The greenfin horse-faced filefish (Thamnaconus septentrionalis) is susceptible to recurrent Amyloodinium ocellatum (AO) infestation over the grow-out production cycle. This parasite breeds mainly on the gills, causing hypoxia in the fish body, and leading to many deaths. The host-parasite response drives a complex immune reaction, which is poorly understood. To generate a model for host-parasite interaction and the pathogenesis of AO in greenfin horse-faced filefish, an RNA-seq approach, differential gene expression, GO, and KEGG analyses were employed. Overall, 624 new genes and 2076 differentially expressed genes (DEGs) were detected, including 942 upregulated and 1134 downregulated genes in the gills. Compared with the control group, the expression of leptin a, GTPase IMAP family member 4, and NLR family CARD domain-containing protein 3 was significantly higher in the AO-infected group. Conversely, cell wall integrity and stress response component 1-like, and hepcidin-like were significantly downregulated in the gills of AO-infected fish. GO and KEGG enrichment analysis indicated that DEGs were significantly enriched in signaling pathways associated with viral protein interaction with cytokine and cytokine receptor and cytokine–cytokine receptor interaction. Collectively, this transcriptomic study provides novel molecular insights into the pathology caused by AO infestation and alternative theories for future research implementing strategies to control and manage AO.

This study evaluated the endpoint biochemical responses and associated physiological status of rainbow trout (Oncorhynchus mykiss) of different body sizes during salinity acclimation under varying temperature and salinity conditions. An L₉ (3⁴) orthogonal design was applied using three nominal body-size levels (100, 250, and 500 g), three temperatures (10, 15, and 20 °C), and three salinities (10, 20, and 30‰) over 60 days. Hepatic superoxide dismutase (SOD), alkaline phosphatase (ALP), and acid phosphatase (ACP) activities and plasma malondialdehyde (MDA), urea nitrogen (BUN), ammonia, alanine aminotransferase (ALT), and aspartate aminotransferase (AST) were measured. For inferential analysis, the three fish sampled from each tank were averaged to obtain one tank-level value, yielding 18 tank-level observations. Tank-level main-effects analysis showed that body size was significantly associated with ALP, ACP, MDA, BUN, ammonia, ALT, and AST. Temperature was significantly associated with SOD, ACP, MDA, BUN, and AST, whereas salinity was significantly associated with MDA, ALT, and AST. MDA and AST were the only endpoints associated with all three factors. The biochemical responses were pathway-specific rather than uniformly directional across treatment combinations. Because interactions could not be independently estimated in the L₉ design, the identified main effects should be interpreted as orthogonal screening associations. Overall, body-size class was associated with the broadest range of endpoints and should be incorporated into future experimental assessments of rainbow trout within the tested salinity range of 10–30‰.

Using a three-factor orthogonal design, we investigated the transcriptomic and histological responses of triploid rainbow trout (Oncorhynchus mykiss) gills across three salinities (10, 20, and 30 ppt) over 60 days, with temperature and body size as background conditions. Results showed that 20 ppt was associated with extensive transcriptional reprogramming, with 3333 differentially expressed transcripts (DETs), whereas 30 ppt induced only 120 DETs; WGCNA further identified salinity-correlated modules involved in ion transport and ribosome biogenesis. Histological alterations remained within physiological ranges with no salinity-dependent severity gradient, as confirmed by semi-quantitative scoring. These findings demonstrate that triploid rainbow trout gills employ distinct molecular strategies at medium versus high salinity. Within the 10–30 ppt range examined, 20 ppt was the salinity at which transcriptional reprogramming was most active, suggesting that this intermediate salinity warrants further investigation as a potential acclimation stage.

The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based on available salmonid studies and relevant evidence from broader fish and aquaculture systems, this review synthesizes current knowledge on salmonid gut microbial composition, nutritional modulation, microbiome–mucosal immune interactions, aquaculture stressors, antibiotic exposure, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metagenomics, multi-omics, and emerging microbiome-informed decision-support tools. Current evidence does not support a universally stable single-core microbiota in these species. Instead, community structure is shaped by developmental stage, freshwater–seawater transition, intestinal segment, digesta versus mucosa sampling, diet, temperature, stress, health status, and methodological workflow. Feed substitution and functional additives can remodel the gut microbiota, but these shifts should be interpreted alongside histology, barrier function, metabolic profiles, immune indicators, and disease-resistance phenotypes. Antibiotic exposure may reduce acute bacterial disease pressure while disturbing community structure and potentially enriching ARGs or ARG–MGE associations. Risk assessment should therefore move beyond ARG abundance toward host–ARG–MGE linkage using shotgun metagenomics, metagenome-assembled genomes, long-read sequencing, Hi-C, and externally validated multi-omics models. Machine learning and artificial intelligence approaches may support feature screening, risk stratification, and decision support, but their application in salmonid gut-health management remains at an early stage and requires external validation across sites, production stages, diets, and seasons.

Rainbow trout (Oncorhynchus mykiss) is a globally cultured cold-water salmonid, yet triploid larvae often develop spinal ventral lordosis and conjoined twin malformations with unclear molecular mechanisms. Here, RNA-seq of 15 dph normal (N), spinal-deformed (SD) and conjoined (CT) triploid larvae yielded 54.13 Gb of valid data, identifying 4292, 3601 and 2699 DEGs for SD vs. N, CT vs. SD and CT vs. N groups, respectively. Five shared disrupted cascades (cell adhesion, neuroactive ligand-receptor interaction, phagosome, cytokine-receptor interaction, and PI3K-Akt signaling) were identified, while potential calcium/MAPK and steroid-biosynthesis-related pathways were predominantly perturbed in SD and CT larvae, respectively. Filtered PPI sub-networks displayed distinct predicted topological phenotype-associated candidate transcripts, with coagulation and complement transcripts forming core hubs in SD larvae and steroid-related transcripts showing weak connectivity in CT groups. Three discriminative transcripts with inverse expression patterns were screened. This study reveals conserved and phenotype-specific transcriptional phenotype-associated candidate transcripts of the two malformations and provides candidate phenotype-associated transcripts for subsequent functional verification of larval malformations. It should be noted that all transcriptomic data originate from whole-larval homogenates; expression signatures of conjoined-twin larvae may be confounded by altered tissue-type proportions rather than malformation-exclusive regulatory mechanisms.