish's MAGs were more specialized for the degradation of proteins. The invertivorous triggerfish's gut MAGs lacked many carbohydrate-degrading capabilities, resulting in them being more specialized and functionally uniform. Across all treatments, several MAGs were able to participate in only individual steps of the degradation of complex polysaccharides, suggestive of microbial community networks that degrade complex inputs.

IMPORTANCE

The benefits of healthy microbiomes for vertebrate hosts include the breakdown of food into more readily usable forms and production of essential vitamins from their host's diet. Compositions of microbial communities in the guts of fish in response to diet have been studied, but there is a lack of a comprehensive understanding of the genome-based metabolic capabilities of specific microbes and how they support their hosts. Therefore, we assembled genomes of several gut microbes collected from the feces of three fish species that were being fed different diets to illustrate how individual microbes can carry out specific steps in the degradation and energy utilization of various food inputs and support their host. We found evidence that fish gut microbial communities share several core functions despite differences in microbial taxonomy. Herbivorous fish harbored a functionally diverse microbial community with plant matter degraders, while the piscivorous and invertivorous fish had microbiomes more specialized in protein degradation.

Effect of ectoparasite Ichthyophthirius multifiliis on the histopathology and gill and gut microbiota of goldfish (Carassius auratus)

Introduction

The ectoparasite Ichthyophthirius multifiliis, is the pathogen of white spot disease in freshwater fish, which parasitizes on gills, fins, and skins of fish, causing tissue damage and death of host. However, whether it influences gill and gut microbiota is still unknow.

Methods

In this study, H&E staining was used to show the gill and gut histopathological characteristics of I. multifiliis-infected and uninfected goldfish (Carassius auratus). Meanwhile, 16S rRNA gene amplicon sequencing was conducted to analyze the difference of gill and gut microbiota between I. multifiliis-infected and uninfected goldfish.

Results

Histopathological examination revealed that I. multifiliis has induced significant damage to the gills of goldfish, characterized by lamellae fusion, cell hyperplasia, cell hyperaemia, inflammatory infiltration, necrosis and desquamation. 16S rRNA gene sequencing result showed that alpha and beta diversity of gill microbiota was significantly reduced in the I. multifiliis-infected group, while no significant changes were observed in gut microbiota. Genus Candidatus Megaira exhibited the highest relative abundance in the I. multifiliis-infected group. Meanwhile, the abundance of opportunistic pathogens Aeromonas and Achromobacter were increased in the intestines of I. multifiliis-infected goldfish.

Discussion

The increased presence of Candidatus Megaira may originate from within the cells of I. multifiliis. The increase of opportunistic pathogens Aeromonas and Achromobacter may pose a threat to the health of goldfish. In summary, this study laid a foundation for further research on the interaction between I. multifiliis and host microbiota.

Effects of Dietary Tea Polyphenols on the Growth, Antioxidant Status, Immune Function, and Intestinal Microbiota of Largemouth Bass (Micropterus salmoides)

This research aimed to explore the impact of tea polyphenol (TP) supplementation on the development, antioxidant properties, immune responses, and gut wellness in largemouth bass (Micropterus salmoides, LMB). Four diets with varying levels of TPs (0.00%, 0.02%, 0.04%, and 0.08%) were devised to feed LMB with an initial weight of 4.3 ± 0.02 g for 56 days, among which the intermittent feeding (IF) group was fed a diet supplemented with TP8 for 7 days, followed by a basal diet for another 7 days, and this was repeated until the end (56th day). The results demonstrated that supplementation with 0.04% or 0.08% TPs in the diet could reduce the crude lipid content and increase the crude protein content of LMB (p < 0.05). The levels of total cholesterol (CHO) and low-density lipoprotein (LDL) in the serum significantly decreased with the addition of 0.08% dietary TPs to the diet (p < 0.05). Dietary TPs can stimulate the activities of antioxidant enzymes such as superoxide dismutase (SOD) and catalase (CAT) and enhance the antioxidant capacity of LMB (p < 0.05). The activities of immune enzymes such as acid phosphatase (ACP) were increased to improve the immune response via the addition of TPs (p < 0.05). Supplementation with 0.02% and 0.04% TPs reduced liver fatty infiltration and alleviated hepatocyte damage. Compared with the control diet, dietary TPs significantly increased villus height (VH), villus width (VW), and lipase (LPS) activity in the intestine (p < 0.05), and supplementation with 0.04% TPs significantly increased muscular layer thickness (MT) (p < 0.05). With the increase in dietary TPs, distinct differences were observed in the intestinal microbial composition and the relative abundance of potential pathogens, especially Clostridiaceae, which decreased, along with the enrichment of pathways related to metabolism, including amino acid metabolism, carbohydrate metabolism, and lipid metabolism. Additionally, intermittent feeding could alleviate the adverse effects caused by a high dosage. In conclusion, dietary TPs of LMB could enhance antioxidant capacity and immunity and improve intestinal health, and intermittent feeding could mitigate the adverse effects caused by a high dosage.

Microbial communities associated with the skin, gill, and gut of large yellow croaker (Larimichthys crocea)

The microbiota inhabiting the surface of fish mucosal tissue play important roles in the nutrition, metabolism and immune system of their host. However, most investigations on microbial symbionts have focused on the fish gut, but the microbiota associated with external mucosal tissues (such as the skin and gill) is poorly understood. This study characterised the traits and dynamic of microbial communities associated with the skin, gill and gut of large yellow croaker (Larimichthys crocea) culturing with net enclosures or pens at different sampling times (with seasonal transition). Results revealed the structure and function of microbial communities differed according to the mucosal tissues of large yellow croaker. The richness and diversity of microbiota in the skin were significantly higher than that in the gill and gut. Discriminative microbial taxa such as Psychrobacter in the skin, Enterobacterales in the gill, and Fusobacterium in the gut, and discriminative predictive functions were identified in the skin, gill and gut. Furthermore, different environmental-related factors (such as sampling time/season and culture method) had impacts on the fish microbiota differently. The diversity and composition of microbiota associated with the skin, gill and gut changed over time, and the difference in skin microbiota across sampling times was most significant among the three tissues. The culture method significantly impacted the diversity and composition of skin microbiota, but no significant difference was found in the gill and gut microbiota between net enclosure and net pen. These results indicated that the skin microbiota of large yellow croaker was more diverse and affected by environmental-related factors than other tissues. This study provides new insights into the structure, environmental response pattern, and relationship with host health of microbiota associated with the mucosal tissues of large yellow croaker.

Impacts of Black Soldier Fly (Hermetia illucens) Larval Meal on Intestinal Histopathology and Microbiome Responses in Hybrid Grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂): A Comprehensive Analysis

This study examined the diversity and responses of intestinal microbiota in hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) fed diets with varying levels of fishmeal replaced by black soldier fly larvae (BSFL). The 10% BSFL substitution (BSFL10) group showed the highest levels of trypsin and amylase. Substituting fishmeal with 30% and 50% BSFL weakened the intestinal wall, resulting in vacuoles, sparse striatal boundaries, and fewer villi. Microbiota diversity, measured through Shannon's index, was higher in the BSFL10 and BSFL50 groups than in the control. 16S rRNA amplicon data revealed the dominance of Firmicutes, Proteobacteria, Bacteroidetes, Spirochaetota, and Verrucomicrobia phyla. The BSFL-replacement groups showed an increase in Proteobacteria, Bacteroidetes, and Spirochaetota compared to the control, but fewer Firmicutes. PICRUSt analysis indicated significant alterations in microbial function, particularly enhanced protein, carbohydrate, lipid, and energy metabolisms in the BSFL-fed group. Substituting 10% fishmeal with BSFL enhanced nutrient metabolism and gut microbiota in juvenile hybrid grouper. Further research is needed to explore factors affecting the efficacy of insect feed as a sustainable aquaculture diet.

Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments

Fish gut microbial communities are important for the breakdown and energy harvesting of the host diet. Microbes within the fish gut are selected by environmental and evolutionary factors. To understand how fish gut microbial communities are shaped by diet, three tropical fish species (hawkfish, Paracirrhites arcatus; yellow tang, Zebrasoma flavescens; and triggerfish, Rhinecanthus aculeatus) were fed piscivorous (fish meal pellets), herbivorous (seaweed), and invertivorous (shrimp) diets, respectively. From fecal samples, a total of 43 metagenome assembled genomes (MAGs) were recovered from all fish diet treatments. Each host-diet treatment harbored distinct microbial communities based on taxonomy, with Proteobacteria, Bacteroidota, and Firmicutes being the most represented. Based on their metagenomes, MAGs from all three host-diet treatments demonstrated a baseline ability to degrade proteinaceous, fatty acid, and simple carbohydrate inputs and carry out central carbon metabolism, lactate and formate fermentation, acetogenesis, nitrate respiration, and B vitamin synthesis. The herbivorous yellow tang harbored more functionally diverse MAGs with some complex polysaccharide degradation specialists, while the piscivorous hawkfish's MAGs were more specialized for the degradation of proteins. The invertivorous triggerfish's gut MAGs lacked many carbohydrate degrading capabilities, resulting in them being more specialized and functionally uniform. Across all treatments, several MAGs were able to participate in only individual steps of the degradation of complex polysaccharides, suggestive of microbial community networks that degrade complex inputs.

Understanding the probiotic potential of Lactobacillus plantarum: Antioxidant capacity, non-specific immunity and intestinal microbiota improvement effects on Manila clam Ruditapes philippinarum

Lactic acid bacteria (LAB) have beneficial effects on aquatic animals, improving their immune system and intestinal microbiota. Nevertheless, the probiotic effects of LAB on the Manila clam Ruditapes philippinarum remain poorly understood. Herein, the effects of administering Lactobacillus plantarum at final doses of 1 × 105 CFU/L (T5 group), 1 × 107 CFU/L (T7 group), and 1 × 109 CFU/L (T9 group) in the rearing water for eight weeks were evaluated for the antioxidant capacity, non-specific immunity, resistance to Vibrio parahaemolyticus infection, and intestinal microbiota of R. philippinarum. The rearing water without the addition of L. plantarum served as a control. The results showed that the T7 and T9 groups demonstrated a significant elevation in the disease resistance of clams against V. parahaemolyticus, in the activities of alkaline phosphatase and lysozyme in the hepatopancreas, and in the expression of antioxidant- and immune-related genes, including SOD, GPx, and GST. Meanwhile, the T7 group showed a significant enhancement in superoxide dismutase and catalase activities and CAT expression, while the T9 group experienced a remarkable elevation in reduced glutathione content. Only catalase activity was markedly elevated in the T5 group. The expression of SOD, CAT, GPx, and GST was significantly elevated in three treatment groups following the V. parahaemolyticus challenge. The T7 group exhibited a significant increase in intestinal microbiota richness. Significant increases were noted in Firmicutes abundance across all three treatment groups and in Actinobacteriota in the T5 and T7 groups. Additionally, the opportunistic pathogen Escherichia-Shigella abundance significantly decreased in three treatment groups. Furthermore, administration of 1 × 107 CFU/L L. plantarum enhanced the stability of the intestinal microecosystem, whereas a dose of 1 × 109 CFU/L might have a negative effect. The application of three doses of L. plantarum significantly enhanced intestinal microbiota functions related to the immune response and oxidative stress regulation, while a higher dose (1 × 109 CFU/L) might inhibit several functions. In conclusion, the application of L. plantarum in the rearing water exerted beneficial effects on the antioxidant capacity, non-specific immunity, resistance to V. parahaemolyticus, and the intestinal microbiota stability and functions of R. philippinarum. The beneficial effects of L. plantarum on R. philippinarum were dose-dependent, and the final dose of 1 × 107 CFU/L exhibited the optimal effects.

Association between Turbot (Scophthalmus maximus) Fish Phenotype and the Post-Larval Bacteriome

Over the past decade, an increasing number of studies have emphasized the importance of the host microbiome in influencing organismal health and development. Aligned with this understanding, our study aimed to investigate the potential association between the turbot (Scophthalmus maximus) phenotypic traits and the post-larval bacteriome. Turbot post-larvae were sampled from twenty randomly selected production cycles thirty days after hatching (DAH) across multiple post-larval production batches over a three-month period (April to June). Fish were selectively sampled based on five phenotypic traits, namely, normal, large, small, malformed, and depigmented. Our results showed that small-sized post-larvae had significantly higher bacterial phylogenetic diversity in their bacterial communities than all other phenotypes. A more in-depth compositional analysis also revealed specific associations between certain bacterial taxa and fish phenotypes. For example, the genera Aliivibrio and Sulfitobacter were enriched in small-sized post-larvae, while the family Micrococcaceae were predominantly found in larger post-larvae. Furthermore, genus Exiguobacterium was linked to depigmented larvae, and genus Pantoea was more prevalent in normal post-larvae. These observations underscore the importance of further research to understand the roles of these bacterial taxa in larval growth and phenotypic differentiation. Such insights could contribute to developing microbiome modulation strategies, which may enhance turbot post-larval health and quality and improve larviculture production.

Interactions between lipid metabolism and the microbiome in aquatic organisms: A review

Marine organisms' lipid metabolism contributes to marine ecosystems by producing a variety of lipid molecules. Historically, research focused on the lipid metabolism of the organisms themselves. Recent microbiome studies, however, have revealed that gut microbial communities influence the amount and type of lipids absorbed by organisms, thereby altering the organism's lipid metabolism. This has highlighted the growing importance of research on gut microbiota. This review highlights mechanisms by which gut microbiota facilitate lipid digestion and diversify the lipid pool in aquatic animals through the accelerated degradation of exogenous lipids and the transformation of lipid molecules. We also assess how environmental factors and pollutants, along with the innovative use of probiotics, interact with the gut microbiome to influence lipid metabolism within the host. We aim to elucidate the complex interactions between lipid metabolism and gut microbiota in aquatic animals by synthesizing current research and identifying knowledge gaps, providing a foundation for future explorations.

Comparative analysis of gut microbiome in Pangasionodon hypopthalmus and Labeo catla during health and disease

The present study was conducted to study the composition of gut microbiome in the advanced fingerling and fingerling stage of striped pangasius catfish and catla during healthy and diseased conditions. Healthy pangasius and catla fishes were obtained from commercial farms and injected with the LD50 dose of A. hydrophila. The intestinal samples from the control and injected group were collected and pooled for 16 s metagenomic analysis. Community analysis was performed by targeting the 16 s rRNA gene to explore and compare the gut microbiota composition of these fishes. The operational taxonomic units (OTUs) consisted of four major phyla: Bacteroidia, Proteobacteria, Firmicutes, and Actinobacteria. Alpha and beta diversity indices were carried out to understand the diversity of microbes within and between a sample. While comparing the advanced fingerling and fingerling stage gut microbiome of Pangasius catfish, the dominance of Proteobacteria was found in fingerlings, whereas Firmicutes and Bacteroides were found in advanced fingerlings. In catla, Proteobacteria and Bacteroides were predominant. Taxonomic abundance of the microbiota in control and diseased Pangasius and catla fishes at phylum, class, order, family, genus, and species levels were also depicted. The present study is the first of its kind, and it will help to identify the diversity of novel potential bacterial species involved in disease protection of fishes. It can lead to the development of sustainable prophylactic measures against (re-)emerging bacterial diseases in aquaculture.

The impacts of microplastics on zebrafish behavior depend on initial personality state

Microplastic pollution is associated with inflammation, gut dysbiosis and behavioral changes in fish. Fish have distinct personality traits but the role of personality in behavioral toxicology is rarely considered. We classified zebrafish on four behavioral axes: boldness, anxiety, sociability and exploration tendency then exposed them to low- or high- concentrations of two types of polyethylene microplastics (low- and high-density) for 28 days. Behaviors, antioxidant enzymes (catalase and superoxide dismutase), and gut microbiome were then measured. There were direct effects of microplastics on boldness, anxiety and sociability. However, fish retained their initial behavioral tendencies. Exposure to all microplastic treatments reduced average swimming speed and decreased the time spent motionless. Microplastic exposure did not affect antioxidant enzymes but did cause significant changes in the composition of the gut microbiome. This study demonstrates that environmentally realistic concentrations of microplastics can alter fish behavior, but much of the variance in response can be explained by personality.

Connection between the gut microbiota of largemouth bass (Micropterus salmoides) and microbiota of the aquaponics system environment

The significant role played by the gut microbiota in fish growth, development, immunity, and overall health has been widely established. Nevertheless, there remains a lack of clarity regarding the interaction and origin between the environmental microbiota and the gut microbiota of aquaculture species within the aquaponics coupling system. Thus, we conducted an analysis of the gut microbiota of largemouth bass (Micropterus salmoides) obtained from an indoor enclosed circulating water aquaponics coupling system located in greenhouses in northern China. Additionally, we examined the microbiota of the fish pond water and tomato rhizosphere soil using high-throughput sequencing of the 16S rRNA gene. Our results demonstrated significant differences in the compositions of fish pond water, rhizosphere soil, and the gut microbiota of largemouth bass. Moreover, these compositions changed throughout the culture period. Approximately 11.99% of the bacterial composition in the gut microbiota of largemouth bass could be attributable to the rhizosphere soil microbiota, while 62.01% of the bacterial composition could be attributable to the fish pond water microbiota. However, the proportion of bacteria in the gut microbiota from the fish pond water microbiota remained respectively 40.90% and 56.15% in May and September, which increased markedly to 88.97% in July. Similarly, the proportion of bacteria in the pond water microbiota from the tomato rhizosphere soil microbiota were respectively 0% and 8.95% in samples collected in May and September, which increased markedly to 69.26% in July, and the proportion of bacteria in the gut microbiota from the tomato rhizosphere soil microbiota were respectively 0.07% and 0% in samples collected in May and September, which increased to 0.45% in July. The research results offer essential insights into the interactions and origins of environmental microbiota and gut microbiota in the aquaponics system of cultured fish. This knowledge could enhance green aquaponics practices for largemouth bass.

In vivo toxicity of upconversion nanoparticles (NaYF4:Yb, Er) in zebrafish during early life stages: Developmental toxicity, gut-microbiome disruption, and proinflammatory effects

Lanthanide-doped upconversion nanoparticles (Ln-UCNPs) have been considered promising materials for various fields, such as biomedical and industrial applications. However, data and reports regarding its toxicity and environmental risks are scarce. Under these circumstances, data must be obtained to fully understand potential toxicity and adverse outcome pathways. In the present study, the toxicity of uncoated Ln-UCNP cores (NaYF4:Yb, Er) was systematically assessed in zebrafish embryos during early developmental stages. Ln-UCNPs were found to have multiple toxic effects, such as effects on survival rates, delayed hatching times, shorter body lengths, altered heart rates and blood circulation (significantly reduced), and neurobehavioral impairments in response to photoperiod stimulation. Bioimaging showed that Ln-UCNPs were distributed on the chorion, eyes, and skin at 72 hpf. However, it accumulates in the pharynx, esophagus, and intestine after oral administration. Ln-UCNPs disrupt the diversity and abundance of host-associated microorganisms (gut microbiota) leading to an increase in the prevalence of harmful bacteria in zebrafish. Transcriptomic and Ingenuity Pathway Analysis (IPA) predicted Interleukin-8 (IL-8) signaling, neuroinflammation, cardiac hypertrophy signaling pathways, immune and inflammation-related response interferon-gamma (ifnγ), and miR-155 as key mediators in regulatory effects. Based on this, a causal network was built showing the strong links between the induced gene expression of differentially expressed genes (DEGs), such as nitric oxide synthase 2 (nos2) and tumor necrosis factor (tnf) upon Ln-UCNPs treatment, and with the downstream adverse outcomes, in particular, the promotion of apoptosis, liver damage, and inflammatory response. Finally, RT-qPCR analysis confirmed the up-regulated expression of nos2 and tnf in the exposed larvae, consistent with the observation of an increased number of fluorescence-labelled neutrophils and macrophages in lyz: DsRed transgenic zebrafish until 120 hpf exposure, which together demonstrated the proinflammatory effects of Ln-UCNPs on organisms. In conclusion, we illustrated the developmental toxicity, disruption of gut-microbiome, and proinflammatory effects of Ln-UCNP cores on zebrafish, and the causal network from IPA analysis may help further elucidate the adverse outcome pathway of Ln-UCNPs.

Impact of wildfire ash on skin and gut microbiomes and survival of Rana dybowskii

Climate change and human activities escalate the frequency and intensity of wildfires, threatening amphibian habitats and survival; yet, research on these impacts remains limited. Wildfire ash alters water quality, introduces contaminants, and may disrupt microbial communities, impacting gut and skin microbiota; however, the effects on gut and skin microbiota remain unclear. Rana dybowskii were exposed to five concentrations (0 g L-1, 1.25 g L-1, 2.5 g L-1, 5 g L-1, and 10 g L-1) of aqueous extracts of wildfire ashes (AEAs) for 30 days to assess AEAs' metal content, survival, and microbiota diversity via Illumina sequencing. Our results showed that the major elements in ash were Ca > K > Mg > Al > Fe > Na > Mn, while in AEA they were K > Ca > Na > Mg > As > Al > Cu. A significant decrease in amphibian survival rates with increased AEA concentration was shown. The beta diversity analysis revealed distinct shifts in microbiota composition. Notably, bacterial genera associated with potential health risks showed increased abundance in skin microbiota, emphasising the potential for ash exposure to affect amphibian health. Functional prediction analyses revealed significant shifts in metabolic pathways related to health and disease, indicating that wildfire ash exposure may influence amphibian health through changes in microbial functions. This study highlights the urgent need for strategies to mitigate wildfire ash impacts on amphibians, as it significantly alters microbiota and affects their survival and health.

Probiotics Alleviate Microcystin-LR-Induced Developmental Toxicity in Zebrafish Larvae

Microcystin-LR (MCLR) poses a significant threat to aquatic ecosystems and public health. This study investigated the protective effects of the probiotic Lactobacillus rhamnosus against MCLR-induced developmental toxicity in zebrafish larvae. Zebrafish larvae were exposed to various concentrations of MCLR (0, 0.9, 1.8, and 3.6 mg/L) with or without L. rhamnosus from 72 to 168 h post-fertilization (hpf). Probiotic supplementation significantly improved survival, hatching, and growth rates and reduced malformation rates in MCLR-exposed larvae. L. rhamnosus alleviated MCLR-induced oxidative stress by reducing reactive oxygen species (ROS) levels and enhancing glutathione (GSH) content and catalase (CAT) activity. Probiotics also mitigated MCLR-induced lipid metabolism disorders by regulating key metabolites (triglycerides, cholesterol, bile acids, and free fatty acids) and gene expression (ppara, pparb, srebp1, and nr1h4). Moreover, 16S rRNA sequencing revealed that L. rhamnosus modulated the gut microbiome structure and diversity in MCLR-exposed larvae, promoting beneficial genera like Shewanella and Enterobacter and inhibiting potential pathogens like Vibrio. Significant correlations were found between gut microbiota composition and host antioxidant and lipid metabolism parameters. These findings suggest that L. rhamnosus exerts protective effects against MCLR toxicity in zebrafish larvae by alleviating oxidative stress, regulating lipid metabolism, and modulating the gut microbiome, providing insights into probiotic-based strategies for mitigating MCLR toxicity in aquatic organisms.

Melodious tuning of microbial dynamics in biofloc, cage, and pond culturing system: a study on Pangasius pangasius fish gut microbiome

Aquaculture, a rapidly expanding sector, meets the global surging demand for aquatic food. Pangasius, a highly valued freshwater species, has seen a significant increase in demand due to its adaptability and potential for high yields, making it a promising candidate for aquaculture in India. This study investigates the gut microbiome composition of Pangasius pangasius fish cultured in three different systems (biofloc, cage, and pond). Metagenomic DNA extraction and 16S rRNA gene-targeted sequencing were performed. Outcomes revealed distinct microbial compositions across culture types, with significant differences in species richness and diversity, specifically in the biofloc system, compared to cages and ponds. Taxonomic analysis identified prevalent phyla such as Firmicutes and Fusobacteriota, with varying abundances among culture systems. The genus-level analysis highlighted dominant genera such as Cetobacterium and WWE3. Functional profiling indicated differences in enzymatic activity and metabolic pathways, emphasizing each culture sample type's unique microbial community structures. Notably, the microbiota from BF samples exhibited significant differences and unique metabolic pathways compared to the microbiota from C and P samples, which showed greater similarity and shared several common metabolic pathways. These findings highlight substantial differences in microbial diversity across the culturing systems, reflecting the microbiota's ability to adapt to specific environments and their potential role in promoting fish growth within those environments. Overall, this study provides insights into the gut microbiome diversity and functionality in Pangasius pangasius across different aquaculture environments, contributing to a better understanding of host-microbe interactions and aquaculture management strategies.

The Response of the Gut Physiological Function and Microbiome of a Wild Freshwater Fish (Megalobrama terminalis) to Alterations in Reproductive Behavior

The fish gut microbiome is well known for its role in degrading nutrients to improve the host's digestion and absorption efficiency. In this study, we focused on the core physiological adaptability during the various reproductive stages of the black Amur bream (Megalobrama terminalis) to explore the interaction mechanisms among the fish host gut mucosal structure, gut enzyme activity, and gut microbial metabolism in the course of the host's reproductive cycle. Our findings showed that M. terminalis exhibited locomotion metabolic type (aids in sporting) in the reproductive stage, and a change to visceral metabolic type (aids in digestion) during non-reproductive and post-reproductive stage phases. The impact of metabolic type selection and energy demand during various reproductive stages on fish nutrition strategy and digestive function was substantial. Our resulted showed that mitochondria in intestinal epithelial cells of reproductive M. terminalis appeared autophagy phenomenon, and the digestive enzyme activities in the intestines of reproductive M. terminalis were lower than those in the non-reproductive and post-reproductive individuals. Moreover, these differences in nutrition strategy have a prominent impact on the gut microbiome of reproductive M. terminalis, compared to non-reproductive and post-reproductive samples. Our findings showed that reproductive females had lower levels of alpha diversity compared to non-reproductive and post-reproductive females. Our results also showed a greater functional variety and an increase in functional genes related to carbohydrate, lipid, amino acid, cofactors, and vitamin metabolic pathways in the NRS and PRS group. It is noteworthy that an enrichment of genes encoding putative enzymes implicated in the metabolism of taurine and hypotaurine was observed in the RS samples. Our findings illustrated that the stability and resilience of the gut bacterial community could be shaped in the wild fish host-microbiome interactions during reproductive life history.

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human

BACKGROUND

Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health.

RESULTS

The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer.

CONCLUSIONS

The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.

Lactococcus G423 improve growth performance and lipid metabolism of broilers through modulating the gut microbiota and metabolites

This study aimed to explore whether Lactococcus G423 could improve growth performance and lipid metabolism of broilers by the modulation of gut microbiota and metabolites. A total of 640 1-day-old AA broilers were randomly divided into 4 groups [Control (CON), Lac_L, Lac_H, and ABX]. Average daily gain (ADG), average daily feed intake (ADFI), feed conversion ratio (FCR), breast muscle, thigh muscle, and abdominal fat pad were removed and weighed at 42 days of age. Serum was obtained by centrifuging blood sample from jugular vein (10 mL) for determining high-density lipoprotein (HDL), total cholesterol (TC), low-density lipoprotein (LDL), and triglyceride (TG) using ELISA. The ileal contents were harvested and immediately frozen in liquid nitrogen for 16S rRNA and LC-MS analyses. Then, the results of 16S rRNA analysis were confirmed by quantitative polymerase chain reaction (qPCR). Compared with the CON group, FCR significantly decreased in the Lac_H group (p < 0.05) in 1-21 days; ADG significantly increased and FCR significantly decreased in the Lac_H group (p < 0.05) in 22-42 days. 42 days weight body and ADG significantly increased in the Lac_H group (p < 0.05) in 42 days. Abdominal fat percentage was significantly decreased by Lactococcus G423 (p < 0.05), the high dose of Lactococcus G423 significantly decreased the serum of TG, TC, and LDL level (p < 0.05), and the low dose of Lactococcus G423 significantly decreased the serum of TG and TC level (p < 0.05). A significant difference in microbial diversity was found among the four groups. Compared with the CON group, the abundance rates of Firmicutes and Lactobacillus in the Lac_H group were significantly increased (p < 0.05). The global and overview maps and membrane transport in the Lac_L, Lac_H, and ABX groups significantly changed versus those in the CON group (p < 0.05). The results of LC-MS demonstrated that Lactococcus could significantly improve the levels of some metabolites (6-hydroxy-5-methoxyindole glucuronide, 9,10-DiHOME, N-Acetyl-l-phenylalanine, and kynurenine), and these metabolites were involved in four metabolic pathways. Among them, the pathways of linoleic acid metabolism, phenylalanine metabolism, and pentose and glucuronate interconversions significantly changed (p < 0.05). Lactococcus G423 could ameliorate growth performance and lipid metabolism of broilers by the modulation of gut microbiota and metabolites.

Comparative studies on the intestinal health of wild and cultured ricefield eel (Monopterus albus)

Fish intestinal health under intensive aquaculture mode plays an important role in growth, development, and immune function. The present study was aimed to systematically investigate the differences of intestinal health between wild and cultured Monopterus albus by biochemical parameters, histomorphology, and molecular biology. A total of 15 healthy M. albus per group, with an average body weight of 45 g, were sampled to analyze intestinal health parameters. Compared with wild fish, the cultured M. albus in the foregut had lower trypsin, lipase, SOD, CAT, T-AOC, and GSH-Px activities (P < 0.05) and higher amylase activity and MDA content (P < 0.05). The villus circumference and goblet cells in the cultured group were significantly lower than those in the wild group (P < 0.05). In addition, the cultured fish showed lower relative expression levels of occludin, zo-1, zo-2, claudin-12, claudin-15, mucin5, mucin15, lysozyme, complement 3, il-10, tgf-β1, tgf-β2, and tgf-β3 (P < 0.05) and higher il-1β, il-6, il-8, tnf-a, and ifnγ mRNA expressions than those of wild fish (P < 0.05). In terms of gut microbiota, the cultured group at the phylum level displayed higher percentages of Chlamydiae and Spirochaetes and lower percentages of Firmicutes, Bacteroidetes, Actinobacteria, Cyanobacteria, and Verrucomicrobia compared to the wild group (P < 0.05). At the genus level, higher abundances of Pseudomonadaceae_Pseudomonas and Spironema and lower abundances of Lactococcus and Cetobacterium were observed in the cultured group than in the wild group (P < 0.05). To our knowledge, this is the first investigation of the intestinal health status between wild and cultured M. albus in terms of biochemistry, histology, and molecular biology levels. Overall, the present study showed significant differences in intestinal health between wild and cultured M. albus and the main manifestations that wild M. albus had higher intestinal digestion, antioxidant capacity, and intestinal barrier functions than cultured M. albus. These results would provide theoretical basis for the subsequent upgrading of healthy aquaculture technology and nutrient regulation of intestinal health of cultured M. albus.

Metagenomic dissection of the intestinal microbiome in the giant river prawn Macrobrachium rosenbergii infected with Decapod iridescent virus 1

Microbiome in the intestines of aquatic invertebrates plays pivotal roles in maintaining intestinal homeostasis, especially when the host is exposed to pathogen invasion. Decapod iridescent virus 1 (DIV1) is a devastating virus seriously affecting the productivity and success of crustacean aquaculture. In this study, a metagenomic analysis was conducted to investigate the genomic sequences, community structure and functional characteristics of the intestinal microbiome in the giant river prawn Macrobrachiumrosenbergii infected with DIV1. The results showed that DIV1 infection could significantly reduce the diversity and richness of intestinal microbiome. Proteobacteria represented the largest taxon at the phylum level, and at the species level, the abundance of Gonapodya prolifera and Solemya velum gill symbiont increased significantly following DIV1 infection. In the infected prawns, four metabolic pathways related to purine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and pentose phosphate pathway, and five pathways related to nucleotide excision repair, homologous recombination, mismatch repair, base excision repair, and DNA replication were significantly enriched. Moreover, several immune response related pathways, such as shigellosis, bacterial invasion of epithelial cells, Salmonella infection, and Vibrio cholerae infection were repressed, indicating that secondary infection in M. rosenbergii may be inhibited via the suppression of these immune related pathways. DIV1 infection led to the induction of microbial carbohydrate enzymes such as the glycoside hydrolases (GHs), and reduced the abundance and number of antibiotic-resistant ontologies (AROs). A variety of AROs were identified from the microbiota, and mdtF and lrfA appeared as the dominant genes in the detected AROs. In addition, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration were the main antibiotic resistance mechanisms. Collectively, the data would enable a deeper understanding of the molecular response of intestinal microbiota to DIV1, and offer more insights into its roles in prawn resistance to DIVI infection.

Dietary Bacillus velezensis T23 fermented products supplementation improves growth, hepatopancreas and intestine health of Litopenaeus vannamei

This study aimed to elucidate the effects of dietary fermented products of Bacillus velezensis T23 on the growth, immune response and gut microbiota in Pacific white shrimp (Litopenaeus vannamei). Shrimp were fed with diets containing fermentation products of B. velezensis T23 at levels of (0, 0.05, 0.1, 0.2, 0.3, 0.4, and 0.5 g/kg) for 4 weeks, to assess the influence on shrimp growth. The results showed that 0.3 and 0.4 g/kg T23 supplementation improved shrimp growth and feed utilization. Based on these results we selected these three diets (Control, 0.3T23 and 0.4T23) to assess the effect on immune response and gut microbiota of shrimp. Compared with the control, the 0.3T23 and 0.4T23 groups enhanced lipase and α-amylase activities in the gut significantly. Moreover, the 0.4T23 group decreased TAG and MDA levels in hepatopancreas, ALT and AST levels of serum significantly (P < 0.05). In hepatopancreas, CAT and SOD activities were improved observably and the MDA content was reduced markedly in both T23 groups. The expressions of antimicrobial related genes, Cru and peroxinectin in the 0.3T23 group, and proPO and peroxinectin in the 0.4T23 group were up-regulated remarkably (P < 0.05). Moreover, hepatopancreas of shrimp fed with a diet amended with T23 showed a significant down-regulated expression of nf-kb and tnf-α genes, while expressions of tgf-β was considerably up-regulated. Furthermore, serum LPS and LBP contents were reduced markedly in T23 groups. Intestinal SOD and CAT were noteworthy higher in T23 groups (P < 0.05). In the intestine of shrimp fed on the diet enriched with T23 the expression of nf-κb and tnf-α exhibited markedly down-regulated, whereas hif1α was up-regulated (P < 0.05). Besides, in the intestine of shrimp grouped under T23, Cru and peroxinectin genes were markedly up-regulated (P < 0.05). Dietary 0.3 g/kg T23 also upregulated the ratio of Rhodobacteraceae to Vibrionaceae in the gut of the shrimp. Taken together, the inclusion of B. velezensis T23 in the diet of shrimp enhanced the growth and feed utilization, enhanced hepatopancreas and intestine health.

Antibiotics alter development and gene expression in the model cnidarian Nematostella vectensis

Background

Antibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative impacts on development and physiology that could offset the positive effects of reducing or eliminating pathogens. Similarly, antibiotics can shift the microbial community due to differential effectiveness on resistant and susceptible bacteria. Though antibiotic application does not typically result in mortality of marine invertebrates, little is known about the developmental and transcriptional effects. These sublethal effects could reduce the fitness of the host organism and lead to negative changes after removal of the antibiotics. Here, we quantify the impact of antibiotic treatment on development, gene expression, and the culturable bacterial community of a model cnidarian, Nematostella vectensis.

Methods

Ampicillin, streptomycin, rifampicin, and neomycin were compared individually at two concentrations, 50 and 200 µg mL-1, and in combination at 50 µg mL-1 each, to assess their impact on N. vectensis. First, we determined the impact antibiotics have on larval development. Next Amplicon 16S rDNA gene sequencing was used to compare the culturable bacteria that persist after antibiotic treatment to determine how these treatments may differentially select against the native microbiome. Lastly, we determined how acute (3-day) and chronic (8-day) antibiotic treatments impact gene expression of adult anemones.

Results

Under most exposures, the time of larval settlement extended as the concentration of antibiotics increased and had the longest delay of 3 days in the combination treatment. Culturable bacteria persisted through a majority of exposures where we identified 359 amplicon sequence variants (ASVs). The largest proportion of bacteria belonged to Gammaproteobacteria, and the most common ASVs were identified as Microbacterium and Vibrio. The acute antibiotic exposure resulted in differential expression of genes related to epigenetic mechanisms and neural processes, while constant application resulted in upregulation of chaperones and downregulation of mitochondrial genes when compared to controls. Gene Ontology analyses identified overall depletion of terms related to development and metabolism in both antibiotic treatments.

Discussion

Antibiotics resulted in a significant increase to settlement time of N. vectensis larvae. Culturable bacterial species after antibiotic treatments were taxonomically diverse. Additionally, the transcriptional effects of antibiotics, and after their removal result in significant differences in gene expression that may impact the physiology of the anemone, which may include removal of bacterial signaling on anemone gene expression. Our research suggests that impacts of antibiotics beyond the reduction of bacteria may be important to consider when they are applied to aquatic invertebrates including reef building corals.

A Well-Established Gut Microbiota Enhances the Efficiency of Nutrient Metabolism and Improves the Growth Performance of Trachinotus ovatus

The gut microbiota has become an essential component of the host organism and plays a crucial role in the host immune system, metabolism, and physiology. Nevertheless, our comprehension of how the fish gut microbiota contributes to enhancing nutrient utilization in the diet and improving host growth performance remains unclear. In this study, we employed a comprehensive analysis of the microbiome, metabolome, and transcriptome to analyze intestines of the normal control group and the antibiotic-treated model group of T. ovatus to investigate how the gut microbiota enhances fish growth performance and uncover the underlying mechanisms. First, we found that the growth performance of the control group was significantly higher than that of the antibiotic-treated model under the same feeding conditions. Subsequent multiomics analyses showed that the gut microbiota can improve its own composition by mediating the colonization of some probiotics represented by Lactobacillus in the intestine, improving host metabolic efficiency with proteins and lipids, and also influencing the expression of genes in signaling pathways related to cell proliferation, which together contribute to the improved growth performance of T. ovatus. Our results demonstrated the important contribution of gut microbiota and its underlying molecular mechanisms on the growth performance of T. ovatus.

Global analysis of the adverse effects of micro- and nanoplastics on intestinal health and microbiota of fish

The wide occurrence of micro- and nanoplastics (MPs/NPs) within aquatic ecosystems has raised increasing concerns regarding their potential effects on aquatic organisms. However, the effects of MPs/NPs on intestinal health and microbiota of fish remain controversial, and there is a lack of comprehensive understanding regarding how the impact of MPs/NPs is influenced by MPs/NPs characteristics and experimental designs. Here, we conducted a global analysis to synthesize the effects of MPs/NPs on 47 variables associated with fish intestinal health and microbiota from 118 studies. We found that MPs/NPs generally exerted obvious adverse effects on intestinal histological structure, permeability, digestive function, immune and oxidative-antioxidative systems. By contrast, MPs/NPs showed slight effects on intestinal microbial variables. Further, we observed that the responses of intestinal variables to MPs/NPs were significantly regulated by MPs/NPs characteristics and experimental designs. For instance, polyvinyl chloride plastics showed higher toxicity to fish gut than polyethylene and polystyrene did. Additionally, larval fish appeared to be more sensitive to MPs/NPs than juvenile fish. Collectively, this study highlights the potential impacts of MPs/NPs on intestinal health and microbiota of fish, and underscores the determinant role of MPs/NPs characteristics and experimental designs in MPs/NPs toxicity.

Integrated microbiome and metabolome analyses reveal the effects of low pH on intestinal health and homeostasis of crayfish (Procambarus clarkii)

Low pH (LpH) poses a significant challenge to the health, immune response, and growth of aquatic animals worldwide. Crayfish (Procambarus clarkii) is a globally farmed freshwater species with a remarkable adaptability to various environmental stressors. However, the effects of LpH stress on the microbiota and host metabolism in crayfish intestines remain poorly understood. In this study, integrated analyses of antioxidant enzyme activity, histopathological damage, 16S rRNA gene sequencing, and liquid chromatography-mass spectrometry (LC-MS) were performed to investigate the physiology, histopathology, microbiota, and metabolite changes in crayfish intestines exposed to LpH treatment. The results showed that LpH stress induced obvious changes in superoxide dismutase and catalase activities and histopathological alterations in crayfish intestines. Furthermore, 16S rRNA gene sequencing analysis revealed that exposure to LpH caused significant alterations in the diversity and composition of the crayfish intestinal microbiota at the phylum and genus levels. At the genus level, 14 genera including Bacilloplasma, Citrobacter, Shewanella, Vibrio, RsaHf231, Erysipelatoclostridium, Anaerorhabdus, Dysgonomonas, Flavobacterium, Tyzzerella, Brachymonas, Muribaculaceae, Propionivibrio, and Comamonas, exhibited significant differences in their relative abundances. The LC-MS analysis revealed 859 differentially expressed metabolites in crayfish intestines in response to LpH, including 363 and 496 upregulated and downregulated metabolites, respectively. These identified metabolites exhibited significant enrichment in 24 Kyoto Encyclopedia of Genes and Genomes pathways (p < 0.05), including seven and 17 upregulated and downregulated pathways, respectively. These pathways are mainly associated with energy and amino acid metabolism. Correlation analysis revealed a strong correlation between the metabolites and intestinal microbiota of crayfish during LpH treatment. These findings suggest that LpH may induce significant oxidative stress, intestinal tissue damage, disruption of intestinal microbiota homeostasis, and alterations in the metabolism in crayfish. These findings provide valuable insights into how the microbial and metabolic processes of crayfish intestines respond to LpH stress.

The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence

The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.

Immunological and molecular diagnostic techniques in fish health: present and future prospectus

Fish health management is critical to aquaculture and fisheries as it directly affects sustainability and productivity. Fish disease diagnosis has taken a massive stride because of advances in immunological and molecular diagnostic tools which provide a sensitive, quick, and accurate means of identifying diseases. This review presents an overview of the main molecular and immunological diagnostic methods for determining the health of fish. The immunological techniques help to diagnose different fish diseases by detecting specific antigens and antibodies. The application of immunological techniques to vaccine development is also examined in this review. The genetic identification of pathogens is made possible by molecular diagnostic techniques that enable the precise identification of bacterial, viral, and parasitic organisms in addition to evaluating host reactions and genetic variation associated with resistance to disease. The combination of molecular and immunological methods has resulted in the creation of novel techniques for thorough evaluation of fish health. These developments improve treatment measures, pathogen identification and provide new information about the variables affecting fish health, such as genetic predispositions and environmental stresses. In the framework of sustainable fish farming and fisheries management, this paper focuses on the importance of these diagnostic techniques that play a crucial role in protecting fish populations and the aquatic habitats. This review also examines the present and potential future directions in immunological and molecular diagnostic techniques in fish health.

Effects of different temperatures on Leiocassis longirostris gill structure and intestinal microbial composition

Fish are poikilothermic vertebrates and their physiological activities are affected by water temperature. In recent years, extreme weather has occurred frequently, and temperature changes have adversely affected the growth of farmed fish. To explore the changes in gill tissue structure caused by changing the water temperature and the relationship between the intestinal microbiota and the Leiocassis longirostris host adaptation mechanism, gill tissue sections and intestinal microbial 16S rRNA amplicon sequencing were conducted under different temperature stress (low temperature 4 °C, normal temperature 26 °C and high temperature 32 °C). The results showed that heat stress and cold stress caused injury and swelling, terminal congestion, cell vacuolation, and necrosis of the gill tissue of L. longirostris. For intestinal microbiota, the abundances of Pseudomonadota and Bacillota increased at the cold stress, while the abundances of Fusobacteriota and Bacteroidota increased at the heat stress. The number of opportunistic bacteria, mainly Aeromonas and Acinetobacter, was the highest under cold stress. In addition, the richness of the intestinal microbiota decreased significantly at heat and cold stresses, while evenness increased. Prediction of intestinal microbiota function showed that most common functions, such as metabolism of cofactors and vitamins, energy metabolism and replication and repair, were decreased significantly at heat stress and cold stress, and phylogenetic relationship analysis revealed significant differences among the groups. In conclusion, the change of temperature altered the gill tissue structure, and affected the structure and homeostasis of the intestinal microbiota, thus affecting the survival time of L. longirostris, and cold stress had a greater effect than heat stress.

Effects of dietary β-glucans on the productive performance, blood parameters, and intestinal microbiota of angelfish (Pterophyllum scalare) juveniles

Among the potential feed additives, β-glucans are known to positively affect the growth performance, blood parameters, and intestinal microbiota of fish, even the ornamental species. Therefore, the present study evaluated the effects of the dietary supplementation of different Saccharomyces cerevisiae β-glucans concentrations (0, 0.05, 0.1, and 0.2%) in juvenile angelfish (Pterophyllum scalare) over a 42-day period. Regarding growth performance, no effects were observed on most parameters. However, 0.2% β-glucans supplementation produced higher condition factor values, indicating a better nutritional status. Furthermore, β-glucans supplementation did not affect blood parameters. Regarding intestinal microbiota, β-glucans supplementation increased the abundance of the potentially beneficial bacterial genus Phascolarctobacterium. The high abundance of bacteria from the phylum Bacteroidetes, which can degrade β-glucans, may be attributed to the increased abundance of Phascolarctobacterium spp. In addition, 0.2% β-glucans supplementation produced more operational taxonomic units and higher Sobs (observed species richness), indicating effects on the overall bacterial community structure. These results demonstrate the potential application of β-glucans as a dietary supplement to improve the performance and modulate the intestinal microbiota of angelfish.

Prometryn exposure disrupts the intestinal health of Eriocheir sinensis: Physiological responses and underlying mechanism

Most toxicity studies of prometryn in non-target aquatic animals have focused on hepatotoxicity, cardiotoxicity, embryonic developmental and growth toxicity, while studies on the molecular mechanisms of intestinal toxicity of prometryn are still unknown. In the current study, the intestinal tissues of the Chinese mitten crab (Eriocheir sinensis) were used to uncover the underlying molecular mechanisms of stress by 96-h acute in vivo exposure to prometryn. The results showed that prometryn activated the Nrf2-Keap1 pathway and up-regulated the expression of downstream antioxidant genes. Prometryn induced the expression of genes associated with non-specific immunity and autophagy, and induced apoptosis through the MAPK pathway. Interestingly, the significant up-or down-regulation of the above genes mainly occurred at 12 h- 24 h after exposure. Intestinal flora sequencing revealed that prometryn disrupted the intestinal normal barrier function mainly by reducing beneficial bacteria abundance, which further weakened the intestinal resistance to exogenous toxicants and caused an inflammatory response. Correlation analyses found that differential flora at the genus level had potential associations with gut stress-related genes. In conclusion, our study contributes to understanding the molecular mechanisms behind the intestinal stress caused by herbicides on aquatic crustaceans.

Profile of the gut microbiota of Pacific white shrimp under industrial indoor farming system

The gut microbial communities interact with the host immunity and physiological functions. In this study, we investigated the bacterial composition in Litopenaeus vannamei shrimp's gut and rearing water under different host (developmental stage: juvenile and adult; health status: healthy and diseased) and environmental factors (temperature 25 °C and 28 °C; and light intensity: low and high). The PCoA analysis showed that all water samples were clustered together in a quarter, whereas the gut samples spread among three quarters. In terms of functional bacteria, gut samples of adult shrimp, healthy adult shrimp, adult shrimp raised at 28 °C, and juvenile shrimp under high light intensity exhibited a higher abundance of Vibrionaceae compared to each other opposite group. Gut samples of juvenile shrimp, infected adult shrimp, juvenile shrimp with low light intensity, and adult shrimp with a water temperature of 25 °C showed a higher abundance of Pseudoaltromonadaceae bacteria compared to each other opposite group. Gut samples of juvenile shrimp, healthy adult shrimp, adult shrimp raised at a water temperature of 28 °C, and juvenile shrimp with high light intensity showed the higher abundance of Firmicutes/Bacteroidota ratio compared to each other opposite group. Our results showed that L. vannamei juveniles are more sensitive to bacterial infections; besides, water temperature of 28 °C and high light intensity groups were both important conditions improving the shrimp gut bacterial composition under industrial indoor farming systems. KEY POINTS: • Bacteria diversity was higher among shrimp intestinal microbiota compared to the rearing water. • Shrimp juveniles are more sensitive to bacterial infection compared to adults. • Water temperature of 28 °C and high light intensity are recommended conditions for white shrimp aquaculture.

Dietary nobiletin regulated cefuroxime- and levofloxacin-associated "gut microbiota-metabolism" imbalance and intestinal barrier dysfunction in mice

Nobiletin (NOB) exhibits significant biological activities and may be a potential dietary treatment for antibiotic-associated gut dysbiosis. In this study, mice were gavaged with 0.2 mL day-1 of 12.5 g L-1 cefuroxime (LFX) and 10 g L-1 levofloxacin (LVX) for a duration of 10 days, accompanied by 0.05% NOB to investigate the regulatory effect and potential mechanisms of NOB on antibiotic-induced intestinal microbiota disorder and intestinal barrier dysfunction. Our results indicated that dietary NOB improved the pathology of intestinal epithelial cells and the intestinal permeability by upregulating the expression of intestinal tight junction proteins (TJs) and the number of goblet cells. Furthermore, dietary NOB reduced the levels of serum lipopolysaccharide (LPS) and pro-inflammatory factors (TNF-α and IL-1β), thereby facilitating the restoration of the intestinal mucosal barrier. Additionally, dietary NOB increased the abundance of beneficial bacteria f_Lachnospiraceae and regulated the metabolic disorders of short-chain fatty acids (SCFAs) and bile acids (BAs). Notably, NOB supplementation resulted in elevated levels of butyric acid and lithocholic acid (LCA), which contributed to the repair of the intestinal mucosal barrier function and the maintenance of intestinal homeostasis. Collectively, our results propose a healthy dietary strategy for the prevention or mitigation of antibiotic-associated gut dysbiosis by dietary NOB.

Adverse effects of fenpropathrin on the intestine of common carp (Cyprinus carpio L.) and the mechanism involved

Fenpropathrin (FEN), a pyrethroid pesticide, is frequently detected in natural water bodies, unavoidable pose adverse effects to aquatic organisms. However, the harmful effects and potential mechanisms of FEN on aquatic species are poorly understood. In this study, common carp were treatment with FEN at 0.45 and 1.35 μg/L for 14 d, and the toxic effects and underlying mechanisms of FEN on the intestine of carp were revealed. RNA-seq results showed that FEN exposure cause a wide range of transcriptional alterations in the intestine and the differentially expressed genes were mainly enrichment in the pathways related to immune and metabolism. Specifically, FEN exposure induced pathological damage and altered submicroscopic structure of the intestine, elevated the levels of Bacteroides fragilis enterotoxin, altered the contents of claudin-1, occludin, and zonula occluden-1 (ZO-1), and causing injury to the intestinal barrier. In addition, inflammation-related index TNF-α in the serum and IL-6 in the intestinal tissues were generally increased after FEN exposure. Moreover, FEN exposure promoted an increase in reactive oxygen species (ROS), altered the levels of superoxide dismutase (SOD), catalase (CAT), and glutathione (GSH), upregulated the contents of malondialdehyde (MDA) in the intestines. The apoptosis-related parameter cytochrome c, caspase-9, and caspase-3 were significantly altered, indicating that inflammation reaction, oxidative stress, and apoptosis may be involved in the toxic mechanism of FEN on carp. Moreover, FEN treatment also altered the intestinal flora community significantly, which may affect the intestinal normal physiological function and thus affect the growth of fish. Overall, the present study help to clarify the intestinal reaction mechanisms after FEN treatment, and provide a basis for the risk assessment of FEN.

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.

Tissue-specific transcriptional response of post-larval clownfish to ocean warming

Anthropogenically driven climate change is predicted to increase average sea surface temperatures, as well as the frequency and intensity of marine heatwaves in the future. This increasing temperature is predicted to have a range of negative physiological impacts on multiple life-stages of coral reef fish. Nevertheless, studies of early-life stages remain limited, and tissue-specific transcriptomic studies of post-larval coral reef fish are yet to be conducted. Here, in an aquaria-based study we investigate the tissue-specific (brain, liver, muscle, and digestive tract) transcriptomic response of post-larval (20 dph) Amphiprion ocellaris to temperatures associated with future climate change (+3 °C). Additionally, we utilized metatranscriptomic sequencing to investigate how the microbiome of the digestive tract changes at +3 °C. Our results show that the transcriptional response to elevated temperatures is highly tissue-specific, as the number of differentially expressed genes (DEGs) and gene functions varied amongst the brain (102), liver (1785), digestive tract (380), and muscle (447). All tissues displayed DEGs associated with thermal stress, as 23 heat-shock protein genes were upregulated in all tissues. Our results indicate that post-larval clownfish may experience liver fibrosis-like symptoms at +3 °C as genes associated with extracellular matrix structure, oxidative stress, inflammation, glucose transport, and metabolism were all upregulated. We also observe a shift in the digestive tract microbiome community structure, as Vibrio sp. replace Escherichia coli as the dominant bacteria. This shift is coupled with the dysregulation of various genes involved in immune response in the digestive tract. Overall, this study highlights post-larval clownfish will display tissue-specific transcriptomic responses to future increases in temperature, with many potentially harmful pathways activated at +3 °C.

Effects of simulated winter short photoperiods on the microbiome and intestinal metabolism in Huanghe carp (Cyprinus carpio haematopterus)

Objective

As one of the most important environmental signals, photoperiod plays a crucial role in regulating the growth, metabolism, and survival of organisms. The photoperiod shifts with the transition of the seasons. The difference in photoperiod between summer and winter is the greatest under natural conditions. However, the effect of photoperiod on Huanghe carp (Cyprinus carpio haematopterus) was paid little attention. We investigated the impact of artificial manipulation of seasonal photoperiod on Huanghe carp by integrating growth performance, intestinal flora, and intestinal metabolome.

Method

We conducted an 8-week culture experiment with summer photoperiod (14 h light:10 h dark, n = 60) as the control group and winter photoperiod (10 h light:14 h dark, n = 60) based on the natural laws.

Results

Winter photoperiod provokes significant weight increases in Huanghe carp. The altered photoperiod contributed to a significant increase in triglyceride and low-density lipoprotein cholesterol levels and the gene expressions of lipid metabolism in the intestine of Huanghe carp. 16s rDNA sequencing revealed that winter photoperiod diminished intestinal flora diversity and altered the abundance. Specifically, the relative abundances of Fusobacteria and Acidobacteriota phyla were higher but Proteobacteria, Firmicutes, and Bacteroidetes phyla were reduced. Analogously, photoperiodic changes induced a significant reduction in the Pseudomonas, Vibrio, Ralstonia, Acinetobacter, and Pseudoalteromonas at the genus level. Additionally, metabolomics analysis showed more than 50% of differential metabolites were associated with phospholipids and inflammation. Microbiome and metabolome correlation analyses revealed that intestinal microbe mediated lipid metabolism alteration.

Conclusion

The winter photoperiod induced intestinal flora imbalance and lipid metabolism modification, ultimately affecting the growth of Huanghe carp. This study provides new insights into the effects of seasonal photoperiodic alteration on the well-being of fish.