Integrated mRNA and miRNA analysis reveals the regulatory network of oxidative stress and inflammation in Coilia nasus brains during air exposure and salinity mitigation.

BACKGROUND: Air exposure is an inevitable source of stress that leads to significant mortality in Coilia nasus. Our previous research demonstrated that adding 10‰ NaCl to aquatic water could enhance survival rates, albeit the molecular mechanisms involved in air exposure and salinity mitigation remained unclear. Conversely, salinity mitigation resulted in decreased plasma glucose levels and improved antioxidative activity. To shed light on this phenomenon, we characterized the transcriptomic changes in the C. nasus brain upon air exposure and salinity mitigation by integrated miRNA-mRNA analysis. RESULTS: The plasma glucose level was elevated during air exposure, whereas it decreased during salinity mitigation. Antioxidant activity was suppressed during air exposure, but was enhanced during salinity mitigation. A total of 629 differentially expressed miRNAs (DEMs) and 791 differentially expressed genes (DEGs) were detected during air exposure, while 429 DEMs and 1016 DEGs were identified during salinity mitigation. GO analysis revealed that the target genes of DEMs and DEGs were enriched in biological process and cellular component during air exposure and salinity mitigation. KEGG analysis revealed that the target genes of DEMs and DEGs were enriched in metabolism. Integrated analysis showed that 24 and 36 predicted miRNA-mRNA regulatory pairs participating in regulating glucose metabolism, Ca2+ transport, inflammation, and oxidative stress. Interestingly, most of these miRNAs were novel miRNAs. CONCLUSION: In this study, substantial miRNA-mRNA regulation pairs were predicted via integrated analysis of small RNA sequencing and RNA-Seq. Based on predicted miRNA-mRNA regulation and potential function of DEGs, miRNA-mRNA regulatory network involved in glucose metabolism and Ca2+ transport, inflammation, and oxidative stress in C. nasus brain during air exposure and salinity mitigation. They regulated the increased/decreased plasma glucose and inhibited/promoted antioxidant activity during air exposure and salinity mitigation. Our findings would propose novel insights to the mechanisms underlying fish responses to air exposure and salinity mitigation.

Integrative analysis of metagenome and metabolome provides new insights into intestinal health protection in Coilia nasus larvae via probiotic intervention.

With the development of large-scale intensive feeding, growth performance and animal welfare have attracted more and more attention. Exogenous probiotics can promote the growth performance of fish through improving intestinal microbiota; however, it remains unclear whether intestinal microbiota influence physiological biomarkers. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of a 90-day Lactiplantibacillus plantarum supplementation to a basal diet (1.0 × 108 CFU/g) on the growth performance, intestinal microbiota and their metabolites, and physiological biomarkers in Coilia nasus larvae. The results showed that the probiotic supplementation could significantly increase weight and body length. Moreover, it could also enhance digestive enzymes and tight junctions, and inhibit oxidative stress and inflammation. The metagenomic analysis showed that L. plantarum supplementation could significantly decrease the relative abundance of Proteobacteria and increase the relative abundance of Firmicutes. Additionally, pathogenic bacteria (Aeromonadaceae, Aeromonas, and Enterobacterales) were inhibited and beneficial bacteria (Bacillales) were promoted. The metabolome analysis showed that acetic acid and propanoic acid were significantly elevated, and were associated with Kitasatospora, Seonamhaeicola, and Thauera. A correlation analysis demonstrated that the digestive enzymes, tight junction, oxidative stress, and inflammation effects were significantly associated with the increased acetic acid and propanoic acid levels. These results indicated that L. plantarum supplementation could improve intestinal microbial community structure and function, which could raise acetic acid and propanoic acid levels to protect intestinal health and improve growth performance in C. nasus larvae.

Metagenomic Insight into the Effect of Probiotics on Nitrogen Cycle in the Coilia nasus Aquaculture Pond Water.

Recently, probiotics have been widely applied for the in situ remediation of aquatic water. Numerous studies have proved that probiotics can regulate water quality by improving the microbial community. Nitrogen cycling, induced by microorganisms, is a crucial process for maintaining the balance of the aquatic ecosystem. Nevertheless, the underlying mechanisms by which probiotics enhance water quality in aquatic systems remain poorly understood. To explore the water quality indicators and their correlation with nitrogen cycling-related functional genes, metagenomic analysis of element cycling was performed to identify nitrogen cycling-related functional genes in Coilia nasus aquatic water between the control group (C) and the groups supplemented with probiotics in feed (PF) or water (PW). The results showed that adding probiotics to the aquatic water could reduce the concentrations of ammonia nitrogen (NH4+-N), nitrite (NO2--N), and total nitrogen (TN) in the water. Community structure analysis revealed that the relative abundance of Verrucomicrobiota was increased from 30 d to 120 d (2.61% to 6.35%) in the PW group, while the relative abundance of Cyanobacteria was decreased from 30 d to 120 d (5.66% to 1.77%). We constructed a nitrogen cycling pathway diagram for C. nasus aquaculture ponds. The nitrogen cycle functional analysis showed that adding probiotics to the water could increase the relative abundance of the amoC_B and hao (Nitrification pathways) and the nirS and nosZ (Denitrification pathways). Correlation analysis revealed that NH4+-N was significantly negatively correlated with Limnohabitans, Sediminibacterium, and Algoriphagus, while NO2--N was significantly negatively correlated with Roseomonas and Rubrivivax. Our study demonstrated that adding probiotics to the water can promote nitrogen element conversion and migration, facilitate nitrogen cycling, benefit ecological environment protection, and remove nitrogen-containing compounds in aquaculture systems by altering the relative abundance of nitrogen cycling-related functional genes and microorganisms.

The Effect of Infertility on the Liver Structure, Endocrinology, and Gene Network in Japanese Flounder.

The liver can synthesize vitellogenin, the precursor of vitellin, which is needed for oocyte development and maturation. Here, we investigated the effects of infertility on liver structure, hormone regulation, and gene and protein networks in Japanese flounder (Paralichthys olivaceus). Results showed that the liver of infertile fish had fewer vacuoles and significantly lower serum vitellogenin (VTG) level than in liver of fertile fish. Whole transcriptomics analysis between infertile and fertile groups identified 2076 significantly differentially expressed (DE) mRNAs, 431 DE lncRNAs, 265 DE circRNAs, and 53 DE miRNAs. Proteomics analysis identified 838 DE proteins. Integrated analysis of whole transcriptomics and proteomics revealed 60 significantly DE genes and proteins associated with metabolism, immunity, signal transduction, and steroid biosynthesis. Moreover, non-coding RNA (miRNAs, circRNA, and lncRNA) transcripts involved in metabolism, immunity, and signal transduction in infertile liver were identified. In conclusion, this study shows that gonadal infertility is associated with not only changes in histological structure and hormone secretion but also changes in metabolism, immunity, and signal transduction networks in the liver. These results provide valuable information concerning the mechanism underlying infertility in fish.