The sub-therapeutic use of antibiotic use in aquaculture disrupts host-microbiota balance and poses ecological risks, though its chronic effects on benthic species remain poorly understood. Here we demonstrate that exposing Chinese longsnout catfish (L. longirostris) to florfenicol at a standard aquaculture dose of 10 mg/kg per day for five days induced severe intestinal dysbiosis and functional impairment. We observed a significant 43.65 % reduction in microbial gene abundance and a 96.16 % decrease in host mRNA expression, accompanied by a marked 69.11 % increase in host DNA contamination, indicating the collapse of the mucosal barrier and loss of microbial ecological function. The core microbiota shifted from beneficial Cetobacterium, which produces antioxidant and neuroprotective metabolites, to opportunistic genera such as Clostridium and Acinetobacter. Metabolically, florfenicol exposure resulted in a significant 29.3 % suppression of functional pathways and a pronounced 5.8-fold upregulation of electron transport genes including petB and fprB, which is associated with the activation of chronic diseases pathways such as Parkinson's, Huntington's and Diabetic cardiomyopathy. These pathways all share common mechanisms with mitochondrial dysfunction and ROS metabolism and further trigger chronic pathological changes including intestinal mucosal injury, mitochondrial oxidative stress and cell apoptosis. Additionally, the loss of Cetobacterium impaired the synthesis of key metabolites such as ascorbic acid and lovastatin acid, exacerbating intestinal structural damage and apoptosis. The transfer risk of antibiotic resistance genes was also significantly elevated. These findings reveal persistent microbiome dysfunction and heightened chronic disease risks following conventional antibiotic exposure, underscoring the urgency of reevaluating antibiotic usage in sustainable aquaculture.

Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the ‘low–temperature–pathogen’ model and shifts focus to mucosal barrier dysfunction and host–microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host–microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.

Percocypris pingi was listed in the China Vertebrate Red List in 2015, and albino P. pingi exhibits remarkable ocular phenotypes due to melanin synthesis defects, including the deficiency of melanin granules in the iris and retinal pigment epithelium (RPE). However, the regulatory mechanism of pigment loss in the eyes of albino P. pingi has not yet been clarified. This study systematically revealed the potential mechanisms underlying the obstruction of ocular melanin synthesis in albino P. pingi through histopathological analysis, transcriptomics, and proteomics techniques. The results showed that the synergistic effects of abnormal H⁺ transport mediated by SLC45A2, excessive activation of retinol metabolism, and cytoskeletal transport disorders led to the inhibition of tyrosinase activity and retention of pigment granules, ultimately causing melanin deficiency in the eyes. This study first elucidates the molecular network of ocular albinism in fish from a multi-omics perspective, providing a new perspective for the mechanistic research of pigmentation disorders in vertebrates.

Venomous spines are widespread defensive structures in fishes, yet the anatomical organization, molecular composition, and cellular basis of venom systems in many catfishes remain poorly characterized. Here, we combined morphology, proteomics, FISH, scRNA-seq, sequence comparison, and in vivo puncture to study L. longirostris spines. Histology revealed a spine architecture with longitudinal grooves, epidermal glands, a basement layer, and internal canals. DIA-MS identified a spine-enriched toxin repertoire in which CTα-L accounted for 95.34% of toxin abundance and was among the top proteins. Based on its sequence characteristics and close relationship to CTα-L homologs from bagrid catfishes, we designated this protein Bagridae toxin-1 (BGT-1). Spatial and single-cell analyses localized CTα-L-family transcripts to glandular and basement-layer compartments, with enrichment in several specialized cellular populations, including proliferating endothelial cells, immature epithelial progenitor cells, and junctional vascular smooth muscle cells. Sequence and structural comparisons revealed that BGT-1 retains conserved features of fish cytolytic toxins while exhibiting a distinctive multidomain architecture containing SNTX-like, Stonustoxin-associated, thioredoxin-like, FNIII, and tandem galectin domains. Structural modeling further identified a predicted pore-compatible architecture within the conserved toxin-associated core and provided a basis for a putative working model of BGT-1-mediated cytolysis. Finally, puncture with active spines caused rapid hemorrhage, edema, myofiber injury, inflammatory infiltration, and increased TUNEL-positive cells in vivo, whereas heat-inactivated spines produced substantially milder tissue damage. Together, these findings link specialized anatomy, a predominant toxin-associated protein, its cellular localization, molecular architecture, and in vivo activity in this venom system, providing a framework for comparative venom studies across catfishes.

Water quality deterioration during the late culture phase remains a key limiting factor for intensive Litopenaeus vannamei farming. This study compared traditional open earthen ponds and recirculating aquaculture systems (RAS) to investigate differences in physiological health, tissue structure, and muscle quality of cultured shrimp between the two culture modes. Using coefficient of variation (CV) as a quantitative metric, we observed that water quality parameters in the RAS group exhibited smaller fluctuation amplitudes, with nitrogenous metabolite concentrations and TCBS-culturable Vibrio-like bacteria loads notably lower than those in open earthen ponds. Shrimp reared in RAS achieved better overall growth performance. In contrast, shrimp in the pond system showed systemic ammonia accumulation across multiple tissues, accompanied by gill lamellar blockage, respiratory epithelial shedding, and disrupted mitochondrial cristae in the hepatopancreas. Histochemical assays further revealed marked glycogen depletion in the hepatopancreas of pond-reared shrimp, along with a “low-protein, high-moisture” muscle profile characterized by porous myofibrillar architecture. Although oxidative stress markers were elevated in the Pond group, plasma lysozyme activity was significantly suppressed. These findings suggest that the superior growth performance and muscle quality observed in the RAS system may be partly associated with lower homeostatic and stress repair costs, which arise from overall differences in rearing conditions between the two culture modes. The present study provides supporting histological and physiological evidence for optimizing shrimp culture strategies and upgrading production models.