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Animals
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Application of Multi-Omics Analysis to Fish Nutrition, Health and Welfare
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Application of Multi-Omics Analysis to Fish Nutrition, Health and Welfare

A Special Issue of Animals (ISSN 2076-2615) belonging to the section "Aquatic Animals".

Deadline for manuscript submissions: 30 April 2027 | Viewed by 1737

Editor

Dr. Jin Xu

E-Mail Website
Guest Editor
Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
Interests: aquaculture animal diseases; etiology; pathogenic mechanism; antibiotic; vaccine; prevention; treatment
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aquaculture serves as a crucial pillar for global food security, yet the industry faces persistent challenges regarding feed optimization, disease outbreaks, and environmental stress. To address these complexities, researchers are increasingly transitioning from single-parameter studies to systems biology approaches. This Special Issue, titled “Application of Multi-Omics Analysis to Fish Nutrition, Health and Welfare”, aims to highlight the latest advances in the application of high-throughput technologies—including genomics, transcriptomics, proteomics, metabolomics, and microbiomics—to aquatic biology.

We invite submissions that utilize these integrated approaches to elucidate the molecular mechanisms underlying fish growth, reproductive physiology, nutrient metabolism, and adaptive responses to environmental stressors. The scope of this issue extends to assessing fish welfare through molecular biomarkers and understanding the complex interactions between the host, its diet, and the microbiome. By bridging the gap between large-scale molecular data and phenotypic traits, this collection aims to provide a robust theoretical basis for precision nutrition, stress management, and improved welfare standards in sustainable aquaculture. We welcome both original research articles and comprehensive reviews.

Dr. Jin Xu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • multi-omics
  • aquaculture
  • fish nutrition
  • environmental stress
  • reproduction
  • animal welfare
  • systems biology
  • gut microbiota

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Published Papers (3 papers)

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Research

20 pages, 7482 KB  
Article
Multi-Tissue Transcriptomics Analysis of the Effects of Ammonia Nitrogen Stress on Metabolism, Immunity, and Comprehensive Stress Responses in Megalobrama amblycephala
by Mingguo Lu, Yang Guo, Silei Xia, Jinjuan Wan, Kun Wu, Hui Cao, Wuxiao Zhang and Aimin Wang
Animals 2026, 16(14), 2139; https://doi.org/10.3390/ani16142139 - 9 Jul 2026
Viewed by 334
Abstract
In order to reveal the molecular response characteristics of different tissues of Megalobrama amblycephala under ammonia nitrogen stress, the liver, gill, muscle, kidney and brain tissues of juvenile Megalobrama amblycephala (12.05 ± 0.04 g) under 25 mg/L ammonium chloride stress were used as [...] Read more.
In order to reveal the molecular response characteristics of different tissues of Megalobrama amblycephala under ammonia nitrogen stress, the liver, gill, muscle, kidney and brain tissues of juvenile Megalobrama amblycephala (12.05 ± 0.04 g) under 25 mg/L ammonium chloride stress were used as the research objects. The transcriptome sequencing technology was used to systematically analyze the transcriptional expression changes. A total of 204.42 Gb transcription data were obtained, and a total of 3039 DEGs were detected, of which 1331 genes were up-regulated and 1708 genes were down-regulated. Ten DEGs were randomly selected for quantitative qRT-PCR analysis, and the results confirmed that the transcriptome results were reliable. Multi-organ synergy analysis suggested that overlapping DEGs (e.g., ZNF239, DMBT1, NLRC3, MHC-I, and CCL8) may exhibit similar or opposing regulatory patterns across organs, potentially reflecting complementary and coordinated mechanisms in immune regulation, inflammatory responses, energy allocation, and detoxification strategies among organ systems. GO and KEGG pathway enrichment analysis of differentially expressed genes showed that ammonia nitrogen mainly affected immune inflammation-related processes, material transport and degradation, protein homeostasis maintenance, oxidative stress defense, membrane lipid metabolism remodeling, and energy metabolism regulation. In different tissues, genes related to specific functions are enriched according to their physiological roles: in the liver, genes related to detoxification and damage clearance are enriched; in the gill, genes related to barrier defense and antioxidant/detoxification are enriched; in the kidney, genes related to damage response and metabolic regulation are enriched; in the brain, genes related to membrane lipid homeostasis and protective stress are enriched; and in the muscle, genes related to energy metabolism and structural function adjustment are enriched. This study elucidated the multi-tissue response characteristics of Megalobrama amblycephala under ammonia nitrogen stress at the transcriptome level, providing fundamental data and references for further clarifying the mechanisms of ammonia nitrogen toxicity in fish and screening stress-responsive marker genes. Full article
(This article belongs to the Special Issue Application of Multi-Omics Analysis to Fish Nutrition, Health and Welfare)
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24 pages, 5699 KB  
Article
Integrated Physiological and Transcriptomic Analyses Suggest Key Adaptive Mechanisms of European Perch (Perca fluviatilis) to Acute Heat Stress
by Geng Chen, Fangyuan Peng, Peng Chen and Jin Xu
Animals 2026, 16(13), 2007; https://doi.org/10.3390/ani16132007 - 1 Jul 2026
Viewed by 401
Abstract
The European perch (Perca fluviatilis) is highly susceptible to heat stress, limiting its sustainable aquaculture. While single-organ thermal responses are partially understood, the systemic, multi-organ cooperative survival mechanisms under acute heat stress remain poorly characterized. To elucidate the underlying tolerance mechanisms [...] Read more.
The European perch (Perca fluviatilis) is highly susceptible to heat stress, limiting its sustainable aquaculture. While single-organ thermal responses are partially understood, the systemic, multi-organ cooperative survival mechanisms under acute heat stress remain poorly characterized. To elucidate the underlying tolerance mechanisms and provide genetic markers for breeding, this study investigated the multi-organ responses of European perch (n = 90; body length: 13.15 ± 1.75 cm; body weight: 30.54 ± 7.17 g) transferred from 24 °C to an acute heat stress challenge (31 °C) at an increasing rate of 2 °C/h, and the histopathological changes (liver and gill), hepatic biochemical biomarkers (CAT, SOD, GSH-Px, GST, LDH, and MDA), and transcriptomic changes (liver and kidney) were evaluated over a 24 h period. Heat stress induced progressive structural damage, including gill lamellar edema and hepatocyte necrosis, accompanied by significant hepatic oxidative stress and lipid peroxidation. RNA-seq transcriptome profiling uncovered distinct sets of genes with significant expression changes, comprising 1343 DEGs in liver tissue and 722 DEGs in kidney samples. Both organs shared a systemic endoplasmic reticulum stress response but exhibited highly divergent survival strategies. The liver underwent severe metabolic reprogramming towards anaerobic glycolysis and gluconeogenesis, coupled with vesicle-mediated membrane repair attempts and apoptosis. Conversely, the kidney adopted a strict “energy triage” strategy, suppressing highly energy-consuming immune and osmoregulatory functions while actively silencing pro-apoptotic signals. These findings highlight organ-specific adaptations and identify potential metabolic markers for the future breeding of new heat-tolerant varieties. Full article
(This article belongs to the Special Issue Application of Multi-Omics Analysis to Fish Nutrition, Health and Welfare)
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20 pages, 3857 KB  
Article
Dietary Supplementation with Methionine and Lysine Enhances Antioxidant Function and Muscle Quality of Hefang Crucian Carp (Carassius auratus)
by Xiao Chen, Yiren Wang, Xubing Wang, Minggui Jiang, Hui Li, Xingyu Huang, Hanyuan Wang, Qianhong Gu, Yonghua Zhou and Yamei Xiao
Animals 2026, 16(11), 1636; https://doi.org/10.3390/ani16111636 - 27 May 2026
Viewed by 466
Abstract
Methionine (Met) and lysine (Lys), as primary limiting amino acids, play important roles in regulating muscle quality in aquatic animals. This study investigated the effects of dietary Met and Lys supplementation on the growth performance, antioxidant function, and muscle quality of Hefang crucian [...] Read more.
Methionine (Met) and lysine (Lys), as primary limiting amino acids, play important roles in regulating muscle quality in aquatic animals. This study investigated the effects of dietary Met and Lys supplementation on the growth performance, antioxidant function, and muscle quality of Hefang crucian carp (HCC) using physiological and transcriptomic analyses. Fish were fed three diets for 8 weeks: a basal diet (LA) and two diets supplemented with DL-methionine at 1.7% (MA) and 3.4% (HA), respectively, while L-lysine supplementation was fixed at 3.4%. The results indicated that dietary Met and Lys supplementation had no significant effect on the growth performance of HCC (p > 0.05), but significantly reduced serum triglyceride (TG) and cholesterol levels (T-CHO) (p < 0.05). Additionally, serum total protein (TP) content was significantly increased in the MA group (p < 0.05). Analysis of serum antioxidant enzyme activities indicated that appropriate Met and Lys supplementation improved antioxidant capacity and upregulated the expression of antioxidant-related genes (Nrf2, GPX1a, GSTO1, GSTP1) in the muscle. Moreover, the MA group exhibited superior muscle hardness and gumminess, while the HA group had higher springiness and chewiness (p < 0.05). Muscle fiber density was significantly increased, whereas diameter and area showed opposite trends in fish fed 1.7% Met and 3.4% Lys (p < 0.05). Furthermore, appropriate Met and Lys supplementation significantly affected muscle fiber development genes (MyoD, MyoG, and MRF4), with MyoG highest in the HA group and MyoD and MRF4 highest in the MA group (p < 0.05). Comparative transcriptomic analysis of muscle tissue showed DEGs were mainly enriched in pathways correlated with muscle quality, involving cardiac muscle contraction, actin cytoskeleton regulation, PPAR signaling pathway and ECM–receptor interaction. Taken together, our findings enhance the understanding of the molecular mechanisms underlying the effects of dietary Met and Lys on muscle quality in HCC, providing valuable insights for the development of nutritional strategies in the aquaculture industry. Full article
(This article belongs to the Special Issue Application of Multi-Omics Analysis to Fish Nutrition, Health and Welfare)
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