Proteomic profiling of yellow catfish (Pelteobagrus fulvidraco) skin mucus identifies differentially-expressed proteins in response to Edwardsiella ictaluri infection

Mucous cell histopathology and label-free quantitative proteomic analysis of skin mucus in fat greenling (Hexagrammos otakii) infected with Vibrio harveyi

Hexagrammos otakii is favored by consumers and aquaculture practitioners because of its strong adaptability and fast growth. However, recently, frequent outbreaks of diseases in the breeding of H. otakii have led to significant economic losses, especially due to bacterial diseases, which limit the healthy breeding of H. otakii. As a luminescent Gram-negative bacterium, Vibrio harveyi is the main pathogenic bacteria of H. otakii. In this study, the histopathology and label-free quantitative proteomics analysis were performed to reveal the changes of skin mucus proteins in H. otakii after infection with V. harveyi. The histopathological changes in the skin of H. otakii showed that when the bacteria were injected into the epithelial cells, it caused an increase in the number of mucous cells and a certain degree of damage and deformation in skin. Moreover, the quantitative proteomics analysis revealed a total of 364 differentially expressed proteins (DEPs), and these DEPs were found to be involved in environmental information processing, metabolism, infectious diseases: bacteria, replication and repair. More importantly, the enrichment analysis of the DEPs revealed that these different proteins were mainly targeted immune-related pathways. After infection of bacteria, the host's immune ability will be weakened, causing V. harveyi to enter the organism more easily, resulting in increased mucus in H. otakii, which will eventually lead to a decline in its physical function. These results provided an insight into a series of physiological changes after the bacterial infection of fish at the proteomic level and basic data for further exploration of the potential mechanism of skin mucus. Taken together, the results indicated more opportunities for the future designs and discoveries of effective antibacterial vaccines and antibacterial drugs for H. otakii.

TBK1 upregulates the interferon response against virus by the TBK1-IRF3/7 axis in yellow catfish (Pelteobagrus fulvidraco)

Yellow catfish (Pelteobagrus fulvidraco) is an important economic species of freshwater fish, widely distributed in China. Recently, viral diseases of yellow catfish have been identified in Chian (Hubei province), arising more attention to the viral immunity in P. fulvidraco. Tumor necrosis factor (TNF) receptor-associated factor NF-κB activator (TANK)-binding kinase 1 (TBK1) plays an essential role in IFN production and innate antiviral immunity. In the present study, we characterized the P. fulvidraco TBK1 (PfTBK1) and reported its function in interferon response. The full-length open reading frame (ORF) is 2184 bp encoding a protein with 727 amino acids, which is composed of four conserved domains, including KD, ULD, CCD1, and CCD2, similar to TBK1 in other species. Pftbk1 was widely expressed in all detected tissues by qPCR and was not inducible by the spring viremia of carp virus (SVCV), a single-strand RNA virus. In addition, the cellular distribution indicated that PfTBK1 was only located in the cytoplasm. Moreover, PfTBK1 induced strong IFN promoter activities through the Jak-stat pathway, and PfTBK1 interacted with and significantly phosphorylated IFN regulatory factor 3/7 (IRF3/7) in P. fulvidraco, promoting the nuclear translocation of pfIRF3 and PfIRF7, and PfTBK1 upregulated IFN response by PfTBK1-PfIRF3/7 axis. Above all, PfTBK1 triggered IFN response and strongly inhibited the replication of SVCV in EPC cells through induction of IFN downstream IFN-stimulated genes (ISGs). Summarily, this work reveals that PfTBK1 plays a positive regulatory role in IFN induction through the TBK1-IRF3/7 axis, laying a foundation for further exploring the molecular mechanism of the antiviral process in P. fulvidraco.

Proteomic profile of epidermal mucus from Labeo rohita reveals differentially abundant proteins after Aeromonas hydrophila infection

We report the proteomic profile of Epidermal Mucus (EM) from Labeo rohita and identified the differentially abundant proteins (DAPs) against Aeromonas hydrophila infection through label-free liquid chromatography-mass spectrometry (LC-MS/MS). Using discovery-based proteomics, a total of 2039 proteins were quantified in nontreated group and 1,328 proteins in the treated group, of which 114 were identified as DAPs in both the groups. Of the 114 DAPs, 68 proteins were upregulated and 46 proteins were downregulated in the treated group compared to nontreated group. Functional annotations of these DAPs shows their association with metabolism, cellular process, molecular process, cytoskeletal, stress, and particularly immune system. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Fisher's exact test between the two groups shows that most of the proteins were immune-related, which were significantly associated with the proteasome, phagosome, and Salmonella infection pathways. Overall, this study shows a basic and primary way for further functional research of the involvement of vitellogenin 2, alpha-2-macroglobulin-like protein, toll-like receptors (TLR-13), calpain, keratin-like proteins, and heat shock proteins against bacterial infection. Nonetheless, this first-ever comprehensive report of a proteomic sketch of EM from L. rohita after A. hydrophila infection provides systematic protein information to broadly understand the biological role of fish EM against bacterial infection.

Effects of ammonia and roxithromycin exposure on skin mucus microbiota composition and immune response of juvenile yellow catfish Pelteobagrus fulvidraco

As an inevitable factor in aquaculture, ammonia plays a critical role in macrolide antibiotic resistance, leading to accumulating of antibiotic-resistant bacteria in fish skin mucus. In this study, four experimental groups were implemented to test the effects of ammonia alone or in combination with roxithromycin for 28 days on skin mucus microbial composition and the immune response of yellow catfish: CON (control), AN (50.00 mg L-1 total ammonia nitrogen, TA-N), ROX (100 μg L-1 roxithromycin), and HR (50.00 mg L-1 TA-N, 100 μg L-1 ROX). This study demonstrated that ammonia or roxithromycin exposure resulted in increased plasma ammonia content and decreased total antioxidant capacity. Compared with AN group, the combined exposure of ammonia and roxithromycin inhibited the skin mucus immune response. Microbial composition analysis showed that combined exposure of ammonia and roxithromycin had no significant effect on skin mucus α-diversity as compared with CON group. The abundance of Cetobacterium, Rhizobiales_Incertae_Sedis_uncultured and Acinetobacter was increased significantly with the combined effect of ammonia and roxithromycin, these bacteria may be potentially antibiotic-resistant. As compared with CON group, the combined exposure of ammonia and roxithromycin did not affect skin goblet cell counts. This study suggests that combined exposure to ammonia and ROX increases the risk of the emergence of antibiotic-resistant bacteria.

Fish Skin Mucus Extracts: An Underexplored Source of Antimicrobial Agents

The slow discovery of new antibiotics combined with the alarming emergence of antibiotic-resistant bacteria underscores the need for alternative treatments. In this regard, fish skin mucus has been demonstrated to contain a diverse array of bioactive molecules with antimicrobial properties, including peptides, proteins, and other metabolites. This review aims to provide an overview of the antimicrobial molecules found in fish skin mucus and its reported in vitro antimicrobial capacity against bacteria, fungi, and viruses. Additionally, the different methods of mucus extraction, which can be grouped as aqueous, organic, and acidic extractions, are presented. Finally, omic techniques (genomics, transcriptomics, proteomics, metabolomics, and multiomics) are described as key tools for the identification and isolation of new antimicrobial compounds. Overall, this study provides valuable insight into the potential of fish skin mucus as a promising source for the discovery of new antimicrobial agents.

The feasibility of skin mucus replacing exosome as a pool for bacteria-infected markers development via comparative proteomic screening in teleost

In fish, skin mucus forms a protective barrier between the body surface and the external water environment, thus providing the most direct and intuitive clues to monitor the subject's health condition. To explore the impact of the Vibrio harveyi pathogen on teleost, the proteome of epidermal mucus from control and sick Cynoglossus semilaevis were screened through iTRAQ followed with LC-MS/MS. 1531 credible proteins were obtained relating to structural, metabolic and immunological functions. 335 different expressed proteins (DEPs) were identified, with 166 up-regulated and 169 down-regulated in MS. 62 proteins were characterized, including 22 up-regulated proteins and 40 down-regulated proteins. Integrated analysis of DE-miRNAs and DEPs from miRomics and proteomics were conducted to show the indirect regulatory relationship. Comparative analysis of DEPs between mucus and exosomes demonstrated that exosomes contributed the most DEPs of all mucus DEPs. 125 proteins are DEPs only in exosomes, which presented minor difference in total mucus. Expression of Aminopeptidase (anpep), Calcium-transporting ATPase, Histone H2B and H2A confirmed implied fine discriminative power with infected C. semilaevis, among which Calcium-transporting ATPase and H2B also appeared in list of exosomal markers. This study might shed the light on effective biomarker digging at other extended screening scenarios.

Three IRF4 paralogs act as negative regulators of type Ⅰ IFN responses in yellow catfish (Pelteobagrus fulvidraco)

IRF4 is a master member of the interferon regulatory factor (IRF) family playing vital regulatory roles in immune system development and function. Tetrapods have a single-copy IRF4 gene, while teleosts harbor duplicated IRF4 genes. This work describes three IRF4 paralogs from yellow catfish (Pelteobagrus fulvidraco), designated PfIRF4A, PfIRF4B and PfIRF4B-like. These genes all contain a typical IRF structural architecture. Phylogenic and synteny analyses indicate that they should arise from the teleost-specific whole-genome duplication. PfIRF4 genes are abundantly expressed in the immune-related tissues and upregulated by PolyI:C, LPS, and Edwardsiella ictaluri. Ectopic expression of these genes inhibits the activation of fish type Ⅰ IFN promoters and downregulates the transcription levels of IFN-responsive genes, thus allowing the efficient replication of a fish rhabdovirus, spring viremia of carp virus (SVCV). PfIRF4s possess a repressive effect on MyD88-mediated activation of IFN and NF-κB. Some differences are observed between each individual paralog. PfIRF4B is the main form expressed across the tissues and the most up-regulated one after pathogen induction. It exerts a stronger inhibitory effect on IFN antiviral response than the other two paralogs. PfIRF4A and PfIRF4B-like are primarily present in the nucleus, while PfIRF4B displays colocalization and direct associations with MyD88 in the cytoplasm. Overall, the data demonstrate that three PfIRF4 paralogs show shared and individual functional properties in the negative regulation of type Ⅰ IFN response.

Proteomic analysis of carp seminal plasma provides insights into the immune response to bacterial infection of the male reproductive system

Aeromonas salmonicida is recognized as a significant bacterial pathogen in ulcerative disease of cyprinid fish. However, the mechanism of immunity to these bacteria in common carp is still not well understood, especially the immune regulation in the gonad to bacterial infection. The aims of our study were to analyze changes in the seminal plasma proteome following A. salmonicida infection in carp males. The observed pathological changes in the tissue (liver, spleen, kidney and testis) morphology and upregulation of immune-related genes (tnfa2, il6a) confirmed the successful infection challenge. Using mass spectrometry-based label-free quantitative proteomics, we identified 1402 seminal plasma proteins, and 44 proteins (20 up- and 24 downregulated) were found to be differentially abundant between infected and control males. Most differentially abundant proteins were involved in the immune response mechanisms, such as acute phase response, complement activation and coagulation, inflammation, lipid metabolism, cell-cell and cell-matrix adhesion, creatine-phosphate biosynthesis and germ cell-Sertoli cell junction signaling. Bacterial infection also caused profound changes in expression of selected genes in the testis and hematopoietic organs, which contributed to changes in seminal proteins. The altered seminal proteins and bacterial proteins in seminal plasma may serve as valuable markers of infection in the testis.

Global gene expression responses of Atlantic salmon skin to Moritella viscosa

Moritella viscosa is a Gram-negative pathogen that causes large, chronic ulcers, known as winter-ulcer disease, in the skin of several fish species including Atlantic salmon. We used a bath challenge approach to profile the transcriptome responses of M. viscosa-infected Atlantic salmon skin at the lesion (Mv-At) and away from the lesion (Mv-Aw) sites. M. viscosa infection was confirmed through RNA-based qPCR assays. RNA-Seq identified 5212 and 2911 transcripts differentially expressed in the Mv-At compared to no-infection control and Mv-Aw groups, respectively. Also, there were 563 differentially expressed transcripts when comparing the Mv-Aw to control samples. Our results suggest that M. viscosa caused massive and strong, but largely infection site-focused, transcriptome dysregulations in Atlantic salmon skin, and its effects beyond the skin lesion site were comparably subtle. The M. viscosa-induced transcripts of Atlantic salmon were mainly involved in innate and adaptive immune response-related pathways, whereas the suppressed transcripts by this pathogen were largely connected to developmental and cellular processes. As validated by qPCR, M. viscosa dysregulated transcripts encoding receptors, signal transducers, transcription factors and immune effectors playing roles in TLR- and IFN-dependent pathways as well as immunoregulation, antigen presentation and T-cell development. This study broadened the current understanding of molecular pathways underlying M. viscosa-triggered responses of Atlantic salmon, and identified biomarkers that may assist to diagnose and combat this pathogen.

Omics Strategies in Current Advancements of Infectious Fish Disease Management

Aquaculture is an important industry globally as it remains one of the significant alternatives of animal protein source supplies for humankind. Yet, the progression of this industry is being dampened by the increasing rate of fish mortality, mainly the outbreak of infectious diseases. Consequently, the regress in aquaculture ultimately results in the economy of multiple countries being affected due to the decline of product yields and marketability. By 2025, aquaculture is expected to contribute approximately 57% of fish consumption worldwide. Without a strategic approach to curb infectious diseases, the increasing demands of the aquaculture industry may not be sustainable and hence contributing to the over-fishing of wild fish. Recently, a new holistic approach that utilizes multi-omics platforms including transcriptomics, proteomics, and metabolomics is unraveling the intricate molecular mechanisms of host-pathogen interaction. This approach aims to provide a better understanding of how to improve the resistance of host species. However, no comprehensive review has been published on multi-omics strategies in deciphering fish disease etiology and molecular regulation. Most publications have only covered particular omics and no constructive reviews on various omics findings across fish species, particularly on their immune systems, have been described elsewhere. Our previous publication reviewed the integration of omics application for understanding the mechanism of fish immune response due to microbial infection. Hence, this review provides a thorough compilation of current advancements in omics strategies for fish disease management in the aquaculture industry. The discovery of biomarkers in various fish diseases and their potential advancement to complement the recent progress in combatting fish disease is also discussed in this review.

Function and association analysis of Cyclophilin A gene with resistance to Edwardsiella ictaluri in yellow catfish

Edwardsiella ictaluri (E. ictaluri) is one of the main bacterial pathogens in catfish which has caused serious economic loss to yellow catfish (Pelteobagrus fulvidraco) in China. In our previous work, we demonstrated that CypA was up-regulated at the early stage of E. ictaluri infection in yellow catfish and displayed strong chemotactic activity for leukocytes in vitro. However, the effect of CypA on E. ictaluri is unknown in vivo. Therefore, two homozygous transgenic zebrafish lines expressing yellow catfish CypA (TG-CypA-1 and TG-CypA-2) were generated. After challenged with E. ictaluri at a dose of 1.0 × 10⁴ CFU per adult fish, both two transgenic lines exhibited a higher resistance to bacterial infection than the wildtype zebrafish. Herein, CypA gene in E. ictaluri-challenged yellow catfish was screened for presence of polymorphisms by sequencing and six single nucleotide polymorphisms (SNPs) were identified. SNP association analysis revealed that 528T/C SNP in the first intron was significantly different in disease-susceptible and -resistant groups, which was confirmed in two independent populations of yellow catfish. Moreover, the relative expression of CypA in the resistant group (CC genotype in 528T/C SNP) was significantly higher than that in the susceptible group (TT genotype in 528T/C SNP) in different immune organs of yellow catfish including spleen, head kidney, body kidney and liver. Our results reveal the potential function of CypA in host defense to bacterial infection and suggest the SNP marker in CypA gene associated with the resistance to E. ictaluri may facilitate the selective breeding of disease-resistant yellow catfish in the future.

Effect of dietary isoleucine on skin mucus barrier and epithelial physical barrier functions of hybrid bagrid catfish Pelteobagrus vachelli × Leiocassis longirostris

The study investigated the effects of dietary isoleucine (Ile) on skin mucus barrier and epithelial physical barrier functions of hybrid bagrid catfish Pelteobagrus vachelli × Leiocassis longirostris. A total of 630 fish (33.11 ± 0.09 g) were fed semi-purified isonitrogenous diets containing 5.0 (control), 7.5, 10.0, 12.5, 15.0, 17.5, and 20.0 g Ile kg ^-1 diet for 8 weeks. The results indicated that dietary Ile increased (P < 0.05) in skin (1) mucus protein content and antimicrobial activity against three gram-negative bacteria (Aeromonas hydrophila, Escherichia coli, and Yersinia ruckeri) and two gram-positive bacteria (Streptococcus agalactiae and Staphylococcus aureus), (2) mucus lysofew information is available about the influencezyme (LZM), acid phosphatase (ACP), and alkaline phosphatase (AKP) activities, and complement 3 and 4 (C3 and C4) and immunoglobulin M (IgM) contents, (3) intelectin 1 (intl1), intelectin 2 (intl2), c-type-lysozyme (c-LZM), g-type-lysozyme (g-LZM), and β-defensin mRNA levels. Dietary Ile decreased (P < 0.05) reactive oxygen species (ROS), malondialdehyde (MDA), and protein carbonyl (PC) contents, and up-regulated (P < 0.05) CuZnSOD, GST, GPX1a, muc5ac, muc5b, zonula occludens-1 (ZO-1), zonula occludens-2 (ZO-2), occludin, and claudin 3 mRNA levels in skin. These results indicated that Ile improved skin mucus barrier function via increasing mucus protein, C3 and C4, and IgM contents and antibacterial factors activities, and promoted epithelial physical barrier function via decreasing skin antioxidant damage and improving tight junction structure in hybrid bagrid catfish.

Dietary inclusion of chestnut (Castanea sativa) polyphenols to Nile tilapia reared in biofloc technology: Impacts on growth, immunity, and disease resistance against Streptococcus agalactiae

A feeding trial was carried out to examine the effects of adding chestnut (Castanea sativa) polyphenols (CSP) on the growth, skin mucus and serum immune parameters of Nile tilapia (Oreochromis niloticus). Five experimental diets with inclusion levels of 0, 1, 2, 4, and 8 g kg^-1 of CSP were fed to Nile tilapia fingerlings (12.77 ± 0.17 g fish^-1) during an eight-week trial. Fish were analyzed on the fourth and eighth week to determine the influences of CSP on growth, skin mucus, and serum immune parameters. Challenging test versus Streptococcus agalactiae was evaluated at the end of the trial. Fish fed with CSP enriched diets displayed a significant increase (P ≤ 0.05) in growth and a decline in feed conversion ratio (P ≤ 0.05). Similarly, skin mucus and serum immune parameters were significantly increased (P ≤ 0.05) in fish fed CSP with respect to the control. The effects were already evident four weeks after the CSP administration. The disease protection test displayed that the fish's survival rate was significantly higher (P < 0.05) in CSP diets over the control. The relative percentage of survival (RSP) was 62.5, 75.0, 58.3, and 37.5 in fish fed diets contained 1, 2, 4, and 8 g kg^-1 CSP, respectively. The best effect on growth, immune response, and disease resistance were shown in Nile tilapia fed with a diet supplementation of 2 g kg^-1 CSP.