Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus)

Exploring the underlying mechanisms of enteritis impact on golden pompano (Trachinotus ovatus) through multi-omics analysis

Enteritis posed a significant health challenge to golden pompano (Trachinotus ovatus) populations. In this research, a comprehensive multi-omics strategy was implemented to elucidate the pathogenesis of enteritis by comparing both healthy and affected golden pompano. Histologically, enteritis was characterized by villi adhesion and increased clustering after inflammation. Analysis of the intestinal microbiota revealed a significant increase (P < 0.05) in the abundance of specific bacterial strains, including Photobacterium and Salinivibrio, in diseased fish compared to the healthy group. Metabolomic analysis identified 5479 altered metabolites, with significant impacts on terpenoid and polyketide metabolism, as well as lipid metabolism (P < 0.05). Additionally, the concentrations of several compounds such as calcitetrol, vitamin D2, arachidonic acid, and linoleic acid were significantly reduced in the intestines of diseased fish post-enteritis (P < 0.05), with the detection of harmful substances such as Efonidipine. In transcriptomic profiling, enteritis induced 68 upregulated and 73 downregulated genes, predominantly affecting steroid hormone receptor activity (P < 0.05). KEGG pathway enrichment analysis highlighted upregulation of SQLE and CYP51 in steroidogenesis, while the HSV-1 associated MHC1 gene exhibited significant downregulation. Integration of multi-omics results suggested a potential pathogenic mechanism: enteritis may have resulted from concurrent infection of harmful bacteria, specifically Photobacterium and Salinivibrio, along with HSV-1. Efonidipine production within the intestinal tract may have blocked certain calcium ion channels, leading to downregulation of MHC1 gene expression and reduced extracellular immune recognition. Upregulation of SQLE and CYP51 genes stimulated steroid hormone synthesis within cells, which, upon binding to G protein-coupled receptors, influenced calcium ion transport, inhibited immune activation reactions, and further reduced intracellular synthesis of anti-inflammatory substances like arachidonic acid. Ultimately, this cascade led to inflammation progression, weakened intestinal peristalsis, and villi adhesion. This study utilized multi-level omics detection to investigate the pathological symptoms of enteritis and proposed a plausible pathogenic mechanism, providing innovative insights into enteritis verification and treatment in offshore cage culture of golden pompano.

Integration of transcriptome, gut microbiota, and physiology reveals toxic responses of the red claw crayfish (Cherax quadricarinatus) to imidacloprid

Imidacloprid enters the water environment through rainfall and causes harm to aquatic crustaceans. However, the potential chronic toxicity mechanism of imidacloprid in crayfish has not been comprehensively studied. In this study, red claw crayfish (Cherax quadricarinatus) were exposed to 11.76, 35.27, or 88.17 μg/L imidacloprid for 30 days, and changes in the physiology and biochemistry, gut microbiota, and transcriptome of C. quadricarinatus and the interaction between imidacloprid, gut microbiota, and genes were studied. Imidacloprid induced oxidative stress and decreased growth performance in crayfish. Imidacloprid exposure caused hepatopancreas damage and decreased serum immune enzyme activity. Hepatopancreatic and plasma acetylcholine decreased significantly in the 88.17 μg/L group. Imidacloprid reduced the diversity of the intestinal flora, increased the abundance of harmful flora, and disrupted the microbiota function. Transcriptomic analysis showed that the number of up-and-down-regulated differentially expressed genes (DEGs) increased significantly with increasing concentrations of imidacloprid. DEG enrichment analyses indicated that imidacloprid inhibits neurotransmitter transduction and immune responses and disrupts energy metabolic processes. Crayfish could alleviate imidacloprid stress by regulating antioxidant and detoxification-related genes. A high correlation was revealed between GST, HSPA1s, and HSP90 and the composition of gut microorganisms in crayfish under imidacloprid stress. This study highlights the negative effects and provides detailed sequencing data from transcriptome and gut microbiota to enhance our understanding of the molecular toxicity of imidacloprid in crustaceans.

Combined effects of norfloxacin and polystyrene nanoparticles on the oxidative stress and gut health of the juvenile horseshoe crab Tachypleus tridentatus

Pollution with anthropogenic contaminants including antibiotics and nanoplastics leads to gradual deterioration of the marine environment, which threatens endangered species such as the horseshoe crab Tachypleus tridentatus. We assessed the potential toxic mechanisms of an antibiotic (norfloxacin, 0, 0.5, 5 μg/L) and polystyrene nanoparticles (104 particles/L) in T. tridentatus using biomarkers of tissue redox status, molting, and gut microbiota. Exposure to single and combined pollutants led to disturbance of redox balance during short-term (7 days) exposure indicated by elevated level of a lipid peroxidation product, malondialdehyde (MDA). After prolonged (14-21 days) exposure, compensatory upregulation of antioxidants (catalase and glutathione but not superoxide dismutase) was observed, and MDA levels returned to the baseline in most experimental exposures. Transcript levels of molting-related genes (ecdysone receptor, retinoic acid X alpha receptor and calmodulin A) and a molecular chaperone (cognate heat shock protein 70) showed weak evidence of response to polystyrene nanoparticles and norfloxacin. The gut microbiota T. tridentatus was altered by exposures to norfloxacin and polystyrene nanoparticles shown by elevated relative abundance of Bacteroidetes. At the functional level, evidence of suppression by norfloxacin and polystyrene nanoparticles was found in multiple intestinal microbiome pathways related to the genetic information processing, metabolism, organismal systems, and environmental information processing. Future studies are needed to assess the physiological and health consequences of microbiome dysbiosis caused by norfloxacin and polystyrene nanoparticles and assist the environmental risk assessment of these pollutants in the wild populations of the horseshoe crabs.

Response of serum biochemical profile, antioxidant enzymes, and gut microbiota to dietary Hong-bailanshen supplementation in horses

Background

Traditional Chinese medicine (TCM) is widely used in humans and animals, which is very important for health. TCM affects the body 's immunity and changes in intestinal flora. This study was conducted to investigate the effects of dietary Hong-bailanshen (HBLS) supplementation in horses on serum biochemical profile, antioxidant enzymes and gut microbiota.

Methods

In this study, five horses were selected. On day 0, 14, 28, blood samples and feces were collected on days 0, 14, and 28 to analyse gut microbiota, serum biochemical and redox indexes.

Results

The results showed that the addition of HBLS to horse diets significantly decreased the level of alanine aminotransferase, alkaline phosphatase, creatine kinase and malondialdehyde (p < 0.05, p < 0.01) and significantly increased the activity of total antioxidant capacity, superoxide dismutase and catalase (p  < 0.05, p  < 0.01). Compared with day 14, the levels of alanine aminotransferase, alkaline phosphatase and creatine kinase were significantly decreased; however, the level of catalase was significantly increased in the horses continuously fed with HBLS for 28 days (p  < 0.05, p < 0.01). Alpha diversity analysis was performed that chao1 (p  < 0.05), observed_specicies, faith'pd and goods_coverage upregulated in the horses fed HBLS. A total of 24 differential genera were detected adding HBLS to diet increased the abundance of Bacillus, Lactobacillaceae, Leuconostocaceae, Christensenellaceae, Peptostreptococcaceae, Faecalibacterium, Erysipelotrichaceae, Pyramidobacter, Sphaerochaeta, WCHB1-25, Bacteria, Oscillospira, and Acetobacteraceae, while reduced Aerococcus, EtOH8, Syntrophomonas, Caulobacter, Bradyrhizobiaceae, W22, Succinivibrionaceae, and Desulfovibrio (p < 0.05, p < 0.01).

Conclusion

Adding HBLS to the diet could be a potentially effective strategy to improve horses' health.

Disruption of intestinal structure, tight junction complex, immune response and microbiota after chronic exposure to copper in swamp eel (Monopterus albus)

As an essential micronutrient, copper is crucial in aquatic organisms' growth and development. Numerous studies have consistently reported that excessive intake of copper can have harmful effects on organisms. However, there are limited studies on the impact of copper on the intestine of the swamp eel (Monopterus albus). This study aimed to investigate the changes of intestinal histopathology, tight junction complex, immune response, and microbiota in swamp eel treated with 0 mg/L Cu2+, 0.05 mg/L Cu2+, and 0.10 mg/L Cu2+ for 56 d. Intestinal histopathology showed major changes such as the increased number of erythrocytes and goblet cells in the lamina propria, and separation of the lamina propria. The expression of genes involved in tight junction complex (ZO-1, Claudin-3, Claudin-12 and Claudin-15) was significantly changed. In addition, copper exposure significantly increased the mRNA levels of TLR3, TLR7, TLR8, NF-κB, I-κB, TNF-α and IL-8, especially in 0.10 mg/L Cu2+ group. In contrast, the relative expression level of anti-inflammatory cytokine TGF-β was significantly decreased after exposure to copper. Analysis of the intestinal microbiome showed the intestinal microbiota of swamp eels in the control and copper exposure groups were dominated by Firmicutes and Proteobacteria at the phylum level. Notably, copper exposure changed the diversity of the intestinal microbiota and decreased the relative abundance of Firmicutes and Proteobacteria in the intestine of swamp eel. Collectively, this study demonstrates that chronic copper exposure induces intestinal pathologic changes and inflammatory response, disrupts the intestinal microbial diversity and microbiota composition, and decreases intestinal barrier function in swamp eel, which enhances our understanding of copper-induced intestinal toxicity in fish.

Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review

The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.

Black soldier fly pulp in the diet of golden pompano: Effect on growth performance, liver antioxidant and intestinal health

Black soldier fly (Hermetia illucens) has been widely researched as a protein source for fish meal replacement in aquaculture, but few studies have focused on its potential as a feed additive for growth and immune enhancement. We conducted a 56-day culture experiment to determine the impact of feed addition of black soldier fly pulp (BSFP, with 86.2% small peptides in dry basis) on growth performance, plasma biochemistry, liver antioxidant levels, intestinal immunity, digestion and microbiota of juvenile golden pompano (Trachinotus ovatus, 5.63 ± 0.02 g). BSFP was added to the basal diet at 0%, 1%, 3%, 5%, 7% and 9% (named Control, BSFP-1, BSFP-3, BSFP-5, BSFP-7, BSFP-9), respectively. BSFP increased the weight gain rate, specific growth rate, protein efficiency ratio and reduced the feed conversion rate of juvenile T. ovatus, the optimal growth performance was reached at BSFP-1, after which a negative feedback phenomenon was observed. Low levels of BSFP upregulated the expression of hepatic antioxidant, intestinal tight junctions, anti-inflammatory related genes and enhanced antioxidant, immune and intestinal digestive enzyme activities, which simultaneously reduced hepatic malondialdehyde and plasma aspartate transaminase and alanine aminotransferase concentrations. However, at BSFP-7, catalase activity was significantly reduced, while NF-κB p65 and pro-inflammatory cytokines transcription was significantly enhanced (P < 0.05). The results suggest that high doses of BSFP addition may damage fish health by inhibiting small peptide uptake, decreasing the activity of antioxidant enzyme and activating the canonical NF-κB pathway. Conversely, low doses of BSFP enhanced intestinal tight junction protein transcription, digestive enzyme activity and immune performance, inhibited pathogenic microbiota, while enhancing liver antioxidant capacity, which was associated with activated Nrf2-Keap1 pathway and suppressed NF-κB pathway, showing its potential as a feed additive to aquafeeds.

Midgut microbiota affects the intestinal barrier by producing short-chain fatty acids in Apostichopus japonicus

Introduction

The intestinal microbiota participates in host physiology and pathology through metabolites, in which short-chain fatty acids (SCFAs) are considered principal products and have extensive influence on intestine homeostasis. It has been reported that skin ulceration syndrome (SUS), the disease of Apostichopus japonicus caused by Vibrio splendidus, is associated with the alteration of the intestinal microbiota composition.

Method

To investigate whether the intestinal microbiota affects A. japonicus health via SCFAs, in this study, we focus on the SCFA profiling and intestinal barrier function in A. japonicus treated with V. splendidus.

Results and discussion

We found that V. splendidus could destroy the mid-intestine integrity and downregulate the expression of tight junction proteins ZO-1 and occludin in A. japonicus, which further dramatically decreased microorganism abundance and altered SCFAs contents. Specifically, acetic acid is associated with the largest number of microorganisms and has a significant correlation with occludin and ZO-1 among the seven SCFAs. Furthermore, our findings showed that acetic acid could maintain the intestinal barrier function by increasing the expression of tight junction proteins and rearranging the tight junction structure by regulating F-actin in mid-intestine epithelial cells. Thus, our results provide insights into the effects of the gut microbiome and SCFAs on intestine barrier homeostasis and provide essential knowledge for intervening in SUS by targeting metabolites or the gut microbiota.

Effects of methomyl on the intestinal microbiome and hepatic transcriptome of tilapia, and the modifying effects of mint co-culture

Methomyl (MET) is an oxime carbamate insecticide that can contaminate aquatic systems resulting in toxicological effects. It can harm some fish species possibly through the anti-oxidative, phagosome pathway. Mint is one of the most widely herbal plants exhibiting antioxidant activities. In this study, we investigated the impact of MET on the antioxidant system of Oreochromis niloticus in presence of mint as a floating bed. Results revealed that the superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase, and glutathione S-transferase significantly decreased and the GSH content significantly increased in the intestine. The hepatic peroxisome proliferator-activated receptor (PPAR) signalling pathway, carbon metabolism, renal phosphoinositide 3-kinase (PI3K)-Akt, mitogen-activated protein kinase (MAPK) signalling pathway, and phagosomes were significantly affected. Upon long-term exposure, circadian rhythm and phagosomes were enriched in the liver and kidney. However, mint increased the enriched pathways of Toll-like receptor, PPAR, p53, NF-kappa B, MAPK, oestrogen, and B cell receptor signalling pathways. MET with different concentrations destroyed the balance of gut microbiota, mint decreased Verrucomicrobia and Akkermansia for the maintenance resulted from MET. Cetobacterium had a positive impact on total nitrogen (TN), chemical oxygen demand (CODMn), and glutathione reductase (GR), while Akkermansia had a positive impact on feed conversion ratio (FCR), SOD and CAT, and the abundance of both decreased due to MET exposure. High mint density removed more concentrations of nitrogen and phosphorus in the tilapia cultivation wastewater. Therefore, planting with mint can alleviate the toxicological effects produced by MET, shape the intestinal microbiota, and strengthen the connection between water quality and the metabolic parameters.

Lead exposure disrupted ileal barrier of developmental Japanese quails(Coturnix japonica): Histopathological damages, microbiota dysbiosis and immune disorder

The gut barrier plays an essential role in maintaining homeostasis and is usually composed of a mechanical barrier, a chemical barrier, an immune barrier, and a biological barrier. However, the impacts of lead (Pb) exposure on avian gut barrier are still unclear. Therefore, the present study tried to determine the toxic effects of Pb on ileal barrier of a biological model-Japanese quail (Coturnix japonica). One-week old quails were exposed to 0, 50, 500 and 1000 ppm Pb in drinking water for 5 weeks. The results showed mechanic barrier in the ileum was disrupted with microstructural deformation featured by epithelial cell abscission, villi contractions and goblet cells reduction as well as ultrastructural changes characterized by swollen mitochondria, blurry tight junctions and microvilli subtraction. Meanwhile, the expression of genes associated with intestinal tight junctions was downregulated in Pb-treated groups indicating tight junction malfunction. Moreover, less mucus and downregulation of expression of mucin2 (Muc2) and Krüppel-like factor 4 (Klf4) indicated chemical barrier disturbance by Pb. In addition, the alteration of microbial diversity and emergence of pathogen bacteria suggested ileal biological barrier disruption by Pb. Furthermore, Pb caused immune dysfunction in the ileum through promoting the expression of pro-inflammatory factors including interleukin 1 beta (IL-1β), interleukin 6 (IL-6), Interferon gamma (IFN-γ), tumor necrosis factor alpha (TNF-α) and nuclear factor kappa B (NF-κB) and inhibiting the expression of anti-inflammatory factor interleukin 10 (IL-10). The present study demonstrated that Pb may pose health risks to birds through gut barrier damages.

Identification and Characterization of a Potential Probiotic, Clostridium butyricum G13, Isolated from the Intestine of the Mud Crab (Scylla paramamosain)

The butyrate-producing bacterium Clostridium butyricum has been proven to be important in improving the growth and health benefits of aquatic animals. In this study, C. butyricum G13 was isolated for the first time from the gut of the mud crab (Scylla paramamosain). The results of this study showed that C. butyricum G13 could produce a high concentration of butyric acid and grow well in a wide range of pHs (4 to 9) and NaCl (1 to 2.5%) and bile salt (0.2 to 1.0%) concentrations. In vitro characterization revealed that C. butyricum G13 is a Gram-positive and gamma-hemolytic bacterium sensitive to most antibiotics and shows hydrophobicity and the capacity to degrade starch. In vitro fermentation using mud crab gut contents showed that C. butyricum G13 alone or in combination with galactooligosaccharides (GOS) and/or resistant starch (RS) significantly increased butyric acid production and beneficially affected the abundance and diversity of intestinal microbiota. In addition, C. butyricum G13 can improve the survival rate of mud crabs and effectively maintain the normal structure of gut morphology after infection with Vibrio parahaemolyticus. In conclusion, C. butyricum G13 can be considered a potential probiotic that improves the immune capacity and confers health benefits on mud crabs. IMPORTANCE With the development of society, more and more aquatic animals are demanded. Intensification in the aquaculture scale is facing problems, such as disease outbreaks, eutrophication of water bodies, and misuse of antibiotics. Among these challenges, disease outbreak is the most important factor directly affecting aquaculture production. It is crucial to explore new approaches effective for the prevention and control of diseases. Probiotics have been widely used in aquaculture and have shown beneficial effects on the host. In this study, the butyrate-producing bacterium Clostridium butyricum G13 was isolated for the first time from the intestine of the mud crab through in vitro fermentation. The bacterium has probiotic properties and changes the gut microbiota to be beneficial to hosts in vitro as well as protecting hosts from Vibrio parahaemolyticus infection in vivo. The outcomes of this study indicate that C. butyricum G13 can be used as a potential probiotic in mud crab aquaculture.

Dietary berberine against intestinal oxidative stress, inflammation response, and microbiota disturbance caused by chronic copper exposure in freshwater grouper (Acrossocheilus fasciatus)

Berberine (BBR) is known for its strong antioxidant, anti-inflammatory, and capacity to preserve intestinal microbiota balance in fish. This study aimed to investigate the protective effects of berberine against copper-induced toxicity in the intestine of freshwater grouper Acrossocheilus fasciatus. The experiment involved four groups: a control group, a Cu group exposed to 0.02 mg/L Cu²⁺, and two BBR groups fed with 100 or 400 mg/kg of berberine diets and exposed to the same Cu²⁺ concentration. Three replicates of healthy fish (initial weight 1.56 ± 0.10 g) were subjected to their respective treatments for 30 days. Results showed that none of the treatments significantly affected the survival rate, final weight, weight gain, and feed intake (P > 0.05). However, supplementation with 100 and 400 mg/kg of BBR significantly lowered the antioxidant activities, and glutathione peroxidase (gpx) and superoxide dismutase (sod) expression levels, as well as reduced malondialdehyde (MDA) content caused by Cu²⁺ exposure (P < 0.05). Berberine inclusion significantly downregulated proinflammatory factors NLR family pyrin domain containing 3 (nlrp3), interleukin 1 beta (il1β), interleukin 6 cytokine family signal transducer (il6st) but upregulated transforming growth factor beta 1 (tgfβ1) and heat shock 70kDa protein (hsp70) expression. Moreover, berberine at both levels maintained the intestinal structural integrity and significantly improved gap junction gamma-1 (gjc1) mRNA level compared to the Cu group (P < 0.05). Based on 16S rDNA sequencing, the richness and diversity of intestinal microbiota in different groups were not significantly influenced. Berberine reduced the Firmicutes/Bacteroidota ratio and stifled the growth of some specific pathogenic bacteria such as Pseudomonas, Citrobacter, and Acinetobacter, while boosting the richness of potential probiotic bacteria, including Roseomonas and Reyranella compared with the Cu group. In conclusion, berberine showed significant protective effects against Cu²⁺-induced intestinal oxidative stress, inflammation response, and microbiota disturbance in freshwater grouper.

Dietary Astragalus polysaccharides improve the growth and innate immune response of giant freshwater prawn Macrobrachium rosenbergii: Insights from the brain-gut axis

Supplementation with Astragalus polysaccharides (APS) has beneficial effects on aquatic animals. Herein, we aimed to investigate the effects of different doses of APS on the growth, innate immune response, and brain-gut axis of Macrobrachium rosenbergii. The molecular weight and the monosaccharide composition of APS were analyzed. APS were added at concentration of 0 (control), 0.05, 0.10, 0.15, and 0.20 % in practical diets. Growth performance increased significantly under 0.05 to 0.20 % APS, with enhanced lipase and protease activities in intestinal tissues. Prawns receiving APS supplementation had significantly lower amounts of pathogenic intestinal bacteria (Vibrio and Aeromonas) and a markedly different microbial community structure compared with those of the control group. The fecal short chain fatty acid (SCFA) and neurotransmitters γ-aminobutyric acid contents increased in the brains of prawns receiving APS, which was potentially associated with increased Lactobacillus and Bacillus levels. Prawns receiving APS supplementation displayed a significantly enhanced immune function (such as total hemocyte count, total protein concentration, phenoloxidase activity, serum agglutination titer, and lysozyme activity) and improved disease resistance to Vibrio anguillarum compared those in the control group. Thus, dietary APS positively affected the gut-brain axis by altering the microbiota composition, increasing the fecal SCFA content, and enhancing prawn immunity.

Diversity and Antimicrobial Activity of Intestinal Fungi from Three Species of Coral Reef Fish

Although intestinal microbiota play crucial roles in fish digestion and health, little is known about intestinal fungi in fish. This study investigated the intestinal fungal diversity of three coral reef fish (Lates calcarifer, Trachinotus blochii, and Lutjanus argentimaculatus) from the South China Sea using a culturable method. A total of 387 isolates were recovered and identified by sequencing their internal transcribed spacer sequences, belonging to 29 known fungal species. The similarity of fungal communities in the intestines of the three fish verified that the fungal colonization might be influenced by their surrounding environments. Furthermore, the fungal communities in different intestines of some fish were significantly different, and the number of yeasts in the hindgut was less than that in fore- and mid-intestines, suggesting that the distribution of fungi in fishes' intestines may be related to the physiological functions of various intestinal segments. In addition, 51.4% of tested fungal isolates exhibited antimicrobial activity against at least one marine pathogenic microorganism. Notably, isolate Aureobasidium pullulans SCAU243 exhibited strong antifungal activity against Aspergillus versicolor, and isolate Schizophyllum commune SCAU255 displayed extensive antimicrobial activity against four marine pathogenic microorganisms. This study contributed to our understanding of intestinal fungi in coral reef fish and further increased the library of fungi available for natural bioactive product screening.

The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats

BACKGROUND

Artificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.

RESULTS

The results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats. In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.

CONCLUSIONS

This study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.

Exposure to nitrate induced growth, intestinal histology and microbiota alterations of Bufo raddei Strauch tadpoles

Nitrate (NO₃^-) is one of the ubiquitous environmental chemicals which multiplies negative impacts on aquatic life such as amphibian larvae. However, the data involving the dynamics of amphibians in response to NO₃-N are scarce. This study investigated the effects of NO₃-N on locomotor ability, growth performance, oxidative stress parameters, intestinal histology, and intestinal microbiota of Bufo raddei Strauch tadpoles. The tadpoles were chronically exposed to different concentrations of NO₃-N (10, 50, 100, and 200 mg/L) from Gosner stage 26 to 38. Our results revealed that NO₃-N exposure caused significantly reduced body weight and length, impaired locomotor activity, and severe oxidative damage to liver tissue. Moreover, the high NO₃-N (50, 100, and 200 mg/L) exposure caused irregular arrangement and indistinct cell borders of mucosal epithelial cells in the tadpoles intestine. The NO₃-N exposure significantly changed the structure of the intestinal microbiota. The phylum Cyanobacteria occupy the main niche of intestinal microbes and have a certain negative correlation with the growth and motility of tadpoles. In addition, the functional prediction revealed that NO₃-N exposure obviously downregulated the metabolism of enzyme families in tadpoles. Our comprehensive research shows the toxicity of NO₃-N exposure in B. raddei Strauch, explores the potential links between development and intestinal microbiota of tadpole, and provides a new framework for the potential health risk of nitrate in amphibians.

Identification of multifunctionality of grass carp (Ctenopharyngodon idella) TBK1 during bacterial infection

TBK1 is an atypical IκB kinase family member with a set of functions. It is involved in congenital immunization and autophagy in mammals. In this study, we reported that grass carp TBK1 gene expression could be upregulated by bacterial infection. Overexpression of TBK1 could decrease the number of adhesive bacteria in CIK cells. TBK1 could promote cellular migration, proliferation, vitality, and anti-apoptosis ability. Furthermore, the expression of TBK1 could activate the NF-κB signaling pathway by inducing inflammatory cytokines. In addition, we found that the grass carp TBK1 could cause the autophagy level of CIK cells within the decreasing level of p62 protein. Our finding indicated that TBK1 participated in grass carp innate immune progress and autophagy. This study provides evidence of the positive regulation of TBK1 in teleost innate immunity with its multiple functions. It thus may provide important information about the defense and immune mechanisms used by teleost against pathogens.

Omics and imaging combinatorial approach reveals butyrate-induced inflammatory effects in the zebrafish gut

BACKGROUND

Prebiotic feed additives aim to improve gut health by influencing the microbiota and the gut barrier. Most studies on feed additives concentrate on one or two (monodisciplinary) outcome parameters, such as immunity, growth, microbiota or intestinal architecture. A combinatorial and comprehensive approach to disclose the complex and multifaceted effects of feed additives is needed to understand their underlying mechanisms before making health benefit claims. Here, we used juvenile zebrafish as a model species to study effects of feed additives by integrating gut microbiota composition data and host gut transcriptomics with high-throughput quantitative histological analysis. Zebrafish received either control, sodium butyrate or saponin-supplemented feed. Butyrate-derived components such as butyric acid or sodium butyrate have been widely used in animal feeds due to their immunostimulant properties, thereby supporting intestinal health. Soy saponin is an antinutritional factor from soybean meal that promotes inflammation due to its amphipathic nature.

RESULTS

We observed distinct microbial profiles associated with each diet, discovering that butyrate (and saponin to a lesser extent) affected gut microbial composition by reducing the degree of community-structure (co-occurrence network analysis) compared to controls. Analogously, butyrate and saponin supplementation impacted the transcription of numerous canonical pathways compared to control-fed fish. For example, both butyrate and saponin increased the expression of genes associated with immune response and inflammatory response, as well as oxidoreductase activity, compared to controls. Furthermore, butyrate decreased the expression of genes associated with histone modification, mitotic processes and G-coupled receptor activity. High-throughput quantitative histological analysis depicted an increase of eosinophils and rodlet cells in the gut tissue of fish receiving butyrate after one week of feeding and a depletion of mucus-producing cells after 3 weeks of feeding this diet. Combination of all datasets indicated that in juvenile zebrafish, butyrate supplementation increases the immune and the inflammatory response to a greater extent than the established inflammation-inducing anti-nutritional factor saponin. Such comprehensive analysis was supplemented by in vivo imaging of neutrophil and macrophage transgenic reporter zebrafish (mpeg1:mCherry/mpx:eGFPi¹¹⁴) larvae. Upon exposure to butyrate and saponin, these larvae displayed a dose-dependent increase of neutrophils and macrophages in the gut area.

CONCLUSION

The omics and imaging combinatorial approach provided an integrated evaluation of the effect of butyrate on fish gut health and unraveled inflammatory-like features not previously reported that question the usage of butyrate supplementation to enhance fish gut health under basal conditions. The zebrafish model, due to its unique advantages, provides researchers with an invaluable tool to investigate effects of feed components on fish gut health throughout life.

Effects of different protein and lipid levels on the growth performance and intestinal microflora of loach (Paramisgurnus dabryanus)

The aim of this study was to examine the effects of dietary protein and lipid levels on the growth performance and homeostasis of the intestinal flora in Paramisgurnus dabryanus. An 8-wk 3 × 3 two-factorial experiment was conducted to investigate the interaction between dietary crude protein (CP: 30%, 35%, 40%) and ether extract (EE: 6%, 10%, 14%) on the growth rate and the intestinal microflora of P. dabryanus. A total of 2,160 fish (5.19 ± 0.01 g) were randomly allotted to 36 aquariums each with 60 fish. Fish were fed the experimental diet twice daily. Results revealed that weight gain rate (WGR), specific growth rate (SGR), protein efficiency ratio and net protein utilization significantly increased when increasing protein levels from 30% to 40% (P < 0.05). Both WGR and SGR enhanced first but reduced thereafter with maximum value at 10% lipid level as dietary lipid increased from 6% to 14% (P < 0.05). Significant interactions between protein and lipid were found with feed conversion rate, lipid efficiency ratio and net lipid utilization (P < 0.05). At the phylum level, Proteobacteria and Actinobacteria were the dominant bacteria; at the genus level, Burkholderia-Caballeronia-Paraburkholderia was the dominant bacteria. Fish fed the diet containing 10% lipid had a higher abundance of Proteobacteria and unclassified_f_Eenterobacteriaceae than those fed the 14% lipid diet, and a higher abundance of Rhodobacter than those fed the 6% lipid diet (P < 0.05). Analysis of the predicted functions showed that metabolism in the intestine of fish in the CP40EE10 group was more active than that in CP30EE14 group. Polynomial regression analysis found that a diet containing 40.87% protein and 9.88% lipid can be considered optimal for P. dabryanus.

Evaluation of Methanotroph (Methylococcus capsulatus, Bath) Bacteria Protein as an Alternative to Fish Meal in the Diet of Juvenile American Eel (Anguilla rostrata)

This study was conducted to evaluate the effects of replacing fish meal (FM) with methanotroph (Methylococcus capsulatus, Bath) bacteria protein (MBP) in the diets of the juvenile American eel (Anguilla rostrata). Trial fish were randomly divided into the MBP0 group, MBP6 group, MBP12 group, and MBP18 group fed the diets with MBP replacing FM at levels of 0, 6%, 12%, and 18%, respectively. The trial lasted for ten weeks. There were no significant differences in weight gain or feed utilization among the MBP0, MBP6, and MBP12 groups (except for the feeding rate in the MBP12 group). Compared with the MBP0 group, the D-lactate level and diamine oxidase activity in the serum were significantly elevated in the MBP12 and MBP18 groups. In terms of non-specific immunity parameters in serum, the alkaline phosphatase activity was significantly decreased in the MBP18 group, and the complement 3 level was significantly elevated in the MBP12 and MBP18 groups. The activities of lipase and protease in the intestine were significantly decreased in the MBP12 and MBP18 groups. Compared with the MBP0 group, the total antioxidant capacity and activities of superoxide dismutase, catalase, and glutathione peroxidase in the intestine were significantly decreased in the MBP18 group, while the malondialdehyde level was significantly increased. The villus height, muscular thickness, and microvillus density were significantly decreased in the MBP12 and MBP18 groups. There were no significant differences in the foresaid parameters between the MBP0 group and the MBP6 group. The intestinal microbiota of the MBP6 group was beneficially regulated to maintain similar growth and health status with the MBP0 group. The adverse effects on the intestinal microbiota were reflected in the MBP18 group. In conclusion, MBP could successfully replace 6% of FM in the diet without adversely affecting the growth performance, serum biochemical parameters, and intestinal health of juvenile American eels.

Impact of aluminum exposure on oxidative stress, intestinal changes and immune responses in red swamp crayfish (Procambarus clarkii)

Aluminum (Al) is an abundant metal that has been classified as a threatening pollutant due to indiscriminate use and anthropogenic activities. This study aimed to evaluate the impacts of Al on crayfish (Procambarus clarkii), including biochemical change, histological alteration, gut microbial community diversification, and immune changes. The bioaccumulation of Al was detected in the hemolymph and intestine of crayfish after Al exposure at different time points. Results showed that Al exposure significantly induced oxidative stress and caused pathohistological changes on intestinal barrier structures in crayfish. It was found that the intestinal microbiota was affected by retained Al and the intestinal community diversity was changed after Al treated in the crayfish. Furthermore, Al exposure affected the immunity in crayfish, by altering the expression of a set of immune-related genes, as well as reducing the phenoloxidase and lysozyme activities. Moreover, Al exposure promoted hemocytes apoptosis and impaired hemophagocytic capacity against Vibro parahamolyticus, resulting in higher mortality of crayfish upon bacterial infection. Taken these results together, we conclude that excessive Al exposure caused adverse effects on multiple biological processes of crayfish and Al pollution is a potential threat to crayfish culture.

Comparative analysis of intestinal microbiota composition and transcriptome in diploid and triploid Carassius auratus

Polyploidy and the microbiome are crucial factors in how a host organism responds to disease. However, little is known about how triploidization and microbiome affect the immune response and disease resistance in the fish host. Therefore, this study aims to identify the relationship between intestinal microbiota composition, transcriptome changes, and disease resistance in triploid Carassius auratus (3nCC). In China's central Dongting lake water system, diploid (2nCC) and triploid Carassius auratus were collected, then 16S rRNA and mRNA sequencing were used to examine the microbes and gene expression in the intestines. 16S rRNA sequencing demonstrated that triploidization altered intestinal richness, as well as the diversity of commensal bacteria in 3nCC. In addition, the abundance of the genus Vibrio in 3nCC was increased compared to 2nCC (P < 0.05). Furthermore, differential expression analysis of 3nCC revealed profound up-regulation of 293 transcripts, while 324 were down-regulated. Several differentially expressed transcripts were related to the immune response pathway in 3nCC, including NLRP3, LY9, PNMA1, MR1, PELI1, NOTCH2, NFIL3, and NLRC4. Taken together, triploidization can alter bacteria composition and abundance, which can in turn result in changes in expression of genes. This study offers an opportunity for deciphering the molecular mechanism underlying disease resistance after triploidization.

New insights into β-glucan-enhanced immunity in largemouth bass Micropterus salmoides by transcriptome and intestinal microbial composition

β-glucan is widely used in aquaculture due to its immunostimulatory effects, but the specific effect and potential regulatory mechanism on largemouth bass (Micropterus salmoides) are still unclear. Here, we evaluated the effects of β-glucan on growth, resistance to Aeromonas schubertii, intestinal health, and transcriptome of largemouth bass to reveal the potential regulators, metabolic pathways, and altered differential microbiota. Four experimental diets were designed with β-glucan supplementation levels of 0 (control), 100 (LA-100), 200 (MA-200), and 300 (HA-300) mg kg^-1, and each diet was fed to largemouth bass (79.30 ± 0.50 g) in triplicate for 70 days, followed by a 3-day challenge experiment. Results showed that different β-glucan supplementations had no significant effects on growth performance and whole-body composition. Fish fed a diet with 300 mg kg^-1 β-glucan significantly increased the activity of lysozyme than those fed diets with 0 and 100 mg kg^-1 β-glucan. In addition, the survival rate of largemouth bass in β-glucan supplementation groups was significantly higher than the control group at 12- and 24-h challenge by Aeromonas schubertii. Transcriptome analysis showed that a total of 1,245 genes were differentially expressed [|log₂(fold change)| ≥1, q-value ≤0.05], including 109 immune-related differentially expressed genes (DEGs). Further analysis revealed that significantly upregulated and downregulated DEGs associated with immunity were mapped into 12 and 24 pathways, respectively. Results of intestinal microflora indicated that fish fed a diet with 300 mg kg^-1 β-glucan had higher bacterial richness and diversity as evaluated by Sobs, Chao, Ace, and Simpson indices, but no significant differences were found in the comparison groups. Furthermore, 300 mg kg^-1 β-glucan significantly increased the relative abundance of Mycoplasma and decreased Proteobacteria (mainly Escherichia-Shigella and Escherichia coli) and Bacillus anthracis in largemouth bass intestinal microflora. The findings of this study provided new insights that will be valuable in future studies to elucidate the mechanism of immunity enhancement by β-glucan.

Significant alterations of intestinal symbiotic microbiota induced by intraperitoneal vaccination mediate changes in intestinal metabolism of NEW Genetically Improved Farmed Tilapia (NEW GIFT, Oreochromis niloticus)

BACKGROUND

After millions of years of coevolution, symbiotic microbiota has become an integral part of the host and plays an important role in host immunity, metabolism, and health. Vaccination, as an effective means of preventing infectious diseases, has been playing a vital role in the prevention and control of human and animal diseases for decades. However, so far, minimal is known about the effect of vaccination on fish symbiotic microbiota, especially mucosal microbiota, and its correlation with intestinal metabolism remains unclear.

METHODS

Here we reported the effect of an inactivated bivalent Aeromonas hydrophila/Aeromonas veronii vaccine on the symbiotic microbiota and its correlation with the intestinal metabolism of farmed adult Nile tilapia (Oreochromis niloticus) by 16S rRNA gene high-throughput sequencing and gas chromatography-mass spectrometry metabolomics.

RESULTS

Results showed that vaccination significantly changed the structure, composition, and predictive function of intestinal mucosal microbiota but did not significantly affect the symbiotic microbiota of other sites including gill mucosae, stomach contents, and stomach mucosae. Moreover, vaccination significantly reduced the relative abundance values of potential opportunistic pathogens such as Aeromonas, Escherichia-Shigella, and Acinetobacter in intestinal mucosae. Combined with the enhancement of immune function after vaccination, inactivated bivalent Aeromonas vaccination had a protective effect against the intestinal pathogen infection of tilapia. In addition, the metabolite differential analysis showed that vaccination significantly increased the concentrations of carbohydrate-related metabolites such as lactic acid, succinic acid, and gluconic acid but significantly decreased the concentrations of multiple lipid-related metabolites in tilapia intestines. Vaccination affected the intestinal metabolism of tilapia, which was further verified by the predictive function of intestinal microbiota. Furthermore, the correlation analyses showed that most of the intestinal differential microorganisms were significantly correlated with intestinal differential metabolites after vaccination, confirming that the effect of vaccination on intestinal metabolism was closely related to the intestinal microbiota.

CONCLUSIONS

In conclusion, this paper revealed the microbial and metabolic responses induced by inactivated vaccination, suggesting that intestinal microbiota might mediate the effect of vaccination on the intestinal metabolism of tilapia. It expanded the novel understanding of vaccine protective mechanisms from microbial and metabolic perspectives, providing important implications for the potential influence of vaccination on human intestinal microbiota and metabolism. Video Abstract.

Response of Intestinal Microbiota to the Variation in Diets in Grass Carp (Ctenopharyngodon idella)

The intestinal microbiota is important for the nutrient metabolism of fish and is significantly influenced by the host’s diet. The effect of ryegrass and commercial diets on the intestinal microbiota of grass carp was compared in this study. In comparison to ryegrass, artificial feed significantly reduced the microbial diversity in the intestine, which was measured by a decrease in the observed OTUs, ACE, Shannon, and the InvSimpson index. Although grass carp fed with ryegrass and artificial feed shared a dominant phyla Firmicutes and Proteobacteria, the microbial composition was clearly distinguishable between the two groups. In grass carp fed with ryegrass, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria predominated, whereas Bacilli was significantly higher in the artificial feed group due to an increase in Weissella and an unassigned Bacillales bacteria, as well as a significant increase in a potential pathogen: Aeromonas australiensis. Grass carp fed with ryegrass exhibited a more complex ecological network performed by the intestinal bacterial community, which was dominated by cooperative interactions; this was also observed in grass carp fed with artificial feed. Despite this, the increase in A. australiensis increased the competitive interaction within this ecological network, which contributed to the vulnerable perturbation of the intestinal microbiota. The alteration of the microbial composition through diet can further affect microbial function. The intestinal microbial function in grass carp fed with ryegrass was rich in amino acids and exhibited an increased energy metabolism in order to compensate for a low-nutrient diet intake, while the artificial feed elevated the microbial lipid metabolism through the promotion of its synthesis in the primary and secondary bile acids, together with a notable enhancement of fatty acid biosynthesis. These results indicated that diet can affect the homeostasis of the intestinal microbiota by altering the microbial composition and the interspecific interactions, whilst microbial function can respond to a variation in diet.

Gut Microbiota Mediates Skin Ulceration Syndrome Outbreak by Readjusting Lipid Metabolism in Apostichopus japonicus

The intestinal tract is the most important location for symbiotes and pathogens, and the microbiota plays a crucial role in affecting the health of the gut and other host organs. Dysbacteriosis in the intestinal system has been proven to be significant in skin ulceration syndrome (SUS) in sea cucumbers. This study investigates whether the gut microbiota and lipid metabolites are relevant to the initiation and progression of SUS in a Vibrio-splendidus-infected sea cucumber model. The tight junction genes were downregulated and the inflammatory factor gene transcriptions were upregulated after V. splendidus infection in the intestinal tissue of the sea cucumber. V. splendidus infection modulated the gut microbiota by interacting with Psychromonas macrocephali, Propionigenium maris, Bacillus cereus, Lutibacter flavus, and Hoeflea halophila. Meanwhile, the metabolites of the long-chain fatty acids in the intestinal tissue, including triglycerides (TG), phosphatidylethanolamines (PE), and phosphatidylglycerols (PG), were altered after V. splendidus infection. V. splendidus engaged in positive interactions with PG and PE and negative interactions with specific TG. These results related to gut microbiota and metabolites can offer practical assistance in the identification of the inflammatory mechanisms related to SUS, and this study may serve as a reference for predicting the disease.

Aged microplastics change the toxicological mechanism of roxithromycin on Carassius auratus: Size-dependent interaction and potential long-term effects

Size effects of microplastics have received extensive attention for their influence on other pollutants and harm to organisms. In this study, we investigated the uptake, elimination, tissue distribution and potential toxicity mechanism of roxithromycin (ROX) in the presence of 0.5, 5 and 50 μm of aged microplastics (AMPs) in Carassius auratus. The results showed that AMPs promoted the ROX bioaccumulation of various tissues in a size-dependent manner. AMPs and ROX significantly induced superoxide dismutase and catalase activities of liver and gut, and inhibited acetylcholinesterase activities of brain. The coexistence of smaller AMPs exacerbated pathological abnormalities in liver, gill and brain induced by ROX, while larger AMPs caused more intestinal damage. Moreover, high-throughput 16S rRNA gene sequencing indicated that the abundance of Proteobacteria in 0.5 μm AMPs and ROX joint treatments and Firmicutes and Bacteroidota in 50 μm AMPs and ROX joint treatments were significantly raised (p < 0.05). Metabolomics revealed that AMPs and ROX had a size-dependent long-term effect on gut microbial metabolites, which was mainly related to galactose metabolism, amino acid metabolism and primary bile acid biosynthesis pathways after a 7-day elimination, respectively. These results provide important insights into the relationship between the size effect of AMPs and interaction mechanism of AMPs and coexisting pollutants on aquatic organisms.

Whole genome analysis of host-associated lactobacillus salivarius and the effects on hepatic antioxidant enzymes and gut microorganisms of Sinocyclocheilus grahami

As a fish unique to Yunnan Province in China, Sinocyclocheilus grahami hosts abundant potential probiotic resources in its intestinal tract. However, the genomic characteristics of the probiotic potential bacteria in its intestine and their effects on S. grahami have not yet been established. In this study, we investigated the functional genomics and host response of a strain, Lactobacillus salivarius S01, isolated from the intestine of S. grahami (bred in captivity). The results revealed that the total length of the genome was 1,737,623 bp (GC content, 33.09%), comprised of 1895 genes, including 22 rRNA operons and 78 transfer RNA genes. Three clusters of antibacterial substances related genes were identified using antiSMASH and BAGEL4 database predictions. In addition, manual examination confirmed the presence of functional genes related to stress resistance, adhesion, immunity, and other genes responsible for probiotic potential in the genome of L. salivarius S01. Subsequently, the probiotic effect of L. salivarius S01 was investigated in vivo by feeding S. grahami a diet with bacterial supplementation. The results showed that potential probiotic supplementation increased the activity of antioxidant enzymes (SOD, CAT, and POD) in the hepar and reduced oxidative damage (MDA). Furthermore, the gut microbial community and diversity of S. grahami from different treatment groups were compared using high-throughput sequencing. The diversity index of the gut microbial community in the group supplemented with potential probiotics was higher than that in the control group, indicating that supplementation with potential probiotics increased gut microbial diversity. At the phylum level, the abundance of Proteobacteria decreased with potential probiotic supplementation, while the abundance of Firmicutes, Actinobacteriota, and Bacteroidota increased. At the genus level, there was a decrease in the abundance of the pathogenic bacterium Aeromonas and an increase in the abundance of the potential probiotic bacterium Bifidobacterium. The results of this study suggest that L. salivarius S01 is a promising potential probiotic candidate that provides multiple benefits for the microbiome of S. grahami.

Staphylococcus sciuri causes disease and pathological changes in hybrid sturgeon acipenser baerii × acipenser schrencki

Hybrid sturgeon is the main species of sturgeon cultured in China, with the advantages of a fast growth rate, early sexual maturity, fertile offspring, and more stable genetic traits. In May 2021, a large number of deaths characterized by superficial hemorrhage and liver damage occurred in a sturgeon farm in Yichang, Hubei Province, which posed a significant risk to hybrid sturgeon captive breeding. We isolated a pathogenic bacterium named D-59 from the diseased sturgeon with apparent symptoms. The pathogen was identified as Staphylococcus sciuri using 16S rRNA gene phylogenetic analysis combined with biochemical identification. Regression experiments showed that D-59 exhibited clinical signs similar to those of diseased sturgeon in the farm after intraperitoneal injection into hybrid sturgeon. High-throughput sequencing of gut microbes in D-59-infected sturgeon showed that the number of gut microbial species decreased in infected sturgeon, the number of some intestinal commensal bacteria decreased, and the balance of the intestinal microorganisms was disrupted. Histopathological sections indicated many inflammatory cells, congestion, and even necrosis in the tissue of diseased sturgeon. Analysis of blood indexes revealed an increase in the proportion of mononuclear cells and a decrease in the proportion of lymphocytes in the peripheral blood of diseased sturgeon. Significantly elevated serum levels of aspartate aminotransferase and alanine aminotransferase, whereas alkaline phosphatase, total protein, albumin, and globulin were decreased in diseased sturgeon. Antimicrobial susceptibility tests demonstrated that D-59 is susceptible to florfenicol, enrofloxacin, and neomycin sulfate. This study aimed to highlight the dangers of Staphylococcus sciuri infection during hybrid sturgeon culture and to provide recommendations for diagnosis and treatment.

Mercury Induced Tissue Damage, Redox Metabolism, Ion Transport, Apoptosis, and Intestinal Microbiota Change in Red Swamp Crayfish (Procambarus clarkii): Application of Multi-Omics Analysis in Risk Assessment of Hg

As one of the most toxic elements, mercury (Hg) is a widespread toxicant in aquatic environments. Crayfish are considered suitable for indicating the impact of heavy metals on aquatic crustaceans. Nevertheless, Hg toxicity on Procambarus clarkii is largely unknown. In this research, the acute Hg-induced alterations of biochemical responses, histopathology, hepatopancreatic transcriptome, and intestinal microbiome of Procambarus clarkii were studied. Firstly, Hg induced significant changes in reactive oxygen species (ROS) and malonaldehyde (MDA) content as well as antioxidant enzyme activity. Secondly, Hg exposure caused structural damage to the hepatopancreas (e.g., vacuolization of the epithelium and dilatation of the lumen) as well as to the intestines (e.g., dysregulation of lamina epithelialises and extension of lamina proprias). Thirdly, after treatment with three different concentrations of Hg, RNA-seq assays of the hepatopancreas revealed a large number of differentially expressed genes (DEGs) linked to a specific function. Among the DEGs, a lot of redox metabolism- (e.g., ACOX3, SMOX, GPX3, GLO1, and P4HA1), ion transport- (e.g., MICU3, MCTP, PYX, STEAP3, and SLC30A2), drug metabolism- (e.g., HSP70, HSP90A, CYP2L1, and CYP9E2), immune response- (e.g., SMAD4, HDAC1, and DUOX), and apoptosis-related genes (e.g., CTSL, CASP7, and BIRC2) were identified, which suggests that Hg exposure may perturb the redox equilibrium, disrupt the ion homeostasis, weaken immune response and ability, and cause apoptosis. Fourthly, bacterial 16S rRNA gene sequencing showed that Hg exposure decreased bacterial diversity and dysregulated intestinal microbiome composition. At the phylum level, there was a marked decrease in Proteobacteria and an increase in Firmicutes after exposure to high levels of Hg. With regards to genus, abundances of Bacteroides, Dysgonomonas, and Arcobacter were markedly dysregulated after Hg exposures. Our findings elucidate the mechanisms involved in Hg-mediated toxicity in aquatic crustaceans at the tissue, cellular, molecular as well as microbial levels.

Sub-lethal concentration of metamifop exposure impair gut health of zebrafish (Danio rerio)

Previous studies have demonstrated that sublethal metamifop exposures induce hepatic lipid metabolism disorder in zebrafish. Whether metamifop will cause adverse effects in zebrafish gut is unknown. In the present study, effects of metamifop on gut heath of zebrafish were investigated after sublethal concentration (0.025, 0.10 and 0.40 mg/L) exposure. Histopathology analysis showed that metamifop induced inflammation and reduction of goblet cells in the gut, indicating that gut health may be impaired. Metamifop exposure could reduce activities of digestive enzymes (lipase and alkaline phosphatase), indicating the capacity of lipid absorption were impaired. Meanwhile, the content of fatty acid-binding protein 2 (FABP2) and mRNA levels of related genes (apoa-1a, apoe-b, fatp4, lpl and fabp2) were reduced in zebrafish gut after exposure to metamifop, suggesting the lipid transportation were decreased. The transcripts of genes associated with inflammation (il-17c, tnf-α and nf-kb) were significantly increased in 0.40 mg/L metamifop treatment group, which were 1.90-, 1.53- and 2.77-fold of the control group, respectively, confirming that metamifop induced inflammatory response in zebrafish gut. Moreover, reduction of mRNA levels of cldn-15 and elevation of lipopolysaccharides (LPS) content were observed in metamifop-treated groups, which suggested that metamifop exposure increased the intestinal permeability. Furthermore, metamifop exposure decreased the relative abundance of beneficial bacteria (Psychrobacter and Aeromonas) and elevated the abundance of pathogenic bacteria (Rhodobacter and Ralstonia) in zebrafish intestine. These results indicated that metamifop exposure at sublethal concentrations would impair zebrafish gut health, via reduction of lipids absorption, inflammatory response, elevation of permeability and microbiota disorder.

Effects of Pelleted and Extruded Feed on Growth Performance, Intestinal Histology and Microbiota of Juvenile Red Swamp Crayfish (Procambarus clarkii)

The study was conducted to evaluate the extruded and pelleting feed production on growth performance, intestinal histology and microbiome analysis of juvenile red swamp crayfish, Procambarus clarkii. Crayfish were fed either pelleted or extruded feeds that were made using the same formula. Crayfish fed extruded feed had a lower feed conversion ratio, as well as significantly higher levels of trypsin and amylase (p < 0.05) than those fed pelleted feed. However, other growth indices and the activity of lipase were not significantly influenced by the feed processing technique (p > 0.05). In comparison with the pelleted feed group, the lamina propria thickness of crayfish fed extruded feed was significantly lower (p < 0.05). Additionally, the abundance of intestinal microbiota in the extruded feed group was higher than that in the pelleted feed group. The dominant phyla in the intestine of both groups were Proteobacteria, Tenericutes, and Firmicutes, and the relative abundance of Proteobacteria in the extruded feed group was significantly higher than that in the pelleted feed group (p < 0.05). These results revealed that P. clarkii fed extruded feed had higher feed utilization and better intestinal health.

The effect of a polystyrene nanoplastic on the intestinal microbes and oxidative stress defense of the freshwater crayfish, Procambarus clarkii

The widespread generation and accumulation of plastic waste has become a globally recognized problem. However, there are limited reports on the adverse effects of nanomaterials on freshwater crustaceans. This study tested the acute effects of different concentrations (0, 5, 10, and 20 mg/L) after 48 h exposure of 75 nm polystyrene nanoplastic on intestinal microbes, and oxidative stress parameters of freshwater crayfish, Procambarus clarkii. High-throughput sequencing analysis revealed the richness, diversity, and composition of intestinal microbiota in P. clarkii exposed to polystyrene nanoplastic. At the genus level, abundances of Lactobacillus, Faecalibaculum, Niveibacterium, and Candidatus Bacilloplasma were significantly different. The reduced abundance of Lactobacillus could affect the balance of intestinal microbes through quantitative disadvantage, which may lead to reduced immunity of P. clarkii. Streptococcus salivarius, Clostridium butyricum and Lachnospiraceae bacterium10-1 in intestinal tract reached maximum abundance at a polystyrene concentration of 20 mg/L. The increase in the number of some pathogenic bacteria may upset the balance of intestinal microorganisms through the number of dominance, and the decrease in the relative abundance of lactic acid bacteria. Probiotics, such as Lactobacillus salivarius, Lactobacillus murinus, Lactobacillus gasseri, Lactobacillus reuteri, Lactobacillus iners AB-1, and Lactobacillus crispatus in the intestinal tract reached the lowest value at a concentration of 10 mg/L. The reduced abundance of Lactobacillus can affect the balance of intestinal microbes through quantitative disadvantage, which may lead to reduced immunity in P. clarkii. At nanoplastic 10 mg/L, the relative abundance of intestinal pathogens increased, while the relative abundance of lactic acid bacteria and other probiotics decreased. With increases in nanoplastic concentrations, the values of glutathione (GSH), superoxide dismutase (SOD), acid phosphatase (ACP), lysozyme (LZM), alkaline phosphatase (AKP), peroxidase (POD), glutathione peroxidase (GPX), and protein carbonylation were significantly changed. Our data suggested that Lactobacillus may play an adjunctive role in the treatment of oxidative stress in P. clarkii exposed to 75 nm polystyrene. This study represents an important step towards a better understanding of the toxic effects of nanoplastics on aquatic crustaceans.

Effects of cadmium exposure on intestinal microflora of Cipangopaludina cathayensis

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

Intestinal changes associated with nitrite exposure in Bufo gargarizans larvae: Histological damage, immune response, and microbiota dysbiosis

Nitrite is a ubiquitous toxic compound in aquatic ecosystems and has negative effects on aquatic organisms. The intestine and the trillions of microbes that inhabit it, play an integral role in maintaining digestive and immune functions. However, the effects of nitrite on intestinal health and microflora have been poorly investigated. Therefore, the present study evaluated the response of intestinal histology, immunity, digestive enzyme activities and microbiota to nitrite exposure in Bufo gargarizans tadpoles. The results showed that nitrite caused damage to the intestine and impaired digestive performance. Significant changes in the transcriptional profiles of genes involved in oxidative stress (sod, gpx and hsp), inflammation, and immunity (socs3, il-27, il-1β and il-17d) were observed in the NO₂-N treatment groups. In addition, exposure to nitrite induced alterations of intestinal microbial diversity, structure and composition, suggesting that nitrite may lead to intestinal microbiota dysbiosis. It is noteworthy that probiotics (e.g., Bacteroidetes and Fusobacteria) were decreased after exposure to nitrite, whereas potentially opportunistic pathogens such as Proteobacteria and Enterobacteriaceae were elevated. Functional prediction and correlation analysis suggested that the above changes may interfere with metabolic function and trigger various diseases. Taken together, we concluded that nitrite exposure induced intestinal microbial dysbiosis, which may lead to immune dysfunction and metabolic disorder, and ultimately to histological damages in B. gargarizans. Further, this study will provide a scientific basis for further understanding the risk of nitrite pollution on the intestinal health of amphibians.

Exploring the gut microbiota composition of Indian major carp, rohu (Labeo rohita), under diverse culture conditions

Gut microbiota of freshwater carps are often investigated for their roles in nutrient absorption, enzyme activities and probiotic properties. However, little is known about core microbiota, assembly pattern and the environmental influence on the gut microbiota of the Indian major carp, rohu. The gut microbial composition of rohu reared in different culture conditions was analysed by 16S rRNA amplicon sequencing. There was variation on gut microbial diversity and composition. A significant negative correlation between dissolved oxygen content (DO) and alpha diversity was observed, thus signifying DO content as one of the key environmental factors that regulated the diversity of rohu gut microbial community. A significant positive correlation was observed between phosphate concentration and abundance of Actinobacteria in different culture conditions. Two phyla, Proteobacteria and Actinobacteria along with OTU750868 (Streptomyces) showed significant (p < 0.05) differences in their abundance among all culture conditions. The Non-metric multidimensional scaling ordination (NMDS) analysis using Bray-Curtis distances, showed the presence of unique gut microbiota in rohu compared to other herbivorous fish. Based on niche breadth, 3 OTUs were identified as core generalists, persistent across all the culture conditions whereas the specialists dominated in the rohu gut microbiota assembly. Co-occurrence network analysis revealed positive interaction within core members while mutual exclusion between core and non-core members. Predicted microbiota function revealed that different culture conditions affected the metabolic capacity of gut microbiota of rohu. The results overall indicated the significant effect of different rearing environments on gut microbiota structure, assembly and inferred community function of rohu which might be useful for effective manipulation of gut microbial communities of rohu to promote better health and growth under different husbandry settings.

Heterogeneity of the Tissue-specific Mucosal Microbiome of Normal Grass Carp (Ctenopharyngodon idella)

Microbiome plays key roles in the digestion, metabolism, and immunity of the grass carp (Ctenopharyngodon idella). Here, we characterized the normal microbiome of the intestinal contents (IC), skin mucus (SM), oral mucosa (OM), and gill mucosa (GM) of the grass carp, as well as the microbiome of the sidewall (SW) of the raising pool, using full-length 16S rRNA sequencing based on the PacBio platform in this specie for the first time. Twenty phyla, 38 classes, 130 families, 219 genera, and 291 species were classified. One hundred four common classified species might be core microbiota of grass carp. Proteobacteria, Bacteroides, and Cyanobacteria were the dominant phyla in the niche of grass carp. Proteobacteria and Bacteroides dominated the taxonomic composition in the SM, GM, and OM, while Proteobacteria, Planctomycetota, and Cyanobacteria preponderated in the IC and SW groups. Microbiota of IC exhibited higher alpha diversity indices. The microbial communities clustered either in SW or the niche from grass carp, significantly tighter in the SW, based on Bray-Curtis distances (P < 0.05). SM, GM, and OM were similar in microbial composition but were significantly different from IC and SW, while IC had similarity with SW due to their common Cyanobacteria (P < 0.05). Differences were also reflected by niche-specific and differentially abundant microorganisms such as Noviherbaspirillum in the SM and Rhodopseudomonas palustris, Mycobacterium fortuitum, and Acinetobacter schindleri in GM. Significantly raised gene expression was found in IC and SM associated with cell cycle control, cell division, chromosome, coenzyme transport and metabolism, replication, recombination and repair, cell motility, post-translational modification, signal transduction mechanisms, intracellular trafficking, secretion, and vesicles by PICRUSt. This work may be of great value for understanding of fish-microbial co-workshops, especially in different niche of grass carp.

Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings

The microbiota of fish skin, the primary barrier against disease, is highly dynamic and modulated by several factors. In fish aquaculture, disease outbreaks occur mainly during early-life stages, with associated high economic losses. Antibiotic treatments sometimes remain the best option to control bacterial diseases, despite many reported negative impacts of its use on fish and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of fingerlings are scarce. We sequenced the bacterial 16S rRNA V4 gene region using a metabarcoding approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with flumequine, on the skin microbiota of farmed seabass (Dicentrarchus labrax) fingerlings. Both infection and antibiotic treatment led to a significant increase in bacterial diversity and core microbial communities and impacted microbiome structure. Dysbiosis was confirmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also significantly affected by flumequine administration, suggesting a detriment to fish skin health. Our results add to an increasing body of literature, showing how fish microbiome response to infection and antibiotics cannot be easily predicted.

Exposed to Sulfamethoxazole induced hepatic lipid metabolism disorder and intestinal microbiota changes on zebrafish (Danio rerio)

Antibiotics are widely used around the world. Pollution of Sulfamethoxazole (SMX) in water poses a great threat to aquatic life. In this study, the toxic effects of SMX on the liver were assessed through RNA sequencing analysis and 16S rRNA sequencing analysis was conducted to determine the influence of SMX on gut microbiota of zebrafish (Danio rerio). Adult male zebrafish were exposed to 0, 5, 90 and 450 μg/L of environmentally relevant concentrations of SMX for 21 days respectively. The results showed that the liver had severe histopathological damages including pyknotic nuclei, cytoplasmic hyalinization and vacuolization and deformed hepatocytes with loose cell-to-cell contact. Transcriptomic analysis revealed that liver function was seriously affected by SMX exposure. Meanwhile, SMX exposure significantly inhibited the expression of genes associated with fatty acid synthesis, oxidation and transport. Besides, exfoliated and dissolved epithelial cells were observed in the gut after SMX treatment. Although there was no significant change on richness and species diversity of intestinal microbial community, the relative abundance of phylum and genus of SMX treatments were significantly different from that of control group. The present study implied that SMX may cause potential health risks to fish through inducing histopathological damages, genetic expression alterations, disorder of fatty acid metabolism and intestinal microbiota dysbiosis.

Health hazards of hexavalent chromium (Cr (VI)) and its microbial reduction

Industrial effluents/wastewater are the main sources of hexavalent chromium (Cr (VI)) pollutants in the environment. Cr (VI) pollution has become one of the world’s most serious environmental concerns due to its long persistence in the environment and highly deadly nature in living organisms. To its widespread use in industries Cr (VI) is highly toxic and one of the most common environmental contaminants. Cr (VI) is frequently non-biodegradable in nature, which means it stays in the environment for a long time, pollutes the soil and water, and poses substantial health risks to humans and wildlife. In living things, the hexavalent form of Cr is carcinogenic, genotoxic, and mutagenic. Physico-chemical techniques currently used for Cr (VI) removal are not environmentally friendly and use a large number of chemicals. Microbes have many natural or acquired mechanisms to combat chromium toxicity, such as biosorption, reduction, subsequent efflux, or bioaccumulation. This review focuses on microbial responses to chromium toxicity and the potential for their use in environmental remediation. Moreover, the research problem and prospects for the future are discussed in order to fill these gaps and overcome the problem associated with bacterial bioremediation’s real-time applicability.

Comparative Study of Bacillus amyloliquefaciens X030 on the Intestinal Flora and Antibacterial Activity Against Aeromonas of Grass Carp

Beneficial microorganisms to control bacterial diseases has been widely used in aquaculture, Bacillus amyloliquefaciens (BaX030) as a probiotic feed additive was a commonly biological control method. Added sucrose promoted the growth of BaX030, and the yield of its antibacterial substance macrolactin A was enhanced by 1.46-fold. A total of 2055 proteins were screened through proteomics, with 143 upregulated and 307 downregulated. Differential protein expression analysis and qRT-PCR verification showed that the pentose phosphate pathway and the fatty acid synthesis pathway were upregulated, thereby providing sufficient energy and precursors for the synthesis of macrolactin A. The influence of some potential regulatory factors (SecG, LiaI, MecG and ComG) on macrolactin A was discovered. After grass carp were fed with BaX030, the abundance of probiotics (Fusobacterium, Proteobacteria, Gemmobacter) were higher than the control group, and the abundance of potential pathogenic bacteria (Planctomycetes, Aeromonas) were significantly lower than the control group. The cell and challenge experiments showed that BaX030 can significantly increase the expression of C3 and IL8 in the liver and kidney, which decreases the risk of immune organ disease. Moreover, BaX030 effectively reduced the mortality of grass carp. The results revealed that BaX030 can significantly improve the structure of the intestinal flora, enhance immunity and it is beneficial to the control of grass carp Aeromonas.

A systematic review of advances in intestinal microflora of fish

Intestinal flora is closely related to the health of organisms and the occurrence and development of diseases. The study of intestinal flora will provide a reference for the research and treatment of disease pathogenesis. Upon hatching, fish begin to acquire a microbial community in the intestine. In response to the environment and the host itself, the fish gut eventually develops a unique set of microflora, with some microorganisms being common to different fish. The existence of intestinal microorganisms creates an excellent microecological environment for the host, while the fish symbiotically provides conditions for the growth and reproduction of intestinal microflora. The intestinal flora and the host are interdependent and mutually restrictive. This review mainly describes the formation of fish intestinal flora, the function of normal intestinal flora, factors affecting intestinal flora, and a series of fish models.

The Characteristics of Intestinal Bacterial Community in Three Omnivorous Fishes and Their Interaction with Microbiota from Habitats

Artificial fishery habitats have been extensively used for fishery resource protection and water habitat restoration, and they could attract a large number of omnivorous fishes to gather together. This study intended to reveal the relationship between bacterial communities in the habitats (water and sediment) and intestines of omnivorous fishes (Oreochromis mossambicus, Toxabramis houdemeri and Hemiculter leucisculus). Therefore, we investigated the bacterial communities of samples collected from intestines, water, and sediments in artificial fishery habitats via 16S rRNA metabarcoding high-throughput sequencing technology. The results showed that there were significant differences in the composition, core indicators, diversity and prediction functions in water, sediments, and intestinal microbial communities of the three omnivorous fish. The microbial diversities were significantly higher in habitats than in intestines. The analysis of similarity (ANOSIM) and nonmetric multidimensional scaling (NMDS) results indicated that the intestine microbial communities (T. houdemeri and H. leucisculus) were more similar to the water microbiota, but the intestine microbial communities (O. mossambicus) were more similar to the sediments. Source tracking analysis also confirmed that the contribution of habitat characteristics to omnivorous fish intestinal microorganisms was different; the sediment had a greater contribution than water to the intestinal microbiota of O. mossambicus, which was consistent with their benthic habit. Moreover, the functional prediction results showed that there were unique core indicators and functions between the bacterial community of habitats and intestines. Altogether, these results can enhance our understanding of the bacterial composition and functions about omnivorous fish intestines and their living with habitats, which have provided new information for the ecological benefits of artificial fishery habitats from the perspective of bacterial ecology and contributed to apply artificial fishery habitats in more rivers.

Sub-chronic exposure to antibiotics doxycycline, oxytetracycline or florfenicol impacts gut barrier and induces gut microbiota dysbiosis in adult zebrafish (Daino rerio)

Antibiotics are widely used in the treatment of bacterial infections and as food additives in the livestock industry. The wide usage of antibiotics causes residues in animal products, like milk, eggs and meat. A number of studies have reported that antibiotic residues exist at high concentrations in watercourses around the world. Doxycycline (DH), oxytetracycline (OTCC) and florfenicol (FF) are the three most commonly used veterinary antibiotics in China. However, studies of the toxic effects of DH, OTCC and FF are limited. In this study, six-moth-old healthy male adult zebrafish were exposed to 0, 10, 30, 100 μg/L DH, OTCC or FF for 21 days. After exposure, some biochemical parameters changed significantly, including total cholesterol (TC), triglyceride (TG), pyruvate and acid phosphatase (ACP). In addition, mucus secretion in the gut decreased and the transcription of related genes also decreased significantly. Moreover, the composition of microbiota in the gut changed significantly. DH, OTCC and FF exposure caused the decrease of diversity of gut microbiota. The relative abundance of Proteobacteria increased significantly after OTCC and FF exposure and Fusobacteria decreased in all antibiotic-treated groups. Further functional prediction analysis also suggested changes in gut microbiota in the OTCC and FF-treated groups, especially those linked to metabolism. To support this idea, we confirmed that some glycolipid related genes also increased significantly in the liver of adult zebrafish after antibiotic exposure. According to these results, DH, OTCC or FF exposure could cause the gut microbiota dysbiosis and dysfunction, and hepatic metabolic disorder in adult male zebrafish.

A High Starch Diet Alters the Composition of the Intestinal Microbiota of Largemouth Bass Micropterus salmoides, Which May Be Associated With the Development of Enteritis

Starch is an inexpensive feed ingredient that has been widely used in fish feed. However, starch utilization by carnivorous fish is limited and excess starch is detrimental to the health of the organism. High starch diets often lead to liver damage, but the effects on the intestine are often overlooked. Therefore, in this study, two isonitrogenous and isolipidic semi-pure diets (NC: 0% α-starch, HC: 22% α-starch) were formulated and fed to largemouth bass (Micropterus salmoides) for 45 days. The effects of the high starch diet on the intestine of largemouth bass were comprehensively investigated by intestinal microbiota, histopathology, ultrastructural pathology, and enzymology analyses. Feeding the HC diet did not affect the growth of largemouth bass during the experimental period. However, the high starch diet led to a reduction in the diversity and abundance of intestinal microbiota in largemouth bass, with a significant increase in the abundance of harmful bacteria (Aeromonas) and a decrease in the abundance of beneficial bacteria (Clostridium, Lactobacillus, and Bifidobacterium). Feeding the HC diet caused the development of enteritis, with goblet cell hyperplasia, epithelial necrosis and detachment and inflammatory cell infiltration, and leading to enlarged apical openings and mitochondrial damage in goblet cells. Long-term feeding of the HC diet inhibited intestinal α-amylase activity. changes in the intestinal microbiota, such as an increase in Aeromonas and a decrease in Clostridium, Lactobacillus, and Bifidobacterium, may be closely related to the development of enteritis. Therefore, adding these beneficial bacteria as probiotics may be an effective way to prevent damage to the intestine of largemouth bass from a high carbohydrate diet. Our results suggest reducing the amount of starch added to the largemouth bass diets. This study provides a reference for protecting the largemouth bass gut during modern intensive culture.

Gut microbiota of homologous Chinese soft-shell turtles (Pelodiscus sinensis) in different habitats

Background

Chinese soft-shell turtle (Pelodiscus sinensis) is an important commercial species for their high nutritional value and unique taste, but it has been a vulnerable species due to habitat loss. In this study, homologous juvenile turtles were allocated to lake, pond and paddy field to investigate the habitat effects on turtles.

Results

The growth, morphology and gut microbial communities were monitored during the 4 months cultural period. It showed higher growth rate of turtles in paddy field and pond. The appearance, visceral coefficients, gut morphology and microbial communities in turtles were distinct among different habitats. The microbial community richness on Chao1 was obviously lower in initial turtle guts from greenhouses, whereas it was relative higher in turtle guts sampled from paddy fields than ponds and lake. Significant differences on dominant microbes were found among initial and subsequent samples from different habitats. Firmicutes was the most abundant phylum in the guts of turtles sampled from the greenhouse initially, while Proteobacteria was the most abundant phylum after cultivation in different habitats, followed by Bacteroidetes. The microbial composition were distinct in different habitats at 60d, and the appearance of dominant phyla and genera was more driven by sampling time than habitats at 120d. Both the sampling time and habitats affected the appearance of dominant phyla and genera during the cultivation. The functional predictions indicated that both habitat type and sampling time had significant effects on metabolic pathways, especially amino acid and carbohydrate metabolism.

Conclusions

The turtles could adapt to natural lakes, artificial ponds and paddy fields. The gut microbial abundance was different among the habitats and sampling time. The species of microbes were significantly more diverse in paddy field specimens than in those from ponds and lakes. Rice-turtle coculture is a potential ecological and economic farming mode that plays important roles in wild turtle protection and food security.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02209-y.

Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals

BACKGROUND

Infectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role in regulating the host immune system, health and physiology, altered gut microbiota compositions are often associated with a diseased status. However, few studies have examined the association between disease severity and degree of gut dysbiosis, especially when the gut is not the site of the primary infection. Moreover, there is a lack of knowledge on whether bath treatment with formalin, a disinfectant commonly used in aquaculture to treat external infections, might affect the gut microbiome as a consequence of formalin ingestion. Here we investigate, through 16S rRNA gene metabarcoding, changes in the distal gut microbiota composition of a captive-reared cohort of 80 Atlantic salmon (Salmo salar L.), in consequence of an external bacterial skin infection due to a natural outbreak and subsequent formalin treatment.

RESULTS

We identified Tenacibaculum dicentrarchi as the causative disease pathogen and we show that the distal gut of diseased salmon presented a different composition from that of healthy individuals. A new, yet undescribed, Mycoplasma genus characterized the gut of healthy salmon, while in the sick fish we observed an increase in terms of relative abundance of Aliivibrio sp., a strain regarded as opportunistic. We also noticed a positive correlation between fish weight and Mycoplasma sp. relative abundance, potentially indicating a beneficial effect for its host. Moreover, we observed that the gut microbiota of fish treated with formalin was more similar to those of sick fish than healthy ones.

CONCLUSIONS

We conclude that external Tenacibaculum infections have the potential of indirectly affecting the host gut microbiota. As such, treatment optimization procedures should account for that. Formalin treatment is not an optimal solution from a holistic perspective, since we observe an altered gut microbiota in the treated fish. We suggest its coupling with a probiotic treatment aimed at re-establishing a healthy community. Lastly, we have observed a positive correlation of Mycoplasma sp. with salmon health and weight, therefore we encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.

Effects of Dietary Protein Level on the Gut Microbiome and Nutrient Metabolism in Tilapia (Oreochromis niloticus)

Dietary protein is one of the most important nutritional factors in aquaculture. The aim of this study was to examine the effects of dietary protein levels on the gut microbiome and the liver and serum levels of metabolites in tilapia. Tilapia were fed a diet with a low (20%), moderate (30%), or high (40%) content of crude protein, and the homeostasis of the gut microbiome and metabolic profile of the liver and serum were analyzed. The results showed no significant differences in the diversity and richness of the gut microbiome among the groups; however, there were differences in the microbial composition of the gut. The metabolome analysis of liver samples revealed a difference in the glucose level among the groups, with the highest glucose level in fish fed a high protein diet. In addition, there were significant differences in the levels of tyrosine, guanosine, and inosine among the metabolome analysis of serum samples of these groups. In summary, diets with different protein levels could affect the composition of gut microbiota and the dynamic balance of microbial communities. Dietary protein content can also affect glycolysis and amino acid metabolism in tilapia.

The Alteration of Intestinal Microbiota Profile and Immune Response in Epinephelus coioides during Pathogen Infection

Epinephelus coioides, or grouper, is a high economic value fish species that plays an important role in the aquaculture industry in Asia. However, both viral and bacterial diseases have threatened grouper for many years, especially nervous necrosis virus, grouper iridovirus and Vibrio harveyi, which have caused a bottleneck in the grouper industry. Currently, intestinal microbiota can provide novel insights into the pathogenesis-related factors involved in pathogen infection. Hence, we investigated the comparison of intestinal microbiota communities in control group and pathogen-infected grouper through high-throughput sequencing of the 16S rRNA gene. Our results showed that microbial diversity was decreased, whereas microbial richness was increased during pathogen infection. The individuals in each group were distributed distinctly on the PLSDA diagram, especially the GIV group. Proteobacteria and Firmicutes were the most abundant bacterial phyla in all groups. Interestingly, beneficial genera, Faecalibacterium and Bifidobacterium, predominated in the intestines of the control group. In contrast, the intestines of pathogen-infected grouper had higher levels of harmful genera such as Sphingomonas, Atopostipes, Staphylococcus and Acinetobacter. Additionally, we investigated the expression levels of innate and adaptive immune-related genes after viral and bacterial infection. The results revealed that immunoglobulin T and proinflammatory cytokine levels in the intestine increased after pathogen infection. Through these unique bacterial compositions in diseased and uninfected fish, we could establish a novel therapeutic approach and bacterial marker for preventing and controlling these diseases.