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Sasikumar R, Saranya S, Lourdu Lincy L, Thamanna L, Chellapandi P. Genomic insights into fish pathogenic bacteria: A systems biology perspective for sustainable aquaculture. FISH & SHELLFISH IMMUNOLOGY 2024; 154:109978. [PMID: 39442738 DOI: 10.1016/j.fsi.2024.109978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 10/12/2024] [Accepted: 10/20/2024] [Indexed: 10/25/2024]
Abstract
Fish diseases significantly challenge global aquaculture, causing substantial financial losses and impacting sustainability, trade, and socioeconomic conditions. Understanding microbial pathogenesis and virulence at the molecular level is crucial for disease prevention in commercial fish. This review provides genomic insights into fish pathogenic bacteria from a systems biology perspective, aiming to promote sustainable aquaculture. It covers the genomic characteristics of various fish pathogens and their industry impact. The review also explores the systems biology of zebrafish, fish bacterial pathogens, and probiotic bacteria, offering insights into fish production, potential vaccines, and therapeutic drugs. Genome-scale metabolic models aid in studying pathogenic bacteria, contributing to disease management and antimicrobial development. Researchers have also investigated probiotic strains to improve aquaculture health. Additionally, the review highlights bioinformatics resources for fish and fish pathogens, which are essential for researchers. Systems biology approaches enhance understanding of bacterial fish pathogens by revealing virulence factors and host interactions. Despite challenges from the adaptability and pathogenicity of bacterial infections, sustainable alternatives are necessary to meet seafood demand. This review underscores the potential of systems biology in understanding fish pathogen biology, improving production, and promoting sustainable aquaculture.
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Affiliation(s)
- R Sasikumar
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - S Saranya
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - L Lourdu Lincy
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - L Thamanna
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - P Chellapandi
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India.
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Iyyappan S, Rather MA, Ahmad I, Ahmad I. Comparative mitochondrial genomics analysis of selected species of Schizothoracinae sub family to explore the differences at mitochondrial DNA level. Comput Biol Chem 2024; 112:108165. [PMID: 39106606 DOI: 10.1016/j.compbiolchem.2024.108165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/09/2024]
Abstract
A comprehensive analysis of the whole mitochondrial genomes of the Schizothoracinae subfamily of the family Cyprinidae has been revealed for the first time. The species analyzed include Schizothorax niger, Schizothorax esocinus, Schizothorax labiatus and Schizothorax plagoistomus. The total mitochondrial DNA (mtDNA) length was determined to be 16585 bp, 16583 bp, 16582 bp and 16576 bp, respectively with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding area genes. The combined mean base compositions of the four species were as follows: A: 29.91 % T: 25.47 % G: 17.65 % C 27.01 %. The range of the GC content is 45-44 %, respectively. All protein coding genes (PCGs) commenced with the typical ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene with GTG. The analysis of vital amino acid biosynthesis genes (COX1, ATPase 6, ATPase 8) in four different species revealed no significant differences. All 13 PCGs had Ka/Ks ratios that were all lesser than one, demonstrating purifying selection on those molecules. These tRNA genes were predicted to fold into the typical cloverleaf secondary structures with normal base pairing and ranged in size from 66 to 75 nucleotides. Additionally, the phylogenetic tree analysis revealed that S. esocinus species that was most alike to S. labiatus. This study provides critical data for phylogenetic analysis of the Schizothoracinae subfamily, which will help to resolve taxonomic difficulties and identify evolutionary links. Detailed mtDNA data are an invaluable resource for studying genetic diversity, population structure, and gene flow. Understanding genetic makeup can help inform conservation plans, identify unique populations, and track genetic variation to ensure effective preservation.
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Affiliation(s)
- S Iyyappan
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil, Ganderbal, Sher-e-Kashmir University of Agricultural Science and Technology, Kashmir 190006, India
| | - Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil, Ganderbal, Sher-e-Kashmir University of Agricultural Science and Technology, Kashmir 190006, India.
| | - Ishtiyaq Ahmad
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil, Ganderbal, Sher-e-Kashmir University of Agricultural Science and Technology, Kashmir 190006, India
| | - Irfan Ahmad
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil, Ganderbal, Sher-e-Kashmir University of Agricultural Science and Technology, Kashmir 190006, India
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Shebl S, Ghareeb DA, Ali SM, Ghanem NBED, Olama ZA. Aerobic phenol degradation using native bacterial consortium via ortho-and meta-cleavage pathways. Front Microbiol 2024; 15:1400033. [PMID: 39161607 PMCID: PMC11330787 DOI: 10.3389/fmicb.2024.1400033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/25/2024] [Indexed: 08/21/2024] Open
Abstract
Effective bioremediation of a phenol-polluted environment harnesses microorganisms' ability to utilize hazardous compounds as beneficial degraders. In the present study, a consortium consisting of 15 bacterial strains was utilized. The current study aims to monitor the phenol biodegradation pathway. The tested consortium showed effective potential in the bioremediation of phenol-contaminated industrial wastewater. The enzymatic studies conducted brought to light that the bacterial consortium under test was proficient in degrading phenol under aerobic conditions while exhibiting the simultaneous expression of both ortho- and meta-cleavage pathways. It was observed that pheA, pheB, and C12O genes were maximally expressed, and the enzymes responsible for phenol degradation, namely, phenol hydroxylase, catechol 1,2-dioxygenase, and catechol 2,3-dioxygenase, reached maximum activity after 48 h of incubation with a 20-ppm phenol concentration. To gain a deeper understanding of the activation of both ortho- and meta-cleavage pathways involved in phenol degradation, a technique known as differential display reverse transcriptase polymerase chain reaction (DDRT-PCR) was applied. This method allowed for the specific amplification and detection of genes responsible for phenol degradation. The expression levels of these genes determined the extent to which both ortho- and meta-cleavage pathways were activated in response to the presence of phenol.
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Affiliation(s)
- Sara Shebl
- Department of Botany & Microbiology, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Doaa A. Ghareeb
- Department of Biochemistry, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Safaa M. Ali
- Nucleic Acid Research Center, City of Scientific Research and Technology Applications, Alexandria, Egypt
| | | | - Zakia A. Olama
- Department of Botany & Microbiology, Faculty of Science, Alexandria University, Alexandria, Egypt
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Li M, Chen B, Xu M, Li F, Geng Y, Chen D, Ouyang P, Huang X, Deng Y. Identification of TonB-dependent siderophore receptor inhibitors against Flavobacterium columnare using a structure-based high-throughput virtual screening method. Front Microbiol 2024; 15:1392178. [PMID: 38835482 PMCID: PMC11148330 DOI: 10.3389/fmicb.2024.1392178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/07/2024] [Indexed: 06/06/2024] Open
Abstract
TonB-dependent siderophore receptors play a critical transport role for Flavobacterium columnare virulence formation and growth, and have become valuable targets for the development of novel antimicrobial agents. Traditional Chinese medicine has demonstrated notable efficacy in the treatment of fish diseases and includes potential antibacterial agents. Herein, we performed molecular docking-based virtual screening to discover novel TonB-dependent siderophore receptor inhibitors from traditional Chinese medicine and provide information for developing novel antibacterial agents. Firstly, we efficiently obtained 11 potential inhibitors with desirable drug-like characteristics from thousands of compounds in the TCM library based on virtual screening and property prediction. The antibacterial activity of Enoxolone, along with its interaction characteristics, were determined via an MIC assay and molecular dynamic simulation. Transcriptional profiling, along with validation experiments, subsequently revealed that an insufficient uptake of iron ions by bacteria upon binding to the TonB-dependent siderophore receptors is the antibacterial mechanism of Enoxolone. Finally, Enoxolone's acceptable toxicity was illustrated through immersion experiments. In summary, we have used virtual screening techniques for the first time in the development of antimicrobial agents in aquaculture. Through this process, we have identified Enoxolone as a promising compound targeting the TonB-dependent siderophore receptor of F. columnare. In addition, our findings will provide new ideas for the advancement of innovative antimicrobial medications in aquaculture.
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Affiliation(s)
- Minghao Li
- Fisheries Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Baipeng Chen
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ming Xu
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fulong Li
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yi Geng
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Defang Chen
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Ouyang
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Huang
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yongqiang Deng
- Fisheries Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
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Liu Y, Zheng C, Su X, Chen J, Li X, Sun C, Nizamani MM. Comparative analysis and characterization of the chloroplast genome of Krascheninnikovia ceratoides (Amarathaceae): a xerophytic semi-shrub exhibiting drought resistance and high-quality traits. BMC Genom Data 2024; 25:10. [PMID: 38287264 PMCID: PMC10826016 DOI: 10.1186/s12863-024-01197-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/23/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Krascheninnikovia ceratoides, a perennial halophytic semi-shrub belonging to the genus Krascheninnikovia (Amarathaceae), possesses noteworthy ecological, nutritional, and economic relevance. This species is primarily distributed across arid, semi-arid, and saline-alkaline regions of the Eurasian continent, encompassing Inner Mongolia, Xinjiang, Qinghai, Gansu, Ningxia, and Tibet. RESULTS We reported the comprehensive chloroplast (cp) genome of K. ceratoides, characterized by a circular conformation spanning 151,968 bp with a GC content of 36.60%. The cp genome encompassed a large single copy (LSC, 84,029 bp), a small single copy (SSC, 19,043 bp), and a pair of inverted repeats (IRs) regions (24,448 bp each). This genome harbored 128 genes and encompassed 150 simple sequence repeats (SSRs). Through comparative analyses involving cp genomes from other Cyclolobeae (Amarathaceae) taxa, we observed that the K. ceratoides cp genome exhibited high conservation, with minor divergence events in protein-coding genes (PCGs) accD, matK, ndhF, ndhK, ycf1, and ycf2. Phylogenetic reconstructions delineated K. ceratoides as the sister taxon to Atriplex, Chenopodium, Dysphania, and Suaeda, thus constituting a robust clade. Intriguingly, nucleotide substitution ratios (Ka/Ks) between K. ceratoides and Dysphania species for ycf1 and ycf2 genes surpassed 1.0, indicating the presence of positive selection pressure on these loci. CONCLUSIONS The findings of this study augment the genomic repository for the Amarathaceae family and furnish crucial molecular instruments for subsequent investigations into the ecological adaptation mechanisms of K. ceratoides within desert ecosystems.
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Affiliation(s)
- Yuping Liu
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of Qinghai-Tibetan Plateau in Qinghai Province, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
| | - Changyuan Zheng
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
| | - Xu Su
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China.
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of Qinghai-Tibetan Plateau in Qinghai Province, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China.
| | - Jinyuan Chen
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
| | - Xiaoli Li
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
| | - Chenglin Sun
- School of Life Sciences, Qinghai Normal University, 38# Wusixi Road, Xining, 810008, Qinghai Province, China
| | - Mir Muhammad Nizamani
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, Guizhou, China.
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Nguyen NH. Genetics and Genomics of Infectious Diseases in Key Aquaculture Species. BIOLOGY 2024; 13:29. [PMID: 38248460 PMCID: PMC10813283 DOI: 10.3390/biology13010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease and species specific and contingent upon a multitude of factors. The fields of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus (WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish, and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease-resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favorable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate-to-high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems and AI algorithms and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.
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Affiliation(s)
- Nguyen Hong Nguyen
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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