The intestinal microbiome of fish under starvation

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

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

Gut physiology of rainbow trout (Oncorhynchus mykiss) is influenced more by short-term fasting followed by refeeding than by feeding fishmeal-free diets

Supplementing a fishmeal-free diet with yeast extract improves rainbow trout (Oncorhynchus mykiss) growth performance and modulates the hepatic and intestinal transcriptomic response. These effects are often observed in the long term but are not well documented after short periods of fasting. Fasting for a few days is a common practice in fish farming, especially before handling the fish, such as for short sorting, tank transfers, and vaccinations. In the present study, rainbow trout were subjected to a 4-day fast and then refed, for 8 days, a conventional diet containing fishmeal (control diet) or alternative diets composed of terrestrial animal by-products supplemented or not with a yeast extract. During the refeeding period alone, most of the parameters considered did not differ significantly in response to the different feeds. Only the expression of claudin-15 was upregulated in fish fed the yeast-supplemented diet compared to the control diet. Conversely, fasting followed by refeeding significantly influenced most of the parameters analyzed. In the proximal intestine, the surface area of villi significantly increased, and the density of goblet cell tended to decrease during refeeding. Although no distinct plasma immune response or major signs of gut inflammation were observed, some genes involved in the structure, complement pathway, antiviral functions, coagulation, and endoplasmic reticulum stress response of the liver and intestine were significantly regulated by refeeding after fasting. These results indicate that short-term fasting, as commonly practiced in fish farming, significantly alters the physiology of the liver and intestine regardless of the composition of the diet.

Potential effects of individual and combined exposure to tetraconazole and cadmium on zebrafish from the perspective of enantioselectivity and intestinal microbiota

As the wide use of pesticides, they could form combined pollution with heavy metals, which would affect their environmental behaviors and toxic effects. Particularly, the effects would be more intricate for chiral pesticides. In this study, the accumulation and dissipation trends of tetraconazole enantiomers in zebrafish were investigated by individual and combined exposure of cadmium (Cd) and tetraconazole (including racemate and enantiomers) after confirming the absolute configuration of tetraconazole enantiomer. For the enantiomer treatments, Cd enhanced the accumulation of S-(+)-tetraconazole, but declined the concentrations of R-(-)-tetraconazole in zebrafish. The dissipation half-lives of tetraconazole enantiomers were extended by 1.65-1.44 times after the combined exposure of Cd and enantiomers. The community richness and diversity of intestinal microbiota were reduced in all treatments, and there were significant differences in R + Cd treatment. There was synergistic effect between Cd and S-(+)-tetraconazole for the effects on the relative abundances of Fusobacteria, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. For R-(-)-tetraconazole, Cd mainly exhibited antagonistic effects. In the combined exposure of Cd and S-(+)-tetraconazole, the relative abundance changes of Cetobacterium (Fusobacteria, increase) and Edwardsiella (Proteobacteria, decrease) might affect the carbohydrate metabolism and energy metabolism, and led to the increase of S-(+)-tetraconazole bioaccumulation concentration. In the combined exposure of Cd and R-(-)-tetraconazole, Cd could increase the relative abundance of Edwardsiella (Proteobacteria), and affect the amino acid metabolism, which might reduce the bioaccumulation concentration of R-(-)-tetraconazole. This study reported for the first time that the abundance of intestinal microbiota in zebrafish might affect the bioaccumulation and dissipation of tetraconazole enantiomers, and would provide new insight for the study of combined pollutions.

Gut microbiome resilience of green-lipped mussels, Perna canaliculus, to starvation

Host gut microbiomes play an important role in animal health and resilience to conditions, such as malnutrition and starvation. These host-microbiome relationships are poorly understood in the marine mussel Perna canaliculus, which experiences significant variations in food quantity and quality in coastal areas. Prolonged starvation may be a contributory factor towards incidences of mass mortalities in farmed mussel populations, resulting in highly variable production costs and unreliable market supplies. Here, we examine the gut microbiota of P. canaliculus in response to starvation and subsequent re-feeding using high-throughput amplicon sequencing of the 16S rRNA gene. Mussels showed no change in bacterial species richness when subjected to a 14-day starvation, followed by re-feeding/recovery. However, beta bacteria diversity revealed significant shifts (PERMANOVA p-value < 0.001) in community structure in the starvation group and no differences in the subsequent recovery group (compared to the control group) once they were re-fed, highlighting their recovery capability and resilience. Phylum-level community profiles revealed an elevation in dominance of Proteobacteria (ANCOM-BC p-value <0.001) and Bacteroidota (ANCOM-BC p-value = 0.04) and lower relative abundance of Cyanobacteria (ANCOM-BC p-value = 0.01) in the starvation group compared to control and recovery groups. The most abundant genus-level shifts revealed relative increases of the heterotroph Halioglobus (p-value < 0.05) and lowered abundances of the autotroph Synechococcus CC9902 in the starvation group. Furthermore, a SparCC correlation network identified co-occurrence of a cluster of genera with elevated relative abundance in the starved mussels that were positively correlated with Synechococcus CC9902. The findings from this work provide the first insights into the effect of starvation on the resilience capacity of Perna canaliculus gut microbiota, which is of central importance to understanding the effect of food variation and limitation in farmed mussels.

Utilizing NMR fecal metabolomics as a novel technique for detecting the physiological effects of food shortages in waterfowl

Metabolomics is the study of small, endogenous metabolites that participate in metabolic reactions, including responses to stressors. Anthropogenic and environmental changes that alter habitat and food supply can act as stressors in wild waterfowl. These alterations invoke a series of physiological processes to provide energy to restore homeostasis and increase survival. In this study, we utilized fecal metabolomics to measure metabolites and identify pathways related to a 6-day feed restriction in captive mallard ducks (Anas platyrhynchos, n = 9). Fecal samples were collected before (baseline) and during feed restriction (treatment). H1 Nuclear Magnetic Resonance (NMR) spectroscopy was performed to identify metabolites. We found that fecal metabolite profiles could be used to distinguish between the feed-restricted and baseline samples. We identified metabolites related to pathways for energy production and metabolism endpoints, and metabolites indicative of gut microbiota changes. We also demonstrated that mallard ducks could utilize endogenous reserves in times of limited caloric intake. Fecal metabolomics shows promise as a non-invasive novel tool in identifying and characterizing physiological responses associated with stressors in a captive wild bird species.

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.

Chronic environmentally relevant concentration of copper exposure induces intestinal oxidative stress, inflammation, and microbiota disturbance in freshwater grouper (Acrossocheilus fasciatus)

The influence of chronic environmentally relevant concentration of Cu2+ exposure on fish intestinal health has been rarely studied. In the present study, freshwater grouper (Acrossocheilus fasciatus) was subjected to 0 (control), 0.01 mg/L Cu2+ (Cu0.01), and 0.04 mg/L Cu2+ (Cu0.04) for 30 days. The Cu0.04 group obtained a significantly reduced survival rate, weight gain, and feed intake compared to the control group (P < 0.05). Both levels of Cu2+ exposure induced oxidative stress, evidenced by increased antioxidant enzymes' activities and malondialdehyde (MDA) contents in the intestine and serum. Based on 16S rDNA analysis, both levels of Cu2+ exposure significantly reduced intestinal microbiota community richness. In the Cu2+ exposure groups, Firmicutes/Bacteroidota ratio, and potentially pathogenic bacteria, such as Proteobacteria, genus Pseudomonas, Citrobacter, Shinella, and Aeromonas were enriched. Meanwhile, the richness of probiotic bacteria, such as Fusobacteriota, Planctomycetota, Cetobacterium, Gemmobacter, and Gemmata were significantly reduced by Cu2+ exposure. Both levels of Cu2+ exposure significantly reduced villus length, lamina propria width, and muscular thickness in the foregut and hindgut, but increased intestinal goblet cell numbers. 0.04 mg/L Cu2+ exposure significantly upregulated superoxide dismutase (sod), pro-inflammation genes nuclear factor kappa b subunit 1 (nfκb1) and interleukin 1 beta (il1β) expression, but downregulated anti-inflammation gene transforming growth factor beta 1 (tgfβ1) expression. In summary, chronic environmentally relevant concentrations of Cu2+ exposure induced intestinal oxidative stress, inflammation, prevalence of pathogen and inhibition of probiotic bacteria, and damage intestinal integrity of freshwater grouper.

Riverine pollution influences the intraspecific variation in the gut microbiome of an invasive fish, Cyprinus carpio (Linn., 1758)

Humans are significantly impacting riverine systems worldwide, prompting us to investigate the effects of water pollution on the gut microbiome of Cyprinus carpio (common carp). Using 16S rRNA gene sequencing, we compared the gut microbiomes of common carp from two sites along river Yamuna with different pollution levels. Water pollution significantly altered the fish gut microbiome structure and microbial composition. Proteobacteria dominated in both sampling sites, while Bacteroidota prevailed in polluted water samples, indicating sewage and fecal contamination. Less polluted samples exhibited Verrucomicrobiae and Planctomycetes, negatively correlated with pollution levels. The polluted site had higher prevalence of potentially pathogenic and heavy metal-resistant bacteria, as well as microbial communities associated with wastewater treatment systems. Functional prediction highlighted the significant role of the gut microbiome in digestion and metabolism, with active enzymes for breaking down various organic substances. Biosynthetic pathways for leucine, valine, and isoleucine were present in both sites, known to be involved fish immunity. The host maintained a stable and diverse bacterial consortium, while microbial diversity became more specialized due to human activities, adapting to anthropogenic stress and selection pressures.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03747-0.

Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning

Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.

Effect of plant polysaccharides (Poria cocos and Astragalus polysaccharides) on immune responses and intestinal microbiota of Dabry's sturgeons

Searching for non-toxic and harmless feed ingredients that can improve growth performance and host immunity has always been the focus of attention in the protected areas for artificially bred Dabry's sturgeons. The present study explored the effect of dietary Poria cocos and Astragalus polysaccharides on the antioxidant status, expression of immune related genes, and composition and putative functions of gut bacterial communities in Dabry's sturgeons for the first time. In this study, Dabry's sturgeons were randomly divided into 3 groups and fed diets of normal, P. cocos polysaccharide-added (200 mg/kg), and Astragalus polysaccharide-added (200 mg/kg) food for 14 days. The results indicated that dietary Astragalus polysaccharide can increase the final body weight of Dabry's sturgeon. Compared with normal breeding individuals, feeding diets containing the P. cocos and Astragalus polysaccharides up-regulated the activity of superoxide dismutase, lysozyme, catalase, and glutathione peroxidase while also decreasing the levels of malondialdehyde. In addition, the Astragalus polysaccharide group had higher gene expression of two inflammatory cytokines, tumor necrosis factor alpha and immunoglobulin M, than the control group. Analysis of intestinal microbiota revealed that the dietary Astragalus polysaccharide improved the richness and diversity of major gut microbiota in Dabry's sturgeons, while the structure in the P. cocos polysaccharide group was clearly distinguished from that of the control group. Our results preliminarily indicated that dietary supplementation of P. cocos and Astragalus polysaccharides may contribute to better performance in growth, development, and inflammatory response for Dabry's sturgeons, and they provide basic guidance for plant polysaccharide additives in artificial breeding of sturgeons.

The role of the microbiome on fish mucosal immunity under changing environments

The environment is crucial for fish as their mucosal surfaces face continuous challenges in the water. Fish mucosal surfaces harbor the microbiome and mucosal immunity. Changes in the environment could affect the microbiome, thus altering mucosal immunity. Homeostasis between the microbiome and mucosal immunity is crucial for the overall health of fish. To date, very few studies have investigated mucosal immunity and its interaction with the microbiome in response to environmental changes. Based on the existing studies, we can infer that environmental factors can modulate the microbiome and mucosal immunity. However, we need to retrospectively examine the existing literature to investigate the possible interaction between the microbiome and mucosal immunity under specific environmental conditions. In this review, we summarize the existing literature on the effects of environmental changes on the fish microbiome and mucosal immunity. This review mainly focuses on temperature, salinity, dissolved oxygen, pH, and photoperiod. We also point out a gap in the literature and provide directions to go further in this research field. In-depth knowledge about mucosal immunity-microbiome interaction will also improve aquaculture practices by reducing loss during environmental stressful conditions.

Effects of Aspergillus-meal prebiotic diet on the growth performance, health status and gut microbiota of Asian seabass, Lates calcarifer

In this study, the growth performance, health status and intestinal microbiota of juvenile Asian seabass, Lates calcarifer, were assessed after dietary administration of a prebiotic product obtained from fermented Aspergillus orizae, Fermacto®. Asian seabass were fed three diets; control (without Aspergillus-meal prebiotic), 0.2% and 0.3% Aspergillus-meal prebiotic for 56 days. Fish were raised in freshwater with acceptable water quality. No significant differences were found in the growth performance and composition of dorsal fish muscle among all groups. Fish fed diets supplemented with 0.3% of Aspergillus-meal prebiotic had a significantly higher survival rate after being challenged with V. alginolyticus than fish fed with the control diet. Supplementation of the Aspergillus-meal prebiotic significantly improved immune responses by inducing higher respiratory burst, superoxide dismutase, phagocytic and lysozyme activity compared to the control group. In addition, prebiotic doses significantly induced an up-regulation of heat shock cognate 70 kDa protein (hsp70) in the liver compared to the control group. Signaling pathways were also affected with significantly higher gene expression of complement c-3 (c3), mechanistic target of rapamycin (mtor), and mammalian lethal with SEC13 protein 8 (mlst-8) in the liver of fish fed 0.3% Aspergillus prebiotic. The pro-inflammatory gene, tumor necrosis factor (tnf) and anti-inflammatory gene, transforming growth factor beta-1 (tfg-β1) were significantly higher in the head kidney of fish offered prebiotic diets. Fish receiving Aspergillus-meal prebiotic revealed significantly higher expression of Mx gene 24 h post nervous necrosis virus injection compared to the control. Additionally, the α-diversity of gut microbiota, including genus, Pielou's evenness, Shannon diversity index, and Margalef's species richness were significantly higher in fish fed 0.3% Aspergillus-meal prebiotic than the control group. The principal component analysis eigenvector plots showed that a high abundance of beneficial bacteria, such as Entercoccus faecium, Lactococcus lactis, Macrococcus caseolyticus and Vagococcus fluvialis, along with potentially pathogenic bacteria, such as Staphylococcus sciuri and L. garvieae subsp. garvieae were present in fish treated with Aspergillus-meal prebiotic. Although dietary Aspergillus-meal prebiotic did not improve the growth performance of Asian seabass, 0.3% of Aspergillus-meal prebiotic is recommended to elevate the immunological status of fish.

Changes in community structures and functions of the gut microbiomes of deep-sea cold seep mussels during in situ transplantation experiment

BACKGROUND

Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete digestive system although symbionts in their gills play vital roles in nutrient supply. This digestive system remains functional and can utilise available resources, but the roles and associations among gut microbiomes in these mussels remain unknown. Specifically, how the gut microbiome reacts to environmental change is unclear.

RESULTS

The meta-pathway analysis showed the nutritional and metabolic roles of the deep-sea mussel gut microbiome. Comparative analyses of the gut microbiomes of original and transplanted mussels subjected to environmental change revealed shifts in bacterial communities. Gammaproteobacteria were enriched, whereas Bacteroidetes were slightly depleted. The functional response for the shifted communities was attributed to the acquisition of carbon sources and adjusting the utilisation of ammonia and sulphide. Self-protection was observed after transplantation.

CONCLUSION

This study provides the first metagenomic insights into the community structure and function of the gut microbiome in deep-sea chemosymbiotic mussels and their critical mechanisms for adapting to changing environments and meeting of essential nutrient demand.

Microplastic pollution destabilized the osmoregulatory metabolism but did not affect intestinal microbial biodiversity of earthworms in soil

Metabolomic and gut microbial responses of soil fauna to environmentally relevant concentrations of microplastics indicate the potential molecular toxicity of microplastics; however, limited data exist on these responses. In this study, earthworms (Eisenia fetida) were exposed to spherical (25-30 μm diameter) polystyrene microplastic-contaminated soil (0.02%, w:w) for 14 days. Changes in weight, survival rate, intestinal microbiota and metabolic responses of the earthworms were assessed. The results showed that polystyrene microplastics did not influence the weight, survival rate, or biodiversity of the gut microbiota, but significantly decreased the relative abundance of Bacteroidetes at the phylum level. Moreover, polystyrene microplastics disturbed the osmoregulatory metabolism of earthworms, as indicated by the significantly decreased betaine, myo-inositol and lactate, and increased 2-hexyl-5-ethyl-furan-3-sulfonic acid at the metabolic level. This study provides important insights into the molecular toxicity of environmentally relevant concentrations of polystyrene microplastics on soil fauna.

Metabolic turnover rate, digestive enzyme activities, and bacterial communities in the white shrimp Litopenaeus vannamei under compensatory growth

The present work aimed to evaluate the effects promoted by a phase of compensatory growth on metabolic turnover rate, digestive enzyme activity, and bacterial biota of the Pacific white shrimp Litopenaeus vannamei kept under different feeding regimes. Three treatments were evaluated as follows: 70% feed restriction during 3 (T3) and 6 (T6) days, followed by a period of feeding to satiety, and a control treatment without restriction periods. The results showed a full compensatory growth in treatments T3 and T6 by day 35 of the bioassay. A significant increase in trypsin and lipase (T6) activities was observed during compensatory growth, whereas specific amylase activity was significantly lower in treatment T6 compared to T3 but not significantly different from the control group. To determine the metabolic turnover rate of nitrogen in muscle tissue, an analysis of nitrogen isotope values (δ¹⁵N) at natural abundance levels was performed. At the end of the experimental period, shrimp under feed restriction had lower metabolic turnover rates and longer nitrogen residence times (t ₅₀) in muscle tissue, as compared to individuals in the control treatment. Regarding the changes in the bacterial communities in shrimp gut, no significant differences were observed at the phylum level, with Proteobacteria being the most abundant bacteria, followed by Actinobacteria. At family taxa level, Rhodobacteraceae presented the highest relative abundance in all treatments, whereas a decrease in Vibrionaceae was observed in treatments T3 and T6 when compared to control shrimps during compensatory growth. At the genus level, a decrease in Celeribacter, Catenococcus, and Epibacterium, and an increase in Ruegeria and Shimia, were identified in shrimp subjected to feed restriction when compared to control organisms during compensatory growth (day 14). At the end of the experimental period, the evaluated parameters showed similar results as those observed in the control treatment, suggesting a normalization of the metabolism and the physiological state. The present findings contribute to a better understanding on the physiological effects produced during compensatory growth in shrimp, which in turn could assist in the development of improved feeding strategies in benefit of the aquaculture industry.

Dietary Sodium Butyrate Improves Intestinal Health of Triploid Oncorhynchus mykiss Fed a Low Fish Meal Diet

This study aimed to determine the effects of dietary sodium butyrate (NaB) on the growth and gut health of triploid Oncorhynchus mykiss juveniles (8.86 ± 0.36 g) fed a low fish meal diet for 8 weeks, including the inflammatory response, histomorphology, and the composition and functional prediction of microbiota. Five isonitrogenous and isoenergetic practical diets (15.00% fish meal and 21.60% soybean meal) were supplemented with 0.00% (G1), 0.10% (G2), 0.20% (G3), 0.30% (G4), and 0.40% NaB (G5), respectively. After the feeding trial, the mortality for G3 challenged with Aeromonas salmonicida for 7 days was lower than that for G1 and G5. The optimal NaB requirement for triploid O. mykiss based on weight gain rate (WGR) and the specific growth rate (SGR) was estimated to be 0.22% and 0.20%, respectively. The activities of intestinal digestive enzymes increased in fish fed a NaB diet compared to G1 (p < 0.05). G1 also showed obvious signs of inflammation, but this inflammation was significantly alleviated with dietary NaB supplementation. In comparison, G3 exhibited a more complete intestinal mucosal morphology. Dietary 0.20% NaB may play an anti-inflammatory role by inhibiting the NF-κB-P65 inflammatory signaling pathway. Additionally, the relative abundance of probiotics was altered by dietary NaB. In conclusion, dietary 0.20% NaB improved the intestinal health of triploid O. mykiss fed a low fish meal diet.

Starvation alters gut microbiome and mitigates off-flavors in largemouth bass (Micropterus salmoides)

The present study aimed to investigate the response of intestinal microbiota during 3 weeks' starvation of largemouth bass (Micropterus salmoides), an economically important freshwater fish, using 16S rRNA gene amplicon sequencing and PICRUSt2 predictive functional profiling. Overall, the microbiota was mainly represented by Mycoplasma, Pseudomonas, Acinetobacter, and Microbacterium in the initial group. This pattern contrasted with that of Cetobacterium and Aeromonas, which were major representative genera in the starved group. Significant differences in the richness and composition of intestinal microbial community induced by starvation were observed. Notably, earthy-musty off-flavor compounds (geosmin and 2-methylisoborneol) were significantly decreased during starvation, which were significantly correlated with the abundance of certain actinobacterial taxa, namely, Microbacterium and Nocardioides. Additionally, the functional pathways involved in synthesis of off-flavor compounds, protein digestion, fatty acid degradation, and biosynthesis of cofactors greatly decreased with starvation, indicating that microbiota modulated the specific metabolic pathway to adapt to food deprivation. These results emphasize that starvation can modulate diversity, community structure, and functions of the intestinal microbiota and mitigate the off-flavors, which has important implications for strategies to eliminate off-flavor odorants through the application of probiotics to manipulate the gut microbiome and ultimately enhance flesh quality of freshwater fish.

Freshwater transfer affected intestinal microbiota with correlation to cytokine gene expression in Asian sea bass

As a catadromous fish, Asian sea bass (Lates calcarifer) juveniles migrate from seawater (SW) to freshwater (FW) for growth and development. During migration, they undergo physiological changes to acclimate to environmental salinity. Thus, it is crucial to understand how SW-to-FW migration affects the gut microbiota of catadromous fish. To the best of our knowledge, no study has revealed the effects of transfer to hypotonic environments on a catadromous fish microbiota. In this study, we aimed to determine the effects of FW transfer on the microbiota and cytokine gene expression in the intestines of juvenile catadromous Asian sea bass. The relationship between the water and the gut microbiota of this euryhaline species was also examined. We found that FW transfer affected both mucosa- and digesta-associated microbiota of Asian sea bass. Plesiomonas and Cetobacterium were dominant in both the mucosa- and digesta-associated microbiota of FW-acclimated sea bass. The pathogenic genera Vibrio, Staphylococcus, and Acinetobacter were dominant in the SW group. Although dominant fish microbes were present in the water, fish had their own unique microbes. Vitamin B6 metabolism was highly expressed in the FW fish microbiota, whereas arginine, proline, and lipid metabolism were highly expressed in the SW fish microbiota. Additionally, the correlation between cytokine gene expression and microbiota was found to be affected by FW transfer. Taken together, our results demonstrated that FW transfer altered the composition and functions of mucosa- and digesta-associated microbiota of catadromous Asian sea bass intestines, which correlated with cytokine gene expression.

Metabolite features of serum and intestinal microbiota response of largemouth bass (Micropterus salmoides) after Aeromonas hydrophila challenge

The enteric morphology, enteric microbiota structure and serum metabolomics of M. salmoides before and after infected by A. hydrophila were analysed to explore the pathogenic mechanism of A. hydrophila infection in M. salmoides. The results revealed that, after the infection of A. hydrophila, the villus boundary of largemouth bass became less obvious; the relative abundance of Proteobacteria and decreasing relative abundance of Tenericutes were increasing; genera relative abundance of putatively beneficial bacteria (Mycoplasma) were decreasing, whereas the genus Aeromonas increased after infection; serum metabolomic analysis showed that infection with A. hydrophila caused disorder to the metabolic processes of largemouth bass, particularly amino acid metabolism, and caused inflammation; several potential pathogen infection-related and significantly differential intestinal microbiota-related metabolite markers were identified, such as 6-hydroxy-5-methoxyindole glucuronide, zalcitabine, bilirubin, aciclovir. This study may provide new insights into the potential association between enteric microbiota and serum metabolism and the pathogenic mechanism of M. salmoides infected by A. hydrophila, providing a scientific basis for disease control in largemouth bass breeding.

Biotherapeutic microbial supplementation for ameliorating fish health: developing trends in probiotics, prebiotics, and synbiotics use in finfish aquaculture

Nutrition demands in aquaculture can be realized through quality aquafeeds as compounded diets that contribute to the growth and health of aquaculture species. Functional additives in feed, notably probiotics, prebiotics, and their admixture synbiotics, have been recently recognized for their biotherapeutic role as immunostimulants capable of conferring disease resistance, stress tolerance, and gastrointestinal health; counteracting the negative effects of anti-nutrients, pathogenic prevalence, and antimicrobials in finfish aquaculture. Formulated diets based on probiotics, prebiotics, and as a supplemental combination for synbiotics can significantly influence fish gut microbiomes, establishing the modalities of microbial dynamics to maximize host-associated benefits. These microbial functional-feed supplements are acclaimed to be biocompatible, biodegradable, and safe for dietary consumption as well as the environment. In fed fish aquaculture, prebiotic appended probiotic diet 'synbiotic' has propounded larger attention for its additional health and nutritional benefits. Synbiotic, prebiotic, and probiotic usage as functional feeds for finfish aquaculture thus provides promising prospects. Developing trends in their intended application are reviewed here forth.

Combined antagonist treatment of glucocorticoid and mineralocorticoid receptor does not affect weight loss of fasting rainbow trout but inhibits a fasting-induced elevation of cortisol secretion

The gastrointestinal system of fish reacts rapidly to food deprivation. The relative masses of digestive organs and activities of digestive enzymes decrease within days of fasting. This is believed to be an energy-conserving strategy as the metabolic cost of maintaining digestive capacity is high. Cortisol is known for its role in energy mobilization following stress exposure, and prolonged elevated cortisol levels have been shown to reduce growth rates in fish. Fish experiencing chronic cortisol elevations show structural changes to their digestive tissues and overall reductions in relative digestive tissue masses. In fish fasting for prolonged periods, circulating cortisol levels have been reported to be downregulated, upregulated, or unchanged compared to feeding fish. This study aimed to investigate if RU486 and spironolactone, antagonists of the glucocorticoid receptor (GR), and mineralocorticoid receptor (MR), respectively, alone or in combination affect circulating cortisol levels during prolonged starvation. In addition, we tested the effects of blocking GR and MR, on the down-regulation of relative digestive tissue mass during starvation, and its effects on weight loss. Three treatment groups of rainbow trout were intraperitoneally implanted with either GR, MR, or GR and MR blockers. A fourth group was implanted with cortisol, while a fifth group served as a control. All treatment groups were sampled over a course of four weeks of food deprivation and compared against each other and fed control fish at day 0 of the trial. Starvation for 2 weeks and longer significantly increased circulating cortisol levels in all groups except for the group implanted with GR and MR antagonists. Loss of body mass occurred most rapidly during the first week of starvation. Spironolactone treatment resulted in significantly reduced loss of mass during the first week, however, over the following weeks, no differences in mass loss were observed in the groups implanted with blockers, while cortisol-treated fish showed the highest decrease in body mass over time. Relative digestive tissue mass decreased in all groups but apparently, the fasting-induced elevation in plasma cortisol levels did not affect the relative weight loss of digestive tissues as no differences were observed between control fish and GR + MR antagonist treated fish. Very high cortisol levels caused by cortisol treatment however caused a faster decrease in the relative mass of some digestive organs, particularly the stomach.

Modulation of gut microbiota, blood metabolites, and disease resistance by dietary β-glucan in rainbow trout (Oncorhynchus mykiss)

BACKGROUND

Prebiotics are known to have a positive impact on fish health and growth rate, and β-glucans are among the most used prebiotics on the market. In this study, rainbow trout (Oncorhynchus mykiss) were treated with a β-1,3;1,6-glucan dietary supplement (at a dose of 0 g, 1 g, 10 g, and 50 g β-glucan per kg of feed). After 6 weeks, the effect of the β-glucan was evaluated by determining the changes in the microbiota and the blood serum metabolites in the fish. The impact of β-glucan on the immune system was evaluated through a challenge experiment with the bacterial fish pathogen Yersinia ruckeri.

RESULTS

The microbiota showed a significant change in terms of composition following β-glucan treatment, notably an increase in the relative abundance of members of the genus Aurantimicrobium, associated with a decreased abundance of the genera Carnobacterium and Deefgea. Furthermore, analysis of more than 200 metabolites revealed that the relative levels of 53 metabolites, in particular compounds related to phosphatidylcholines, were up- or downregulated in response to the dietary supplementation, this included the amino acid alanine that was significantly upregulated in the fish that had received the highest dose of β-glucan. Meanwhile, no strong effect could be detected on the resistance of the fish to the bacterial infection.

CONCLUSIONS

The present study illustrates the ability of β-glucans to modify the gut microbiota of fish, resulting in alteration of the metabolome and affecting fish health through the lipidome of rainbow trout.

Developmental stage variation in the gut microbiome of South China tigers

South China tigers (Panthera tigris amoyensis, SC) are the most threatened tiger subspecies in the world. All the living SCs are captive in zoos or reserves and depend on artificial feeding. The composition of the gut microbiome plays an important role in sustaining the health of the host. A comprehensive understanding of the composition and development of the microbial community of SC is helpful to improve the feeding of captive SC. In this study, we collected 47 fecal samples, 37 of which were from SC of three developmental stages, 5 from adult Amur tigers (Am), and 5 from adult Bengal tigers (Bg), which were all housed in the same zoo. We investigated the diversity, richness, and composition of the bacterial microbiomes and we found that the gut microbiome of SC is strongly affected by host aging. The composition of the gut microbiome of juvenile SC experienced dramatic changes from 5 months old to 1 year old, and it showed much less difference when compared to the samples of 1 year old and the subadult. No significant differences were observed between the samples of subadult and the adult groups. The predominant phylum of 5-month-old SC is Fusobacteriota (33.99%) when the juvenile tigers were older than 5 months, and Firmicutes, but not Fusobacteriota, became the predominant phylum of bacteria in their gut. The gut microbiome of SC, Am, and Bg is possibly affected by their genetic variation; however, the core microbiome of these three subspecies is the same. Our data suggest that the gut microbiome of SC undergoes a developmental progression: a developmental phase (cub), a transitional phase (subadult), and a stable phase (adult). These results expand our understanding of the role of age in the development of the gut microbiome of SC.

Resveratrol Improves the Digestive Ability and the Intestinal Health of Siberian Sturgeon

The lack of detailed information on nutritional requirement results in limited feeding in Siberian sturgeon. In this study, resveratrol, a versatile natural extract, was supplemented in the daily diet, and the digestive ability and microbiome were evaluated in the duodena and valvular intestines of Siberian sturgeon. The results showed that resveratrol increased the activity of pepsin, α-amylase, and lipase, which was positively associated with an increase in the digestive ability, but it did not influence the final body weight. Resveratrol improved the digestive ability probably by distinctly enhancing intestinal villus height. Microbiome analysis revealed that resveratrol changed the abundance and composition of the microbial community in the intestine, principally in the duodenum. Random forests analysis found that resveratrol significantly downregulated the abundance of potential pathogens (Citrobacter freundii, Vibrio rumoiensis, and Brucella melitensis), suggesting that resveratrol may also improve intestinal health. In summary, our study revealed that resveratrol improved digestive ability and intestinal health, which can contribute to the development of functional feed in Siberian sturgeon.

Multi-dimensional investigation and distribution characteristics analysis of gut microbiota of different marine fish in Fujian Province of China

The gut microbiota plays an important role in animal health and behavior. In marine fish, the composition of the gut microbiota is affected by many complex factors, such as diet, species, and regional factors. Since more than one hundred fish species have been cultured in fish farms along with the 3,324 km coastline of Fujian Province in South China, we chose this region to study the gut microbiota composition of marine commercial fishes because sufficient different species, diets, and regional factors were observed. We investigated the distribution characteristics of the gut microbiota of seven cultured species (Epinephelus akaara, Epinephelus coioides, Epinephelus lanceolatus ♂ × Epinephelus fuscoguttatus ♀, Siganus fuscescens, Pagrus major, Lateolabrax japonicus, and Acanthopagrus schlegelii) living in the same aquatic region and one species (E. akaara) living separately in five regions separated by latitude. The impacts of diet, region, and species factors on fish gut microbiota were also evaluated. Diversity and multivariate analyses showed that the patterns of the microbiota were significantly different in different fish species within the same habitat and E. akaara with five latitude regions. Mantel analysis showed that AN, SiO₃^2–, DO, and NO₂^– were the principal factors affecting the microbial community of E. akaara in the five habitats. Additionally, similar distribution characteristics occurred in different gut parts of different fishes, with an increasing trend of Proteobacteria and Vibrionaceae abundance and a decreasing trend of Firmicutes and Bacillaceae abundance from the foregut to the hindgut. Vibrionaceae was the most abundant family in the content. This study highlights that a persistent core microbiota was established in marine commercial fishes spanning multiple scales. The factors with the greatest effect on fish gut microbiota may be (i) host genetics and (ii) geographic factors rather than the microbiota in the diet and water environment. These core microbes regularly colonized from the foregut to the hindgut, which was driven by their underlying functions, and they were well adapted to the gut environment. Moreover, the microbiota in the content may have contributed more to the gut microbial communities than previously reported. This study could complement basic data on the composition of marine commercial fishes and facilitate relatively complete investigations, which would be beneficial for the healthy and sustainable development of aquaculture.

Compositional Dynamics of Gastrointestinal Tract Microbiomes Associated with Dietary Transition and Feeding Cessation in Lake Sturgeon Larvae

Compromised nutritional conditions associated with dietary transitions and feeding cessation in the wild and during fish aquaculture operations are common and can impact growth and survival. These effects are especially prevalent during early ontogenetic stages. We quantified phenotypic and GI tract microbial community responses with an emphasis on protease-producing bacteria of lake sturgeon (Acipenser fulvescens) larvae, a species of aquacultural and conservational importance. To quantify responses associated with experimental food transition and feeding cessation, we performed a 36-day feeding experiment using two treatments: control and diet transition. However, larvae in the diet transition treatment failed to undergo transition and ceased feeding. Larvae in the diet transition treatment exhibited lower growth (total length and body weight) and survival than control larvae. Treatment had a greater effect than ontogenetic changes on taxonomic composition and diversity of the GI tract microbial community. Proteobacteria dominated the GI tract microbial community of the diet transition larvae whereas Firmicutes dominated the GI tracts of control larvae. Most of the 98 identified protease-producing isolates in both treatments were from genera Pseudomonas and Aeromonas: taxonomic groups that include known fish pathogens. Overall, failing to transition diets affected responses in growth and GI tract microbiome composition and diversity, with the later dysbiosis being an indicator of morbidity and mortality in larval lake sturgeon. Thus, microbiological interrogations can characterize responses to dietary regimes. The results can inform fish culturalists and microbiologists of the importance of dietary practices consistent with the establishment and maintenance of healthy GI tract microbiota and optimal growth during early ontogeny.

Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic salmon

Background

Rapidly spreading parasitic infections like amoebic gill disease (AGD) are increasingly problematic for Atlantic salmon reared in aquaculture facilities and potentially pose a risk to wild fish species in surrounding waters. Currently, it is not known whether susceptibility to AGD differs between wild and farmed salmon. Wild Atlantic salmon populations are declining and this emerging disease could represent an additional threat to their long-term viability. A better understanding of how AGD affects fish health is therefore relevant for the accurate assessment of the associated risk, both to farming and to the well-being of wild populations. In this study, we assessed the impact of natural exposure to AGD on wild, hybrid and farmed post-smolt Atlantic salmon reared in a sea farm together under common garden conditions.

Results

Wild fish showed substantially higher mortality levels (64%) than farmed fish (25%), with intermediate levels for hybrid fish (39%) suggesting that AGD susceptibility has an additive genetic basis. Metabolic rate measures representing physiological performance were similar among the genetic groups but were significantly lower in AGD-symptomatic fish than healthy fish. Gut microbial diversity was significantly lower in infected fish. We observed major shifts in gut microbial community composition in response to AGD infections. In symptomatic fish the relative abundance of key taxa Aliivibrio, Marinomonas and Pseudoalteromonas declined, whereas the abundance of Polaribacter and Vibrio increased compared to healthy fish.

Conclusions

Our results highlight the stress AGD imposes on fish physiology and suggest that low metabolic-rate fish phenotypes may be associated with better infection outcomes. We consider the role increased AGD outbreak events and a warmer future may have in driving secondary bacterial infections and in reducing performance in farmed and wild fish.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00203-x.

Metagenomics Reveal Microbial Effects of Lotus Root-Fish Co-Culture on Nitrogen Cycling in Aquaculture Pond Sediments

Feed input leads to a large amount of nitrogen-containing sediment accumulating in the substrate in the pond culture process, threatening the safety of aquaculture production. Planting lotus roots (Nelumbo nucifera Gaertn.) in ponds can accelerate the removal of bottom nitrogen, while the role of nitrogen cycle-related microorganisms in the removal is still unclear. In this study, eight yellow catfish (Pelteobagrus fulvidraco) culture ponds with the same basic situation were divided into fishponds with planted lotus roots and ponds with only fish farming. Sediment samples were taken from the fishponds with planted lotus roots and the ponds with only fish farming before and after fish farming, marked as FPB, FPA, FOB, and FOA, respectively, and subjected to physicochemical and metagenomic sequencing analyses. The results show that the contents of NH4+, NO2−, TN, TP, and OM were significantly lower (p < 0.05) in FPA than in FOA. The abundance of metabolic pathways for inorganic nitrogen transformation and ammonia assimilation increased considerably after culture compared to the sediments before culture. A total of eight ammonia production pathways and two ammonia utilization pathways were annotated in the sediments of the experimental ponds, with a very high abundance of ammonia assimilation. Acinetobacter and Pseudomonas (34.67%, 18.02%) were the dominant bacteria in the pond sediments before culture, which changed to Thiobacillus (12.16%) after culture. The FPA had significantly higher relative abundances of Thiobacillus denitrificans and Sulfuricella denitrificans, and the FOA had significantly a higher abundance of Microcystis aeruginosa compared to other samples. The massive growth of Microcystis aeruginosa provided two new inorganic nitrogen metabolic pathways and one organic nitrogen metabolic pathway for FOA. The relative abundances of these three microorganisms were negatively correlated with NH4+ content (p < 0.01) and significantly positively correlated with AP, OM content, and pH value. Compared with ponds with only fish farming, lotus root−fish co-culture can significantly reduce the nitrogen content in sediment, increase the abundance of denitrifying bacteria, and inhibit algae growth. Still, it has little effect on the abundance of nitrogen cycle-related enzymes and genes. In summary, it is shown that, although lotus roots promote the growth of denitrifying microorganisms in the sediment, nitrogen removal relies mainly on nutrient uptake by lotus roots.

Gut Microbiome as a Potential Biomarker in Fish: Dietary Exposure to Petroleum Hydrocarbons and Metals, Metabolic Functions and Cytokine Expression in Juvenile Lates calcarifer

The gut microbiome of fish contains core taxa whose relative abundances are modulated in response to diet, environmental factors, and exposure to toxicogenic chemicals, influencing the health of the host fish. Recent advances in genomics and metabolomics have suggested the potential of microbiome analysis as a biomarker for exposure to toxicogenic compounds. In this 35-day laboratory study, 16S RNA sequencing and multivariate analysis were used to explore changes in the gut microbiome of juvenile Lates calcarifer exposed to dietary sub-lethal doses of three metals: vanadium (20 mg/kg), nickel (480 mg/kg), and iron (470 mg/kg), and to two oils: bunker C heavy fuel oil (HFO) (1% w/w) and Montara, a typical Australian medium crude oil (ACO) (1% w/w). Diversity of the gut microbiome was significantly reduced compared to negative controls in fish exposed to metals, but not petroleum hydrocarbons. The core taxa in the microbiome of negative control fish comprised phyla Proteobacteria (62%), Firmicutes (7%), Planctomycetes (3%), Actinobacteria (2%), Bacteroidetes (1%), and others (25%). Differences in the relative abundances of bacterial phyla of metal-exposed fish were pronounced, with the microbiome of Ni-, V-, and Fe-exposed fish dominated by Proteobacteria (81%), Firmicutes (68%), and Bacteroidetes (48%), respectively. The genus Photobacterium was enriched proportionally to the concentration of polycyclic aromatic hydrocarbons (PAHs) in oil-exposed fish. The probiotic lactic acid bacterium Lactobacillus was significantly reduced in the microbiota of fish exposed to metals. Transcription of cytokines IL-1, IL-10, and TNF-a was significantly upregulated in fish exposed to metals but unchanged in oil-exposed fish compared to negative controls. However, IL-7 was significantly downregulated in fish exposed to V, Ni, Fe, and HFOs. Fish gut microbiome exhibits distinctive changes in response to specific toxicants and shows potential for use as biomarkers of exposure to V, Ni, Fe, and to PAHs present in crude oil.

Dynamics of the Gut Microbiome and Transcriptome in Korea Native Ricefish (Oryzias latipes) during Chronic Antibiotic Exposure

Antibiotics have been widely used to inhibit microbial growth and to control bacterial infection; however, they can trigger an imbalance in the gut flora of the host and dysregulate the host gene regulatory system when discharged into the aquatic environment. We investigated the effects of chronic exposure to a low concentration of erythromycin and ampicillin, focusing on gut microbiome and global gene expression profiles from Korea native ricefish (Oryzias latipes). The proportion of Proteobacteria (especially the opportunistic pathogen Aeromonas veronii) was significantly increased in the ricefish under the chronic exposure to erythromycin and ampicillin, whereas that of other bacterial phyla (i.e., Fusobacteria) decreased. In addition, the expression of genes involved in immune responses such as chemokines and immunocyte chemotaxis was significantly influenced in ricefish in the aquatic environment with antibiotics present. These results show that the internal microbial flora and the host gene expression are susceptible even at a low concentration of chronic antibiotics in the environment, supporting the importance of the appropriate use of antibiotic dose to maintain the sustainable and healthy aquaculture industry and water ecosystem.

Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms

BACKGROUND

Microplastics are a pervasive pollutant widespread in the sea and freshwater from anthropogenic sources, and together with the presence of pesticides, they can have physical and chemical effects on aquatic organisms and on their microbiota. Few studies have explored the combined effects of microplastics and pesticides on the host-microbiome, and more importantly, the effects across multiple trophic levels. In this work, we studied the effects of exposure to microplastics and the pesticide deltamethrin on the diversity and abundance of the host-microbiome across a three-level food chain: daphnids-damselfly-dragonflies. Daphnids were the only organism exposed to 1 µm microplastic beads, and they were fed to damselfly larvae. Those damselfly larvae were exposed to deltamethrin and then fed to the dragonfly larvae. The microbiotas of the daphnids, damselflies, and dragonflies were analyzed.

RESULTS

Exposure to microplastics and deltamethrin had a direct effect on the microbiome of the species exposed to these pollutants. An indirect effect was also found since exposure to the pollutants at lower trophic levels showed carry over effects on the diversity and abundance of the microbiome on higher trophic levels, even though the organisms at these levels where not directly exposed to the pollutants. Moreover, the exposure to deltamethrin on the damselflies negatively affected their survival rate in the presence of the dragonfly predator, but no such effects were found on damselflies fed with daphnids that had been exposed to microplastics.

CONCLUSIONS

Our study highlights the importance of evaluating ecotoxicological effects at the community level. Importantly, the indirect exposure to microplastics and pesticides through diet can potentially have bottom-up effects on the trophic webs.

The Occurrence of Microplastics and the Formation of Biofilms by Pathogenic and Opportunistic Bacteria as Threats in Aquaculture

Aquaculture is the most rapidly growing branch of animal production. The efficiency and quality of the produced food depends on sustainable management, water quality, feed prices and the incidence of diseases. Micro- (MP < 5 mm) and nanoplastic (NP < 1000 nm) particles are among the current factors causing serious water pollution. This substance comes solely from products manufactured by humans. MP particles migrate from the terrestrial to the aquatic environment and adversely affect, especially, the health of animals and humans by being a favorable habitat and vector for microbial pathogens and opportunists. More than 30 taxa of pathogens of humans, aquacutural animals and plants, along with opportunistic bacteria, have been detected in plastic-covering biofilm to date. The mobility and durability of the substance, combined with the relatively closed conditions in aquacultural habitats and pathogens’ affinity to the material, make plastic particles a microbiological medium threatening the industry of aquaculture. For this reason, in addition to the fact of plastic accumulation in living organisms, urgent measures should be taken to reduce its influx into the environment. The phenomenon and its implications are related to the concept of one health, wherein the environment, animals and humans affect each other’s fitness.

Infection and antibiotic treatment have prolonged effect on gut microbiota, muscle and hepatic fatty acids in rainbow trout (Oncorhynchus mykiss)

AIMS

The aim of the present study was to investigate the gastrointestinal (GI) microbiota and bacterium-specific fatty acid occurrence in the muscle and hepatic lipids of rainbow trout Oncorhynchus mykiss (Walbaum, 1792), both healthy and those naturally infected with bacterial pathogens.

METHODS AND RESULTS

From June 2017 (L1) to September 2018 (L8), 74 specimens of rainbow trout Oncorhynchus mykiss (with the average weight from 139.2 ± 7.1 g (L1) to 2191.7 ± 85.1 g (L8)) were studied. Amplicon sequencing targeted to the V3-V4 region of 16S rRNA gene fragments is used for identification of taxonomic composition of gut bacterial communities. Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes, and Fusobacteria were the major phyla. Besides behavioural and physiological manifestations of the bacterial mixed disease (yersiniosis, pseudomonosis, and flavobacteriosis), some disorders induced both the infection and followed antibiotic treatment were detected in the host organism, including (1) a progressive decrease in the content of odd-chain saturated fatty acids of bacterial origin within the trout lipid molecules and (2) abnormalities in trout GI tract microbiota, such as the elimination of LAB and progressive occurrence of certain bacterial taxa, particularly Mycoplasmataceae.

CONCLUSIONS

The GI bacterial flora varied principally due to Mycoplasmataceae and Lactobacillaceae, which could be considered in the search for bioindicators. The content of specific bacterium-derived fatty acids incorporated into the lipids of trout muscle and hepatic seems to be related to the prevalence of bacterial taxa, and their deficit could be regarded as an early warning sign of microbiota disturbance.

SIGNIFICANCE AND IMPACT OF STUDY

Our results demonstrated that infectious disease and antibiotic treatment of reared species can cause pertinent imbalance in their gut microbiota and reduce the abundance of specific fatty acids. This can be useful for the sustainable aquaculture industry due to development of early indication technologies for rapid disease diagnosis.

Gut Microbes Reveal Pseudomonas Medicates Ingestion Preference via Protein Utilization and Cellular Homeostasis Under Feed Domestication in Freshwater Drum, Aplodinotus grunniens

With strong demand for aquatic products, as well as a rapid decrease in global fishery resources and capture fisheries, domesticating animals to provide more high-quality proteins is meaningful for humans. Freshwater drum (Aplodinotus grunniens) is widely distributed in the wild habitats of North America. However, the research on A. grunniens and the feed domestication with diets composed of artificial compounds remains unclear. In this study, a 4-month feeding domestication experiment was conducted with A. grunniens larvae to evaluate the underlying mechanism and molecular targets responsible for alternations in the ingestion performance. The results indicated that a significant increase in the final body weight was exhibited by the feed domesticated group (DOM, 114.8 g) when compared to the group that did not ingest the feed (WT, 5.3 g) as the latest version we raised From the result, the final body weight exhibited significant increase between unfavorable with the feed (WT, 5.3 g) and feed domesticated group (DOM, 114.8 g). In addition, the enzyme activity of digestive enzymes like amylase, lipase, and trypsin was increased in DOM. Genes related to appetite and perception, such as NPY4R, PYY, and LEPR, were activated in DOM. 16s rRNA gene sequencing analysis revealed that Pseudomonas sp. increased from 58.74% to 89.77% in DOM, which accounts for the dominant upregulated microbial community at the genus level, followed by Plesiomonas. Analogously, Mycobacterium, Methylocystis, and Romboutsia also accounted for the down-regulated microbes in the diversity. Transcriptome and RT-PCR analysis revealed that feed domestication significantly improved protein digestion and absorption, inhibited apoptosis by AGE-RAGE signaling, and activated extracellular matrix remodeling by relaxin signaling. Integrated analysis of the microbiome and host transcriptome revealed that Pseudomonas-mediated ingestion capacity, protein utilization, and cellular homeostasis might be the underlying mechanism under feed domestication. These results indicate Pseudomonas and its key genes relating to food ingestion and digestion could serve as the molecular targets for feed domestication and sustainable development in A. grunniens.

Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World's Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)

The symbiosis between a host and its microbiome is essential for host fitness, and this association is a consequence of the host’s physiology and habitat. Sinocyclocheilus, the largest cavefish diversification of the world, an emerging multi-species model system for evolutionary novelty, provides an excellent opportunity for examining correlates of host evolutionary history, habitat, and gut-microbial community diversity. From the diversification-scale patterns of habitat occupation, major phylogenetic clades (A–D), geographic distribution, and knowledge from captive-maintained Sinocyclocheilus populations, we hypothesize habitat to be the major determinant of microbiome diversity, with phylogeny playing a lesser role. For this, we subject environmental water samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus species, both from the wild and after being in captivity for 6 months, to bacterial 16S rRNA gene profiling using Illumina sequencing. We see significant differences in the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types; gut microbiomes too, were influenced by host-related factors. There is no significant association between the gut microbiomes and host phylogeny. However, there is some microbiome related structure at the clade level, with the most geographically distant clades (A and D) being the most distinct, and the two overlapping clades (B and C) showing similarities. Microbes inhabiting water were not a cause for significant differences in fish-gut microbiota, but water quality parameters were. Transferring from wild to captivity, the fish microbiomes changed significantly and became homogenized, signifying plastic changes and highlighting the importance of environmental factors (habitat) in microbiome community assembly. The core microbiome of this group, at higher taxonomic scale, resembled that of other teleost fishes. Our results suggest that divergent natural environments giving rise to evolutionary novelties underlying host adaptations, also includes the microbiome of these fishes.

Histopathology and transcriptome analysis reveals the gills injury and immunotoxicity in gibel carp following acute deltamethrin exposure

More and more evidences proved that deltamethrin (Del) exposure induced adverse effects and damaged immune function to the aquatic animals in the parasite killing process with increasing insecticide application. However, little is currently known of the negative effect on mucosal immunity, especially in gills tissue. Therefore, this study was aimed to reveal the tissue injury and immunotoxicity in the gill of gibel carp following acute deltamethrin exposure. The LC50 of deltamethrin on gibel carp at 96 h was determined to be 6.194 μg/L, and then juvenile gibel carp (Carassius auratus gibelio) (8.8 ± 1.0 g) were exposed to four Del exposure groups (0.61, 1.22, 2.44, and 4.88 μg/L) for 12 h and 24 h. We measured the lysozyme (LYZ) contents and myeloperoxidase (MPO) activities and found that with increased concentration of Del exposure, the LYZ contents were found to increase in the 1.22 μg/L Del group initially significantly and then gradually significantly decrease in the 4.88 μg/L Del group. And the activities of MPO were significantly lifted in a dose-dependent manner. The histological analysis showed that Del exposure caused serious desquamation and necrosis in the surface of epithelial cells, accompanied by interlamellar cellular mass degenerative. In addition, the mucous cells were significantly decreased in the high Del concentration group (2.44 μg/L and 4.88 μg/L Del group) by AB-PAS staining. Additionally, totally 2857 DEGs (including 1624 up-regulated and 1233 down-regulated genes) were identified between the control group and 4.88 μg/L Del exposure group using transcriptional analysis. Among these, some genes involved in innate immune molecules, complement activation, apoptosis-related molecules, cytokine, and adaptive immune molecules, were also down-regulated. Importantly, we found immune system process and tumor necrosis factor receptor (superfamily) binding pathways were downregulated based on the GO and KEGG enrichment analysis. Meanwhile, we detected the expression of pro-inflammatory cytokines (TNF-α, IFN-γ, IL-1β, and IL-8), anti-inflammatory cytokines (TGF-β), LYZ, IgM, and Hsp70 in the gills tissue at 12 h and 24 h after Del exposure, which were consistent with our sequencing results. Collectively, these results demonstrated that the gills injury and immunotoxicity were induced by Del exposure and provided novel insight for explaining to some extent why Del-exposure fish are more susceptible to concurrent or secondary viral or bacterial infections.

Starvation causes changes in the intestinal transcriptome and microbiome that are reversed upon refeeding

BACKGROUND

The ability of animals and their microbiomes to adapt to starvation and then restore homeostasis after refeeding is fundamental to their continued survival and symbiosis. The intestine is the primary site of nutrient absorption and microbiome interaction, however our understanding of intestinal adaptations to starvation and refeeding remains limited. Here we used RNA sequencing and 16S rRNA gene sequencing to uncover changes in the intestinal transcriptome and microbiome of zebrafish subjected to long-term starvation and refeeding compared to continuously fed controls.

RESULTS

Starvation over 21 days led to increased diversity and altered composition in the intestinal microbiome compared to fed controls, including relative increases in Vibrio and reductions in Plesiomonas bacteria. Starvation also led to significant alterations in host gene expression in the intestine, with distinct pathways affected at early and late stages of starvation. This included increases in the expression of ribosome biogenesis genes early in starvation, followed by decreased expression of genes involved in antiviral immunity and lipid transport at later stages. These effects of starvation on the host transcriptome and microbiome were almost completely restored within 3 days after refeeding. Comparison with published datasets identified host genes responsive to starvation as well as high-fat feeding or microbiome colonization, and predicted host transcription factors that may be involved in starvation response.

CONCLUSIONS

Long-term starvation induces progressive changes in microbiome composition and host gene expression in the zebrafish intestine, and these changes are rapidly reversed after refeeding. Our identification of bacterial taxa, host genes and host pathways involved in this response provides a framework for future investigation of the physiological and ecological mechanisms underlying intestinal adaptations to food restriction.

Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish

The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.

Trophic and symbiotic links between obligate-glacier water bears (Tardigrada) and cryoconite microorganisms

Insights into biodiversity and trophic webs are important for understanding ecosystem functions. Although the surfaces of glaciers are one of the most productive and biologically diverse parts of the cryosphere, the links between top consumers, their diet and microbial communities are poorly understood. In this study, for the first time we investigated the relationships between bacteria, fungi and other microeukaryotes as they relate to tardigrades, microscopic metazoans that are top consumers in cryoconite, a biologically rich and productive biogenic sediment found on glacier surfaces. Using metabarcoding (16S rDNA for bacteria, ITS1 for fungi, and 18S rDNA for other microeukaryotes), we analyzed the microbial community structures of cryoconite and compared them with the community found in both fully fed and starved tardigrades. The community structure of each microbial group (bacteria, fungi, microeukaryotes) were similar within each host group (cryoconite, fully fed tardigrades and starved tardigrades), and differed significantly between groups, as indicated by redundancy analyses. The relative number of operational taxonomic units (ZOTUs, OTUs) and the Shannon index differed significantly between cryoconite and tardigrades. Species indicator analysis highlighted a group of microbial taxa typical of both fully fed and starved tardigrades (potential commensals), like the bacteria of the genera Staphylococcus and Stenotrophomonas, as well as a group of taxa typical of both cryoconite and fully fed tardigrades (likely part of the tardigrade diet; bacteria Flavobacterium sp., fungi Preussia sp., algae Trebouxiophyceae sp.). Tardigrades are consumers of bacteria, fungi and other microeukaryotes in cryoconite and, being hosts for diverse microbes, their presence can enrich the microbiome of glaciers.

Characterization of Microbiological Quality of Whole and Gutted Baltic Herring

There is growing interest in Baltic herring (Clupea harengus membras) and other undervalued, small-sized fish species for human consumption. Gutting or filleting of small-sized fish is impractical; hence, the aim of this study was to explore the suitability of the whole (ungutted) herring for food use. The microbiological quality of commercially fished whole and gutted herring was analysed with culture-dependent methods combined with identification of bacterial isolates with MALDI-TOF Mass Spectrometry and culture-independent 16S rRNA gene amplicon sequencing. Whole and gutted herring had between 2.8 and 5.3 log₁₀ CFU g⁻¹ aerobic mesophilic and psychrotrophic bacteria and between 2.2 and 5.6 log₁₀ CFU g⁻¹ H₂S-producing bacteria. Enterobacteria counts remained low in all the analysed herring batches. The herring microbiota largely comprised the phyla Proteobacteria, Firmicutes, and Actinobacteria (71.7% to 95.0%). Shewanella, Pseudomonas, and Aeromonas were the most frequently isolated genera among the viable population; however, with the culture-independent approach, Shewanella followed by Psychrobacter were the most abundant genera. In some samples, a high relative abundance of the phylum Epsilonbacteraeota, represented by the genus Arcobacter, was detected. This study reports the bacterial diversity present in Baltic herring and shows that the microbiological quality was acceptable in all the analysed fish batches.

Feed microbiome: confounding factor affecting fish gut microbiome studies

There is an increasing interest in the impact of feed on the fish gut microbiome. Most of the studies are based on sequencing the bacterial housekeeping gene 16S rRNA from extracted total DNA, including resident and non-resident live bacteria as well as dead bacteria. It has not been a common practice to include the feed as control, although it contains various nutritious ingredients that microorganisms can use before or after feed preparation. Thus, study designs using digesta as a proxy for the intestinal microbiome raise the concern that composition of the gut microbiome might be biased by carry-over of microbial DNA from the feed itself. Here we report analysis of 15 feeds and representative intestinal digesta of Atlantic salmon (Salmo salar) from five independent case studies. This allowed us to identify "feed microbiomes" that were microbially diverse and shared taxa with digesta microbiomes. Digesta-specific microbiomes were identified, though they were mainly enriched by a few taxa, such as Mycoplasma and Ruminococcaceae. Overall, findings are consistent with a model wherein gut microbial profiles are to a different degree influenced by bacterial DNA present in the feed itself through a "feed microbiome" carry-over effect.

Genome-wide identification of seven superoxide dismutase genes in the marine rotifer Brachionus rotundiformis and modulated expression and enzymatic activity in response to microplastics and nutritional status

Microplastics (MPs) pollution has attracted worldwide attention. Superoxide dismutase (SOD) is a sensitive indicator for assessing the toxic effects of MPs in aquatic organisms. However, few studies have been performed to identify all genes encoding SOD in aquatic invertebrates. Especially, effects of MPs on SOD activity and expression in aquatic organisms under starvation or a subsequent refeeding status are unclear. In the present study, all full-length genes encoding SOD were cloned and characterized from the marine rotifer Brachionus rotundiformis, including CuZnSOD1, CuZnSOD2, CuZnSOD3, CuZnSOD4, CuZnSOD5, MnSOD1, and MnSOD2. The CuZnSOD1, CuZnSOD2 and MnSOD2 are homologous to SODs from vertebrates and the other SOD proteins are rotifer-specific according to the results from the phylogenetic tree. The conserved signature sequences and binding sites of Cu²⁺, Zn²⁺and Mn²⁺ were also identified in the seven SOD proteins. Compared with feeding, starvation down-regulated SOD activity and mRNA expression of CuZnSOD2, CuZnSOD4, CuZnSOD5, MnSOD1 and MnSOD2 while refeeding maintained SOD activity comparable to the feeding level and up-regulated CuZnSOD5 and MnSOD2. Intake of MPs by B. rotundiformis was observed by examining fluorescence signals from the fluorescently-labeled microplastics under different nutritional status. Exposure to MPs reduced rotifer density and increased malondialdehyde (MDA) content and SOD activity in the rotifers under the refeeding condition, but did not affect these indicators under the feeding and starvation conditions. However, mRNA expression of some tested genes was responsive to MPs in the fed, starved and refed rotifers. The present study for the first time demonstrated a nutritional status-dependent effect of MPs on oxidative stress response, and provided more sensitive molecular biomarkers for assessing the toxicity of MPs using B. rotundiformis as a model animal.

Stress responses of the intestinal digestion, antioxidant status, microbiota and non-specific immunity in Songpu mirror carp (Cyprinus carpio L.) under starvation

Songpu mirror carp, Cyprinus carpio L., is a new variety of common carp that has become an economically important freshwater fish in China. However, it remains unknown how its metabolism is regulated under starvation. Here, we investigated how intestinal digestion, antioxidant status, microbiota and immune activities were affected under starvation stress. The feeding regimes were designed as follows: ST0 comprised fish allowed to feed continuously; ST1 comprised fish starved for 1 week; ST2 comprised fish starved for 2 weeks; ST3 comprised fish starved for 3 weeks; ST4 comprised fish starved for 4 weeks. Our results showed a significant decrease in the level of intestinal amylase, lipase, and protease activities in the group ST4 (P < 0.05). Compared with the control group, intestinal antioxidant enzyme activities were significantly increased during short-term starvation. The gene expression levels of interleukin 1β (IL-1β), interleukin 8 (IL-8) and tumor necrosis factor-alpha (TNF-α) were elevated in the groups ST3 and ST4. We also detected the reduction in the expression levels of interleukin 10 (IL-10) and transforming growth factor β (TGF-β2) compared with those of the group ST0. Notably, the gut microbial composition was dominated by Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The relative abundance of the dominant microbial phyla changed significantly under starvation stress. Taken together, our results suggest that starvation can induce the change of intestinal digestion, non-specific immunity and microbiota in Songpu mirror carp, and provide new insights into its habitat selection and adaptation to environmental changes.

Cupriavidus in the intestinal microbiota of Tibet endemic fish Glyptosternum maculatum can help it adapt to habitat of the Qinghai Tibet Plateau

Background

Gut microbes play an important role in the growth and development of fish. The Tibetan Plateau fish Glyptosternum maculatum is a unique species of sisorid catfish living in the river up to 4200 m altitude.

Results

To understand the mechanisms underlying the ability of G. maculatum to adapt to the high-altitude habitat, the intestinal microbiota of G. maculatum was studied. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms of wild and cultured G. maculatum to explore the characteristics of intestinal microorganisms and compared the gut microbial community of wild and cultured G. maculatum. The results showed that the α-diversity and richness of the intestinal microbiome were higher in wild G. maculatum than in cultured fish. The most abundant phylum in both G. maculatum were Fusobacteria, Proteobacteria, Firmicutes, and Bacteroidetes; Cetobacterium and Cupriavidus are the most dominant genus. The membership and structure of intestinal bacterial communities in wild G. maculatum are similar to the cultured fish, suggesting that a core microbiota is present in both G. maculatum intestinal bacterial communities. Metastats analysis showed that six genera were differentially represented between the wild and cultured G. maculatum.

Conclusions

The most interesting characteristic of the intestinal microbial communities of G. maculatum is that there were large numbers of Cupriavidus, which may play an important role in the adaptation of G. maculatum to the water of the Yarlung Zangbo River with a high Cu content. This result, in turn, can guide us on breeding G. maculatum.

Tartrazine exposure results in histological damage, oxidative stress, immune disorders and gut microbiota dysbiosis in juvenile crucian carp (Carassius carassius)

Tartrazine (TZ) is an azo dye widely used in foods, cosmetics, beverages, textile, and leather. In recent years, there are reports on detecting azo dyes in the aquatic environment, so the impact of these compounds on aquatic organisms could not be ignored. In this study, we aimed to evaluate the adverse effects of TZ exposure on teleosts' embryo development and juvenile's health by using crucian carp (Carassius carassius) as the experimental fish. The results showed that embryos exposed to TZ (0.19, 0.76 and 1.5 mM) exhibited a deformity, delayed egg resorption and decreased fertilization and hatching rate. When the juvenile fish were exposed to TZ at a level higher than those present in water for 30 days caused severe histopathological damages of the gill, intestine, kidney and liver. Antioxidant enzymes (CAT, SOD and GSH-Px) activities in the gill, intestine and liver, exhibited a decreasing trend after TZ exposure, while MDA contents elevated. TZ exposure also resulted in the upregulation of pro-inflammatory cytokines (il1 and il6), lysozymes (lyz), complement component 3 (c3), and β-defensin 3 (defb3). In addition, TZ exposure also affected the intestinal microbiota structure. In summary, the data in the present study indicated that TZ exposure  reduce the embryo fertilization and hatching rate; cause histopathological damage of tissues, trigger oxidative stress, innate immune disorders and dysbiosis of gut microbiota in juvenile crucian carp. Therefore, it is necessary to be informed about the hazards of TZ exposure and the discharge of the dye into waters should be strictly administrated to prevent environmental pollution.

Interleukin 1 receptor type I (IL-1RI) is involved in the innate immune response of olive flounder (Paralichthys olivaceus) to resist pathogens

The pleiotropic cytokine IL -1 is involved in important immune responses such as thymocyte proliferation and B cell growth and differentiation. Activation of the IL -1 pathway requires its functional receptor IL -1RI, making IL -1RI the critical point of the IL -1 pathway. In-depth study of IL -1RI will help to understand the immune mechanism involved in IL -1. In this study, we identified the cDNA of the IL -1RI gene of olive flounder (PoIL-1RI). The total length of the PoIL-1RI cDNA is 2490 bp, the open reading frame is 1689 bp long and encodes a protein of 562 amino acids. The protein has three Ig domains and a typical TIR domain, as in other mammals and fish. We found that PoIL-1RI is widely expressed in the tissues studied and shows a significant immune response after stimulation with bacteria and pathogen-associated molecular patterns (PAMPs) both in vitro and in vivo. After PoIL-1RI was overexpressed in olive flounder embryonic cell line (FEC), pro-inflammatory cytokines (IL -1β, IL -6, IL -8, TNF-α) and interferon (IFN-α, IFN-γ) were significantly upregulated. And we found that after overexpressing PoIL-1RI in FEC, the antibacterial ability of FEC was significantly stronger than that of the control group, and we found that overexpression of PoIL-1RI gene significantly increased the activity of NF-κB signaling pathway. These results suggest that PoIL-1RI plays an important role in innate immune response.

Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream (Sparus aurata) Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization

New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However, some drawback effects on feed conversion and inflammatory systemic markers were reported in different degrees with PAP- and non-PAP-based feed formulations. Here, we focused on the effects of control and two experimental diets on gut mucosal-adherent microbiota, and how it correlated with host transcriptomics at the local (intestine) and systemic (liver and head kidney) levels. The use of tissue-specific PCR-arrays of 93 genes in total rendered 13, 12, and 9 differentially expressed (DE) genes in the intestine, liver, and head kidney, respectively. Illumina sequencing of gut microbiota yielded a mean of 125,350 reads per sample, assigned to 1,281 operational taxonomic unit (OTUs). Bacterial richness and alpha diversity were lower in fish fed with the PAP diet, and discriminant analysis displayed 135 OTUs driving the separation between groups with 43 taxa correlating with 27 DE genes. The highest expression of intestinal pcna and alpi was achieved in PAP fish with intermediate values in non-PAP, being the pro-inflammatory action of alpi associated with the presence of Psychrobacter piscatorii. The intestinal muc13 gene was down-regulated in non-PAP fish, with this gene being negatively correlated with anaerobic (Chloroflexi and Anoxybacillus) and metal-reducing (Pelosinus and Psychrosinus) bacteria. Other inflammatory markers (igm, il8, tnfα) were up-regulated in PAP fish, positively correlating the intestinal igm gene with the inflammasome activator Escherichia/Shigella, whereas the systemic expression of il8 and tnfα was negatively correlated with the Bacilli class in PAP fish and positively correlated with Paracoccus yeei in non-PAP fish. Overall changes in the expression pattern of il10, galectins (lgals1, lgals8), and toll-like receptors (tlr2, tlr5, tlr9) reinforced the anti-inflammatory profile of fish fed with the non-PAP diet, with these gene markers being associated with a wide range of OTUs. A gut microbiota-liver axis was also established, linking the microbial generation of short chain fatty acids with the fueling of scd1- and elovl6-mediated lipogenesis. In summary, by correlating the microbiome with host gene expression, we offer new insights in the evaluation of fish diets promoting gut and metabolism homeostasis, and ultimately, the health of farmed fish.

Disruption of Intestinal Homeostasis Through Altered Responses of the Microbial Community, Energy Metabolites, and Immune System in Zebrafish After Chronic Exposure to DEHP

Di-(2-ethylhexyl) phthalate (DEHP) is ubiquitously reported in global water bodies and exhibits various environmental and human health risks. However, the effects of DEHP chronic exposure on the intestinal microbiota and associated host health concerns in aquatic species are still largely unexplored. In this study, chronic exposure to DEHP at environmental levels significantly increased the body weight, length, and body mass index (BMI), especially in male fish. The microbial community was disrupted with the relative abundance of phylum Firmicutes and genera diversity for Prevotella-7, Deefgea, PeM15, Halomonas, Akkermansia, Chitinibacter, and Roseomonas, which are significantly activated in zebrafish after exposure to DEHP. The height of the gut villus, the thickness of muscularis layer, and the number of goblet cells per villus were significantly decreased, as well as showed differences between female and male zebrafish. Further, the levels of energy-related metabolites in gut tissues were increased, compared to the control group. The expression levels of immune-related genes (interleukin 8, il-8, also referred to as cxcl8a), microbial defense-related genes (lysozyme, lyz, interleukin 10, and il-10), and obesity-related genes (aquaporin 8a, aqp8, mucin 2.1, muc2.1, fibroblast growth factor 2, fgf2, and proopiomelanocortin a, pomca) were significantly up-regulated in zebrafish, except the down-regulated expressions of toll-like receptor-5 (tlr-5) and interleukin 1β (il-1β) in the females and pomca in the males, respectively. Importantly, Spearman's correlation analyses revealed that the levels of metabolites and gene expressions in the gut were closely related to the dominant microbial genera, such as Aeromonas, Deefgea, Akkermansia, PeM15, Mycobacterium, and Rhodobacter. Taken together, chronic exposure to DEHP at environmental levels disturbed bacterial composition accompanied by the altered expressions of intestinal metabolites and the critical immune and intestinal function-related genes, which provided novel insights into DEHP effects on perturbation of gut microbiota and metabolic homeostasis in zebrafish.

Maternal and environmental microbes dominate offspring microbial colonization in the giant freshwater prawn Macrobrachium rosenbergii

Microbial colonization is vital for physiological equilibrium in animals. However, the impact of maternal and environmental microbes on microbial succession in the early developmental stages of Macrobrachium rosenbergii remains elusive. In this study, the effects of maternal and environmental microbes on the embryonic and larval microbiota of M. rosenbergii were evaluated by high-throughput sequencing. The results showed that Proteobacteria and Firmicutes were the dominant phyla in the intestine, gonads, and hepatopancreases of maternal prawn. In addition, Actinobacteria was dominant in the intestine while Actinobacteria, Bacteroidetes, and Acidobacteria were dominant in gonads of maternal prawn. During the embryonic stages, Proteobacteria, Actinobacteria, and Bacteroidetes became the dominant phyla. In post-larval stages, Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes tended to dominate. In the water, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla at 7, 14, and 21 dph water. Maternal microbes prominently impacted the microbial composition during the embryonic stages. Specifically, microbial colonization during embryonic stages was directly related to the maternal hepatopancreas according to source-tracking models. When the post-larvae developed to 7 days, the high contribution to the larval microbiota mimicked the environment. These results indicated that microbial colonization in embryonic and post-larval stages was attributed to the maternal and environmental microbe community, respectively. This study provides a theoretical basis for microbial community manipulation to promote prawn growth and physiological health in aquaculture.