Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

{"title":"Proteomic analysis reveals the mechanism of cold tolerance in black porgy (Acanthopagrus schlegelii) via ribosome hibernation, metabolic remodeling, and antioxidant coordination","authors":"Jingyang Li ,&nbsp;Ruijian Sun ,&nbsp;Tongxuan Zhao ,&nbsp;Xiaojian Tang ,&nbsp;Bo Gao ,&nbsp;Guangping Xu ,&nbsp;Yue Wang ,&nbsp;Han Yu ,&nbsp;Qian Meng ,&nbsp;Zhiwei Zhang","doi":"10.1016/j.cbd.2026.101748","DOIUrl":"10.1016/j.cbd.2026.101748","url":null,"abstract":"<div><div>Low-temperature stress poses a critical challenge to the overwintering survival of black porgy (<em>Acanthopagrus schlegelii</em>), a commercially important marine fish distributed across the coastal waters of West Pacific region, including the continental shelves of China, Japan, and the Korean Peninsula. To unravel the molecular mechanisms underlying cold adaptation, this study employed quantitative proteomics was employed to analyze hepatic protein profiles of black porgy between three groups: control group (CG, 15 °C), cold-sensitive group (CS, 3.8 °C), and cold-tolerant group (CT, 2.8 °C). A total of 4437 proteins were identified, with 1616 differentially expressed protein (DEPs) detected among the groups. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and trend analysis, revealed distinct adaptive strategies between CT and CS groups. The CT group exhibited a coordinated “energy conservation - metabolic remodeling - antioxidation” strategy: (1) significant downregulation of ribosomal subunits and protein export pathways to reduce Adenosine Triphosphate (ATP) consumption from protein synthesis (called “ribosomal hibernation”); (2) upregulation of Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathway and peroxisomal functions to enhance fatty acid β-oxidation and ketone body production, facilitating efficient energy supply; (3) activation of antioxidant systems to mitigate damage induced by reactive oxygen species (ROS). In contrast, the CS group showed dysregulated energy metabolism, characterized by enhanced but inefficient glycolysis, impaired endoplasmic reticulum function, and excessive inflammatory responses, which may contribute to protential proteotoxic stress and metabolic dysfunction. Key DEPs and pathways, such as ribosomal proteins, PPAR family proteins, and peroxisomal enzymes, were identified as protential core regulators of cold tolerance in black porgy. This study provides the first comprehensive proteomic insights into the molecular mechanisms of cold tolerance in black porgy, highlighting the evolutionary significance of energy allocation and metabolic plasticity in teleosts. These findings offer potential molecular markers for breeding cold-tolerant strains, addressing critical challenges in aquaculture sustainability.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101748"},"PeriodicalIF":2.2,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive transcriptomic analysis reveals detoxification gene expansion and adaptive genetic variation in the emerging pest Acanthotomicus suncei","authors":"Lulu Dai,&nbsp;Jiao Li,&nbsp;Weiyi Pan,&nbsp;Fangyuan Shen,&nbsp;Dejun Hao","doi":"10.1016/j.cbd.2026.101749","DOIUrl":"10.1016/j.cbd.2026.101749","url":null,"abstract":"<div><div>The bark beetle <em>Acanthotomicus suncei</em> is an emerging destructive pest of the introduced American sweetgum (<em>Liquidambar styraciflua</em>) in China. The molecular mechanisms underlying its successful adaptation to this exotic host, particularly its ability to overcome plant chemical defenses, remain largely unknown. We conducted a comprehensive transcriptomic analysis of <em>A. suncei</em>. Our assembly yielded 30,557 unigenes (N50 = 2175 bp). We identified a significant expansion of genes within three major detoxification enzyme families: 122 cytochrome P450 monooxygenases (P450s), 75 carboxylesterases (COEs), and 47 glutathione S-transferases (GSTs). This repertoire is notably larger than that of many compared curculionid beetles. Phylogenetic analyses revealed complex evolutionary relationships, with <em>A. suncei</em> clustering closely with <em>Dendroctonus</em> species in some P450 and GST clades, while showing considerable divergence in others. Furthermore, we uncovered abundant genetic variation, with single nucleotide polymorphisms (SNPs) being highly prevalent within the coding sequences of these detoxification genes, especially P450s. Simple sequence repeat (SSR) analysis indicated a predominance of A/T-rich motifs. The remarkable expansion and substantial genetic variation observed in the detoxification gene families of <em>A. suncei</em> provide a compelling molecular basis for its potent detoxification capacity. These findings suggest that an enriched and highly adaptable detoxification system likely facilitates this beetle's successful colonization of the exotic host L. <em>styraciflua</em>. This study offers crucial insights into the molecular mechanisms of host adaptation in an emerging forest pest and identifies potential genetic targets for future management strategies.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101749"},"PeriodicalIF":2.2,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics dissection of large-size formation in Eriocheir sinensis: Insights from RNA, metabolite profiling, and ceRNA regulatory networks","authors":"Fujun Xuan ,&nbsp;Xinyue Zhang ,&nbsp;Jinghao Hu ,&nbsp;Xuguang Li ,&nbsp;Yuchen Chen ,&nbsp;Aiming Zhang ,&nbsp;Ruifang Wang ,&nbsp;Qian Ren ,&nbsp;Tao Wu ,&nbsp;Weibing Guan ,&nbsp;Yongxu Cheng ,&nbsp;Jun Zhou ,&nbsp;Rongchen Liu","doi":"10.1016/j.cbd.2026.101750","DOIUrl":"10.1016/j.cbd.2026.101750","url":null,"abstract":"<div><div><em>Eriocheir sinensis</em> (Chinese mitten crab) is a key economic species in China's freshwater aquaculture industry. Individual body size is a critical trait that determines both market price and production profitability. Large-sized crabs exhibit substantial commercial advantages; however, the underlying molecular mechanisms regulating size formation remain poorly understood. In this study, we conducted an integrative multi-omics analysis combining whole-transcriptome data (mRNA, miRNA, and lncRNA) and untargeted metabolomics across two aquaculture cohorts (cohort2023 and cohort2024). Our results revealed a systemic downregulation of glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid oxidation, and glycerol metabolism in large-sized crabs, suggesting a “low consumption–high storage” metabolic strategy. In contrast, pathways related to organismal development, exoskeleton reconstruction, steroid hormone biosynthesis, and nutrient absorption were significantly upregulated, indicating enhanced growth potential and nutrient assimilation efficiency. ceRNA network modeling and cis-acting lncRNA analysis identified multiple core regulatory genes (e.g., <em>PTGS1</em>, <em>TPI1</em>, <em>POR</em>) as targets of complex non-coding RNA interactions involved in body size regulation. Enzyme activity assays for key rate-limiting steps in carbohydrate and lipid catabolism, along with extensive qPCR validation, further corroborated the transcriptomic findings. Taken together, our study provides the first comprehensive multi-omics perspective on the molecular basis of body size differentiation in <em>E. sinensis</em>, proposing a tripartite mechanism involving suppressed catabolism, stimulated growth and morphogenesis, and improved nutrient acquisition. These findings offer theoretical insight into crustacean growth regulation and provide molecular targets to support selective breeding of high-value, large-sized mitten crab strains.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101750"},"PeriodicalIF":2.2,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative transcriptome analysis reveals molecular mechanism of temperature effect on body color of red swamp crayfish (Procambarus clarkii)","authors":"Guoliang Chang ,&nbsp;Fanqian Kong ,&nbsp;Songyue Gao ,&nbsp;Huajie Cai ,&nbsp;Long Wang ,&nbsp;Huaiyu Ding ,&nbsp;Yongxu Cheng ,&nbsp;Jiayao Li","doi":"10.1016/j.cbd.2026.101751","DOIUrl":"10.1016/j.cbd.2026.101751","url":null,"abstract":"<div><div>The carapace coloration is of great significance to <em>Procambarus clarkii</em>, and the molecular mechanism of temperature affecting carapace color has not yet been reported. In this study, comparative transcriptome was used to study molecular mechanism of temperature-induced changes in carapace coloration of <em>P. clarkii</em>. This study identified many genes (such as <em>tyrosinase</em>, <em>APOD</em>) and signaling pathways (such as tyrosine metabolism) related to pigment accumulation. As an important environmental factor, temperature can change metabolism and accumulation of pigment in <em>P. clarkii</em> by changing expression patterns of related genes and pathways. High temperature can damage transport of related proteins (such as ABC transporters), thus affecting the metabolism of carotenoids and melanin, and finally lead to the change of body color of <em>P. clarkii</em>. Oxidative stress caused by high temperature can destroy pigment metabolism and accumulation, resulting in changes in body color. The results of this study revealed molecular mechanism of temperature affecting body color of <em>P. clarkii</em>, provided basic data for subsequent selective breeding and practical production, and provided new insights for crustacean body color formation and change.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101751"},"PeriodicalIF":2.2,"publicationDate":"2026-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative transcriptomic analysis across ovarian developmental stages in Sepiella japonica provides novel insights into its molecular regulatory mechanisms","authors":"An Xu ,&nbsp;Zhenming Lü ,&nbsp;Jing Liu ,&nbsp;Tianwei Liu ,&nbsp;Jing Yu ,&nbsp;Yijing Yang ,&nbsp;Kun Huang ,&nbsp;Li Gong ,&nbsp;Fenghui Li ,&nbsp;Denghui Zhu ,&nbsp;Hongling Ping ,&nbsp;Huilai Shi ,&nbsp;Liqin Liu","doi":"10.1016/j.cbd.2026.101746","DOIUrl":"10.1016/j.cbd.2026.101746","url":null,"abstract":"<div><div><em>Sepiella japonica</em> is a cephalopod of significant commercial value, commonly found throughout China's coastal waters, ranging from southern Hong Kong to the Korean Peninsula and western regions of Japan. However, under captive conditions, <em>S. japonica</em> frequently exhibits precocious sexual maturation, which can result in reduced adult body size and severely limit aquaculture development. Therefore, elucidating the molecular mechanisms on ovarian development has become a critical priority. In this study, RNA sequencing was performing of the ovary tissue of female <em>S. japonica</em> collected across four key ovarian developmental stages: oogonium production (stage I), protoplasmic growth (stage II), interstitial growth (stage III), and trophoplasmic growth (stage IV). A total of 354,393,214 clean reads (Q20&gt;98.58%) were obtained from 16 samples. Pairwise comparative analyses of I vs II, II vs III, and III vs IV identified 10050, 2564, 2278 differentially expressed genes (DEGs), respectively. Through differential expression analysis, we identified 13,319 differentially expressed genes (DEGs), among of which exhibited consistently high expression across four developmental stages, such as <em>FOXL2</em>, <em>HSD17B2</em>, and <em>BMP1</em>, suggesting their critical roles in regulating ovarian development in <em>S. japonica</em>. Gene Ontology (GO) enrichment analysis showed that these DEGs were significantly enriched in processes including protein targeting to the ER, response to estradiol, oxidative phosphorylation, and female pregnancy. KEGG pathway analysis revealed that DEGs were significantly enriched in key functional pathways, such as Ribosome, Prolactin signaling, FOXO signaling, and Lysosome. Furthermore, the “response to estradiol” pathway was consistently enriched across multiple developmental stage comparisons, suggesting that genes associated with steroid-related signaling may play conserved roles during ovarian development in <em>S. japonica</em>. This study clarified the regulation of transcript expression and molecular mechanisms in the ovary of <em>S. japonica</em> at different ovarian development stages, thereby offering theoretical guidance for enhancing reproductive efficiency in mollusk aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101746"},"PeriodicalIF":2.2,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis revealed the effects of dietary faba bean (Vicia faba L.) on muscle quality of Nile tilapia (Oreochromis niloticus)","authors":"Qingqing Li ,&nbsp;Yao Huang ,&nbsp;Xi Xie ,&nbsp;Shaowen Liang ,&nbsp;Li Lin","doi":"10.1016/j.cbd.2026.101747","DOIUrl":"10.1016/j.cbd.2026.101747","url":null,"abstract":"<div><div>Nile tilapia (<em>Oreochromis niloticus</em>) is a widely farmed freshwater fish. Feeding with faba bean (<em>Vicia faba</em> L.) for 90–120 days can improve the muscle quality of tilapia. However, the underlying mechanism remain unclear. In the present study, tilapia were fed a faba bean–based diet for 120 days to induce muscle crisped, and ordinary tilapia fed a conventional diet were used as controls. Muscle histological characteristics were evaluated using hematoxylin and eosin staining, and transcriptome sequencing was conducted to explore molecular changes associated with the crisped muscle phenotype. The results showed that, as compared to ordinary tilapia, the fiber diameter and area were significantly reduced in crisped tilapia (<em>p</em> &lt; 0.05), while the muscle fiber density was significantly increased (<em>p</em> &lt; 0.05). In total, 576 differentially expressed genes (DEGs) were identified (FDR &lt; 0.05), of which 211 were significantly up-regulated and 365 significantly down-regulated. Further analysis showed that DEGs associated with myofibroblast proliferation were up-regulated in crisped tilapia, while the glycolytic pathway was inhibited. The expression levels of muscle-related genes (i.e., actc1, myo7a, cib2, abcf2, and pfkfb2) were significantly higher in crisped tilapia than ordinary tilapia (<em>p</em> &lt; 0.05), whereas the expression levels of gapdh, pgam2, eno3, and g6pi were significantly decreased (<em>p</em> &lt; 0.05). Several DEGs and signaling pathways were identified. These findings provide transcriptomic evidence linking dietary faba bean feeding to muscle fiber remodeling and metabolic modulation in tilapia, offering a molecular basis for improving fillet quality through nutritional strategies.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101747"},"PeriodicalIF":2.2,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and characterization of HSP90, HSP60 and HSP40 family genes in Riptortus pedestris (Hemiptera: Alydidae)","authors":"Wenhao Dong ,&nbsp;Huaijun Xue ,&nbsp;Yipeng Ren","doi":"10.1016/j.cbd.2026.101745","DOIUrl":"10.1016/j.cbd.2026.101745","url":null,"abstract":"<div><div>To the best of our knowledge, heat shock proteins (HSPs) serve as molecular chaperones and play vital roles in providing protection under numerous physiological processes and environmental stressors, such as temperature, mechanical injury, chemical agents, and so on. Although their functional roles in hemipteran insects have been identified, comprehensive genome-wide identification and characterization of <em>HSP</em> family genes remain poorly understood in heteropteran pests, especially in <em>R. pedestris</em>, which has led to significant and widespread issues with soybean quality and yield through its sucking stylet, thus inducing a staygreen-like syndrome. In this study, four <em>HSP90</em>, fourteen <em>HSP60</em> and twenty-six <em>HSP40</em> family genes were obtained from the <em>R. pedestris</em> genome. Next, phylogenetic analysis, combined with conserved and domain characterization, supported our classification results. Chromosomal mapping indicated that all these <em>HSP</em> genes are distributed across the six chromosomes of <em>R. pedestris</em>, and a Ka/Ks ratio of &lt;1 provides essential information for purifying selection acting on two duplicated <em>Hsp90</em> genes in <em>R. pedestris</em>. Through data mining of transcriptome data, we obtained the expression patterns of three <em>HSP</em> family genes across all developmental stages and analyzed their expression differences during changes in feeding conditions in the whole body and gut of <em>R. pedestris</em>, respectively. Finally, a miRNA–mRNA interaction network of four significantly differentially expressed (DE) <em>HSPs</em> and corresponding regulatory miRNAs was constructed, of which one miRNA, novel-miRNA-927-3p, exhibited significant downregulation and combined with significantly DE <em>Hsp60a</em> and <em>DnaJA1</em> in one comparison group, suggesting their underlying relationships in response to antibiotic feeding in the <em>R. pedestris</em> gut. Overall, these findings provide valuable insights into how the three types of <em>HSP</em> genes in <em>R. pedestris</em> are involved in developmental and environmental adaptation at the transcriptional and posttranscriptional levels.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101745"},"PeriodicalIF":2.2,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular insights into hydrogen sulfide defense: A tissue-resolved transcriptomic study in the crab Eriocheir sinensis","authors":"Jian Tian ,&nbsp;Zihan Zhou ,&nbsp;Mingming Han ,&nbsp;Yi Juin Tay ,&nbsp;Mengyu Bao ,&nbsp;Longlong Fu ,&nbsp;Qichen Jiang","doi":"10.1016/j.cbd.2026.101743","DOIUrl":"10.1016/j.cbd.2026.101743","url":null,"abstract":"<div><div>The increasing prevalence of multiple abiotic stressors in aquatic ecosystems has raised significant ecological concerns. While molecular responses to hydrogen sulfide (H₂S) have been investigated in some aquatic species, the tissue-specific regulatory mechanisms in the Chinese mitten crab (<em>Eriocheir sinensis</em>) remain poorly understood. Following a 48-h exposure to varying concentrations of H₂S (0, 0.1, and 5 mg/L), four key tissues—hepatopancreas, gill, muscle, and intestine—were collected for an integrated analysis of transcriptomic sequencing and physiological/biochemical assays. Our results demonstrated significant enrichment of pathways related to serine endopeptidase activity and tyrosine metabolism in affected tissues, highlighting their potential role in mitigating H₂S-induced damage. Furthermore, high-concentration H₂S exposure substantially elevated the activities of antioxidant enzymes (SOD, CAT, GSH-PX) and up-regulated the expression of associated genes (<em>SOD1</em>, <em>GPX1</em>, <em>HO-1</em>), while simultaneously suppressing cytochrome <em>c</em> oxidase expression. These coordinated changes indicate that H₂S toxicity triggers pronounced oxidative stress alongside disrupted energy metabolism. The present study provides novel experimental insights into the molecular mechanisms of H₂S toxicity in crustaceans and offers a scientific foundation for ecological risk assessment and sustainable aquaculture management.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101743"},"PeriodicalIF":2.2,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated multi-omics analyses reveals physiological and gut microbiota responses of Litopenaeus vannamei to graded levels of dietary bile acids","authors":"Peng Tan ,&nbsp;Lei Zhang ,&nbsp;Jinzhi Zhang ,&nbsp;Aizhi Cao ,&nbsp;Dongdong Xu ,&nbsp;Aijun Zhu ,&nbsp;Zhili Ding ,&nbsp;Qingjun Shao","doi":"10.1016/j.cbd.2026.101744","DOIUrl":"10.1016/j.cbd.2026.101744","url":null,"abstract":"<div><div>Despite being sterol auxotrophs that lack de novo steroid synthesis pathways, the specific physiological roles of exogenous bile acids (BAs) in crustaceans remain to be fully elucidated. This study investigated the effects of dietary BAs on the antioxidant capacity, immune regulation, and intestinal microbiota of the Pacific white shrimp, <em>Litopenaeus vannamei</em>. Shrimp were fed diets supplemented with graded levels of BAs (0–1000 mg kg⁻¹) for 56 days. Integrated multi-omics analyses were employed, where the 200 mg kg⁻¹ physiological optimum was used for transcriptomic profiling to decipher signaling pathways, while the 1000 mg kg⁻¹ group was analyzed to assess high-dose tolerance and microbial composition changes. Results showed that dietary BAs significantly enhanced non-specific immune parameters, specifically hemolymph lysozyme activity and total antioxidant capacity, without inducing histological damage to the hepatopancreas or intestine even at the highest dosage. Transcriptomic analysis showed an upregulation of antioxidant-related genes, such as <em>sod1</em>, <em>gst</em> and <em>nos1</em>, suggesting that BAs enhance the host's transcriptional potential to cope with oxidative stress. Furthermore, dietary BAs modulated immune signaling by upregulating the NF-κB inhibitor gene <em>nfkbia</em> and downregulating the adaptor <em>myd88</em>, indicating a potential mechanism for maintaining immune homeostasis and suppressing pro-inflammatory responses. In the intestine, BAs significantly increased the Shannon diversity index by promoting community evenness rather than species richness, and reduced the relative abundance of the opportunistic pathogen <em>Vibrio</em> while enriching beneficial genera such as <em>Ruegeria</em>. These findings indicate that exogenous BAs exert a protective role in L. <em>vannamei</em> by priming antioxidant defenses, modulating inflammatory signaling pathways, and stabilizing the intestine microbial ecosystem. These results suggest that BAs can be used as effective feed additives to improve health and intestine stability in shrimp farming.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101744"},"PeriodicalIF":2.2,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145968045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolomic insights into fish osmoregulation: Unveiling adaptive mechanisms to salinity change","authors":"Xiaoli Chen ,&nbsp;Youdi Tang ,&nbsp;Xue Du ,&nbsp;Ivone Giffard-Mena ,&nbsp;Quanquan Cao","doi":"10.1016/j.cbd.2025.101742","DOIUrl":"10.1016/j.cbd.2025.101742","url":null,"abstract":"<div><div>Salinity fluctuation is a major environmental driver influencing fish physiology and aquaculture performance. Metabolomics offers a systems perspective on the small molecule networks underlying osmoregulation. This review synthesizes studies across fish species to identify conserved metabolic responses to salinity change, including shifts in energy metabolism, amino acid turnover, and organic osmolyte synthesis. We evaluate the strengths and limitations of current analytical platforms (NMR, LC–MS, GC–MS) in metabolite coverage and identification, and highlight emerging approaches such as spatial metabolomics, multi-omics integration, and machine learning. By linking metabolic patterns to physiological and aquacultural outcomes, this work clarifies the molecular basis of salinity adaptation and offers actionable guidance for improving salinity tolerance in aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101742"},"PeriodicalIF":2.2,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}