Abstract
Nowadays, fish production through aquaculture and wild capture is escalating due to the higher fish protein demand for human consumption. Thus, the needs for fish products to be improved in scale and quality are becoming increasingly important to meet the nutrition requirements. The negative impacts caused by pathogens infection both in hatchery and grow-out ponds, have resulted in low aquaculture productivity and economic losses for the farmers. Therefore, a systematic study exploring relevant omics datasets through a systems biology approach will enable scientist to describe the complexity and characteristics of interactions in the host-pathogen network, leading to identifying new targets or biomarkers for diseases infection caused by bacteria, viruses, and parasites. The use of different approaches and emerging technologies as a powerful tool in obtaining a new knowledge for sustainable aquaculture production has been increasingly applied by many researchers over the years. In this paper, several omics approaches used to assess the fish immune response were reviewed. A brief description is provided for the omics approaches applicable to aquacultures, such as genomics, transcriptomics, proteomics, and metabolomics. Each tool used are contributes to develop better treatment and prevention strategies to overcome aquaculture disease due to the microbial infections. In genomics and transcriptomics analysis, their parallel approach involving gene expression studies play important role in identifying immune-related genes of the host, response to infectious diseases. While for proteomics and metabolomics approaches, these omics will provide information on the biomarker discovery and understanding the immune-related biosynthetic pathway during pathogen infection. Additionally, examples of the integrative analysis of multi-omics tools required for researchers to better understand the biological systems of aquatic animals especially fish, will also be provided.
Highlights
The dramatic increase in seafood products’ demands in the past few decades has affected the fisheries capture industry and global aquaculture production
Omics approaches have given us high throughput databases and more holistic methodologies than traditional methods. These omics approaches are known for investigating molecular pathways and the identification and quantification of differentially expressed genes or molecules in animals exposed to infectious diseases
Several proteins identified as IL-13 receptor alpha-1 (IL-13Rα1), GTPase IMAP family member 7 (GIMAP7), ferritin, CD209, VDAC2, proteasome subunit alpha type (PSMA1) and annexin ANXA11s could have the potential to act as a biomarker during aminoacyl-tRNA biosynthesis, nucleotide metabolism and proteasome in rainbow trout when infected with A. salmonicida (Long et al, 2015)
Summary
Omics approaches have given us high throughput databases and more holistic methodologies than traditional methods. A total of 1,036 genes and 133 proteins were analyzed, and the correlation between the transcriptomic and proteomic data indicated that 17 proteins showed consistent expression at the RNA and protein levels From these results, several proteins identified as IL-13 receptor alpha-1 (IL-13Rα1), GTPase IMAP family member 7 (GIMAP7), ferritin, CD209, VDAC2, proteasome subunit alpha type (PSMA1) and annexin ANXA11s could have the potential to act as a biomarker during aminoacyl-tRNA biosynthesis, nucleotide metabolism and proteasome in rainbow trout when infected with A. salmonicida (Long et al, 2015). Several proteins identified as IL-13 receptor alpha-1 (IL-13Rα1), GTPase IMAP family member 7 (GIMAP7), ferritin, CD209, VDAC2, proteasome subunit alpha type (PSMA1) and annexin ANXA11s could have the potential to act as a biomarker during aminoacyl-tRNA biosynthesis, nucleotide metabolism and proteasome in rainbow trout when infected with A. salmonicida (Long et al, 2015) In another omics integrated study, metabolomics and proteomics methods were used to elucidate and understand the effects of ammonia toxicity in marine medaka, Oryzias melastigma. These provide opportunities and make it relatively easier for researchers to obtain and discover new vaccination, anti-bacterial, anti-viral and anti-parasite products in the aquaculture field (Ye et al, 2018)
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