Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Bioactivity of green-synthesized zinc oxide nanoparticles using Fusarium oxysporum extract on the expression of extended-spectrum beta-lactamase and biofilm-associated genes in the pathogen Klebsiella pneumoniae","authors":"Amani Kenaan Abd-Alrahman,&nbsp;Huda SA. AL-Hayanni","doi":"10.1016/j.jgeb.2025.100645","DOIUrl":"10.1016/j.jgeb.2025.100645","url":null,"abstract":"<div><div>Multidrug-resistant <em>Klebsiella pneumoniae</em> poses a serious clinical threat because of its ability to form biofilms and generate extended-spectrum beta-lactamase enzymes (ESBLs). This research investigated the influence of biosynthesized zinc oxide nanoparticles made from <em>Fusarium oxysporum</em> alcohol extract (FOE) on ESBL genes (<em>bla</em>TEM, <em>bla</em>CTX-M, <em>bla</em>SHV) and the biofilm-associated genes <em>mrk</em>A and <em>lux</em>S. The presence of the 16S rRNA, ESBL and biofilm genes was confirmed through subsequent polymerase chain reaction of the isolates. The FOE and zinc oxide nanoparticles both demonstrated significant antibacterial activity, with zinc oxide nanoparticles exhibiting greater inhibition with a minimum inhibitory concentration (MIC) of 26 μg/ml. Compared with untreated and FOE-treated isolates, those treated with sub-MIC concentrations of zinc oxide nanoparticles expressed significantly fewer ESBL and biofilm-related genes. The expression levels of the genes <em>bla</em>TEM, <em>bla</em>CTX-M, <em>bla</em>SHV, <em>mrk</em>A and <em>lux</em>S were downregulated below a ratio of 1.0 in each of the bacterial isolates. The biosynthesized zinc oxide nanoparticles demonstrated strong antibacterial and antibiofilm effects through the downregulation of bacterial antibiotic resistance and virulence genes in <em>K. pneumoniae</em>. The findings of this study demonstrate the ability of biosynthesized zinc oxide nanoparticles to function as a green and apotential alternative or support the role of antibiotcs for the treatment of multidrug-resistant (MDR) bacteria.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100645"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ResSGA-Net: A deep learning approach for enhanced brain tumor detection and accurate classification in healthcare imaging systems","authors":"Yucheng Guan ,&nbsp;Ahmad Alshammari ,&nbsp;Yu Wang ,&nbsp;Jahan Zeb Gul ,&nbsp;Azhar Imran","doi":"10.1016/j.jgeb.2026.100658","DOIUrl":"10.1016/j.jgeb.2026.100658","url":null,"abstract":"<div><div>Accurate and reliable brain tumor classification from magnetic resonance imaging (MRI) is a critical component of computer-aided diagnosis systems, directly impacting clinical decision-making and patient outcomes. This study presents ResSGA-Net, a hybrid deep learning framework that integrates a ResNet50 backbone with dual attention mechanisms (global and gated) and a Swin Transformer to capture both fine-grained local features and long-range contextual dependencies effectively. A fusion strategy is employed to unify convolutional, attention-refined, and transformer-enhanced representations into a robust feature space for multi-class classification. The proposed model is evaluated on two publicly available benchmark datasets, including a four-class and a three-class brain tumor classification task, using stratified cross-validation. Extensive quantitative analysis demonstrates that ResSGA-Net achieves state-of-the-art performance, with accuracies exceeding 98% on Dataset I and strong generalization on Dataset II (accuracy of 93.18% and macro-averaged AUC of 0.989). Comprehensive statistical significance testing confirms that the observed improvements are highly significant and not attributable to random chance. Ablation studies further validate the individual contributions of attention mechanisms and data augmentation strategies, demonstrating that performance gains arise from tumor-specific feature learning rather than artificial data diversity. Qualitative analyses, including confusion matrices, training dynamics, ROC curves, and confidence-based visualizations, confirm stable convergence, robust generalization, and reliable decision confidence across tumor classes. These results indicate that ResSGA-Net provides an accurate, stable, and clinically meaningful solution for automated brain tumor classification, with strong potential for integration into real-world diagnostic imaging workflows.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100658"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic underpinnings of type-2 diabetes (T2D) with colorectal cancer (CRC): In-silico discovery of common molecular signatures, pathogenetic processes and therapeutic candidates","authors":"Reaz Ahmmed ,&nbsp;Umme Samia Antu ,&nbsp;Tasfia Noor ,&nbsp;Md.Fahim Faysal ,&nbsp;Arnob Sarker ,&nbsp;Sabkat Mahmud ,&nbsp;Alvira Ajadee ,&nbsp;Md.Nurul Haque Mollah","doi":"10.1016/j.jgeb.2026.100667","DOIUrl":"10.1016/j.jgeb.2026.100667","url":null,"abstract":"<div><div>Type-2 diabetes (T2D) is a risk factor for colorectal cancer (CRC) and the incidence rate of CRC in T2D patients is significantly higher than in control patients. It may be associated with the overlapping dysregulated genetic factors. The management of CRC becomes complicated with T2D compare to without T2D due to the conflict of therapeutic priorities for both diseases.​ However, studies on overlapping dysregulated genetic factors and their therapeutic priorities during their co-incidence/existence, are very limited. This study aimed to identify those overlapping dysregulated genetic factors with their functions, pathways and regulators through which T2D may stimulate the development and progression of CRC, for exploring effective shared drug therapies (polypharmacological agents) against both diseases, since a disease specific drug may conflict with other diseases during their co-existence. In order to explore repurposable common drugs for both T2D and CRC, we identified both diseases causing top-ranked 8 sKGs (CD44, COL18A1, CLDN5, PLS3, PTK2, THBS1, CAV1, and EFEMP1) as the drug targets through transcriptomics analysis. The relationship of sKGs with T2D and CRC were also verified through the literature review, expression analysis with independent datasets, functional enrichment analysis with KEGG-pathways and GO-terms, regulatory network analysis with microRNAs and transcription factors (TFs), DNA methylation and immune infiltration analysis based on independent databases. Finally, sKGs-guided top-ordered four candidate drugs (irinotecan, leucovorincalcium, regorafenib and Fenretinide) were recommended as the shared treatments for both CRC and T2D during their co-existence. The recommended drug therapy might be effective to reduce drug burden from the patients. Therefore, the findings demand experimental and clinical validations for taking a proper treatment plan against CRC with T2D as comorbidity.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100667"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147395712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncovering evolutionary and phylogenetic relationships in Glyptothorax species through comparative mitochondrial genomics","authors":"Somasundaram Iyyappan,&nbsp;Suvadip Ghara,&nbsp;Irfan Ahmad Bhat,&nbsp;Irfan Ahmad Khan,&nbsp;Mohd Ashraf Rather","doi":"10.1016/j.jgeb.2025.100629","DOIUrl":"10.1016/j.jgeb.2025.100629","url":null,"abstract":"<div><div>The mitochondrial genome serves as a crucial molecular marker for studying phylogenetic relationships and molecular evolution in fish. Despite their ecological significance in freshwater ecosystems, <em>Glyptothorax</em> fishes have limited evolutionary research, with only a few complete mitochondrial genomes reported. The present study examines the complete mitochondrial DNA (mtDNA) of <em>Glyptothorax cavia</em>, <em>G. trilineatus</em>, <em>G. annandalei</em>, <em>G. sinensis</em>, and <em>G. granosus</em>, with sequence lengths of 16,529 base pairs (bp), 16,539 bp, 16,541 bp, 16,531 bp, and 16,540 bp, respectively. Our comprehensive analysis reveals that most protein-coding genes (PCGs) begin with the ATG codon and terminate with the TAA stop codon, although some exhibit incomplete stop codons (T/TA). The majority of the 13 protein-coding genes (PCGs) display a negative guanine-cytosine (GC) skew, except for the (Skew value: 0.53–0.60) NADH dehydrogenase subunit 6 (ND6) gene. In terms of adenine–thymine (AT) (AT Skew value: 0–0.007), eight PCGs have positive values, while cytochrome <em>c</em> oxidase subunit 1 (COX1-), NADH dehydrogenase subunit 3 (ND3), NADH dehydrogenase subunit 4L (ND4L), NADH dehydrogenase subunit 4 (ND4), NADH dehydrogenase subunit 5 (ND5), and cytochrome <em>b</em> (Cytb) exhibit negative values. Genetic distance and non-synonymous to synonymous substitution ratio (Ka/Ks) analyses indicate purifying selection acting on the 13 PCGs, with selection pressures potentially influenced by environmental adaptations. Phylogenetic and evolutionary analyses identify <em>G. sinensis</em>, <em>G. annandalei</em>, and <em>G. granosus</em> as closely related species.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100629"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioreactors expansion of human mesenchymal stromal cell therapies: platforms, parameters, challenges and opportunities","authors":"Hong Yu ,&nbsp;Gang Gary Hao","doi":"10.1016/j.jgeb.2025.100638","DOIUrl":"10.1016/j.jgeb.2025.100638","url":null,"abstract":"<div><div>Human mesenchymal stromal cells (MSC) have garnered significant interest as cell therapy for a multitude of indications. Despite their clinical potential, the development and commercialization of MSC-based products have been hampered by the challenge in scalable production of MSC ex vivo. At present, bioreactor expansion represents the most significant technical hurdle during the MSC manufacturing process. Intrinsic properties of MSCs, e.g. cell senescence, donor heterogeneity, and shear stress-sensitivity lead to suboptimal productivity and inconsistent quality, that often confounded the clinical efficacy readout. Herein we review the key aspects in bioreactor cultivation of MSCs, including the instrument platforms, critical process parameters, process scale-up, downstream and analytics. Cell senescence, the key limitation in ex vivo MSC expansion, was also discussed along with emerging strategies to circumvent the obstacle. Technological improvement and mechanistic understanding of MSC expansion in bioreactors will accelerate the clinical development of MSC as regenerative medicine.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100638"},"PeriodicalIF":2.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phytochemical screening and inhibitory effects of Catha edulis Forsk extracts on oxidation, growth, biofilm and quorum sensing of selected pathogens","authors":"Yonatan Nesru ,&nbsp;Muktar Ahmed ,&nbsp;Adam Mengistu ,&nbsp;Mohammed Naimuddin","doi":"10.1016/j.jgeb.2025.100560","DOIUrl":"10.1016/j.jgeb.2025.100560","url":null,"abstract":"<div><div>The treatment of infectious diseases is increasingly challenging due to the emergence and re-emergence of antibiotic-resistant bacteria. Plant-derived natural products are being explored as potential solutions to this global threat. This study investigated the phytochemical composition of <em>Catha edulis</em> and biological properties of its extracts, focusing on their potential as antioxidants and antimicrobials. Gas chromatography/mass spectrometry (GC/MS) of the methanol extract (MeOHE) fractions revealed 11 compounds in dichloromethane fraction (DCMF) and 30 compounds in ethyl acetate fraction (EAF), many of which possess bioactive functions as antioxidants and antimicrobials. Phytol was detected at 60.32 %, not reported before in <em>C. edulis</em>. The antioxidation potential of extracts was assayed by radical scavenging activity (RSA), and the IC₅₀ values ranged from 68.2 to 89.3 µg/mL, respectively indicating good antioxidant potency. In the disc diffusion assay against representative pathogenic bacteria, the extracts exhibited an inhibition order of EAF &gt; DCMF &gt; MeOHE in the 31–75 % range. The minimum inhibitory concentration (MIC) for MeOHE and DCMF were in the 0.5 − &gt;1 mg/mL range, while the minimum bactericidal concentration (MBC) were from 2 to &gt; 2 mg/mL. EAF showed a MIC and MBC in the 0.5–––1 mg/mL and 1–––2 mg/mL range, suggesting better inhibition potential. The tolerance test values showed bactericidal activity against all the tested bacteria. The minimum biofilm inhibitory concentration (MBIC) values of DCMF were 250 to &gt; 500 µg/mL, while EAF ranged from 125 to 500 µg/mL, indicating effective inhibition of biofilm formation. The anti-quorum sensing (anti-QS) activity of DCMF and EAF on <em>P. aeruginosa</em> showed 55.8 % and 51.4 % inhibition of pyocyanin production at 500 µg/mL. These results suggest that DCMF and EAF of <em>C. edulis</em> are potent antioxidants and antimicrobials, potentially reducing the load of pathogens. To our best knowledge, this is the first report of antibiofilm and anti-QS activities of <em>C. edulis</em> extracts on pathogenic bacteria included in the Pathogen Priority List.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100560"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144913946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene editing using gamma modified PNA: HBB gene as a model","authors":"Noha Eltaweel ,&nbsp;Ghada Elkamah ,&nbsp;Nesma Elaraby ,&nbsp;Iman Hassan ,&nbsp;Ahmed Wassel ,&nbsp;Nahla Abdel-Aziz ,&nbsp;Khalda Amr","doi":"10.1016/j.jgeb.2025.100562","DOIUrl":"10.1016/j.jgeb.2025.100562","url":null,"abstract":"<div><div>PNAs have emerged as a powerful tool in gene editing, particularly for correcting monogenic disorders by enhancing targeted recombination and genomic modifications. This study <strong>aimed to</strong> establish a gene editing technique using Peptide Nucleic Acid (PNA)/donor DNA-loaded poly lactic-co-glycolic acid (PLGA) nanoparticles at our genomic facilities, with the ultimate goal of correcting disease-causing mutations. <strong>Methods</strong> involved culturing skin fibroblasts from a healthy Egyptian volunteer without HBB gene mutations in two separate 12-well plates. Oligonucleotides were designed, and nanoparticles were formulated and characterized before being used to treat the cultured fibroblasts. DNA and RNA were extracted from treated cells, followed by molecular analyses to confirm the edits. <strong>Results</strong> indicated successful encapsulation of nanoparticles and modest, sustained introduction of the desired mutation, accompanied by functional impairment in HBB gene expression. The study successfully established PNA gene editing technology, potentially paving the way for future treatment studies of single-gene disorders.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100562"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145158117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the role of oncogenic FAM83A as a prognostic biomarker in lung adenocarcinoma: Insights from smoker and non-smoker cohorts","authors":"Prithvi Singh ,&nbsp;Aanchal Rathi ,&nbsp;Mohammad Masood ,&nbsp;Md.Imtaiyaz Hassan ,&nbsp;Mohammad Mahfuzul Haque ,&nbsp;Ravins Dohare ,&nbsp;Anas Shamsi","doi":"10.1016/j.jgeb.2025.100581","DOIUrl":"10.1016/j.jgeb.2025.100581","url":null,"abstract":"<div><div>Lung adenocarcinoma (LUAD) in smokers and non-smokers presents distinct clinical characteristics, including differences in genetics, treatment response, and prognosis. To explore these differences, we conducted a <em>meta</em>-analysis using publicly accessible LUAD datasets, identifying <em>meta</em>-differentially expressed genes (DEGs) in smokers and non-smokers. A total of <span><math><mrow><mn>29</mn><mspace></mspace></mrow></math></span> <em>meta</em>-DEGs were discovered, with seven (<em>CLDN2</em>, <em>CLDN18</em>, <em>CYP4B1</em>, <em>CYP4X1</em>, <em>FAM83A</em>, <em>HLF</em>, and <em>PLA2G1B</em>) demonstrating prognostic significance in the TCGA-LUAD cohort. Among these, <em>FAM83A</em> was particularly noteworthy for its amplification in LUAD samples and its negative correlation with immune cell infiltration. Functional enrichment analysis revealed key pathways, such as cytochrome P450 metabolism and cell–cell adhesion, which may be critical in LUAD progression. Our findings highlight <em>FAM83A</em> as a potential prognostic biomarker with significant implications for treatment strategies, especially concerning immune modulation. This study offers a more comprehensive insight into the molecular differences in LUAD in smokers and non-smokers and lays the groundwork for targeted therapies tailored to these subgroups.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100581"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145265931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microencapsulation of Annona crassiflora extract using maltodextrin: Material design and evaluation of antioxidant, antiglycation, and antiaging properties in vitro and in silico","authors":"Kamille Daleck Spera ,&nbsp;Pedro Henrique Gorni ,&nbsp;João Luiz Bronzel-Junior ,&nbsp;Filipe Oliveira Granero ,&nbsp;Célia Cristina Malaguti Figueiredo ,&nbsp;Hugo Henrique Santos ,&nbsp;Luciana Pereira Silva ,&nbsp;Patrizia Perego ,&nbsp;Paulo Eduardo Amaral Debiagi ,&nbsp;Nilson Nicolau-Junior ,&nbsp;Regildo Márcio Gonçalves da Silva","doi":"10.1016/j.jgeb.2025.100579","DOIUrl":"10.1016/j.jgeb.2025.100579","url":null,"abstract":"<div><div><em>Annona crassiflora</em>, a native Brazilian Cerrado fruit tree, is rich in bioactive compounds, particularly phenolic compounds and flavonoids, known for their antioxidant capabilities. The research addresses the limitations of seasonal fruit production by exploring the bioactive potential of leaves, aiming for sustainable harvesting practices. In view of this, the study aimed to investigate the antioxidant, antiglycation, and antiaging properties of <em>A. crassiflora</em> leaf extract (AcHE), exploring its potential for microencapsulation using maltodextrin. The methodology included the preparation of a hydroethanolic extract (AcHE) from <em>A. crassiflora</em> leaves, phytochemical analysis to determine total polyphenol, flavonoid, and tannin content using spectrophotometric techniques and GC–MS analysis. Antioxidant activity was assessed through DPPH radical scavenging, ferric ion reducing power (FRAP), inhibition of lipid peroxidation (TBARS assay), nitric oxide radical scavenging activity, and oxidative hemolysis tests. Antiglycation activity was evaluated by quantifying free amino groups using the OPA method in a glycation reaction mixture of bovine serum albumin (BSA) and ribose. The study showed the efficacy of AcHE in preventing oxidative stress, glycation, and premature aging, which are linked to chronic diseases. It also demonstrated the optimization of the microencapsulation process with maltodextrin, showing enhanced stability, bioavailability, and efficacy of the bioactive compounds present in <em>A. crassiflora</em> leaves for potential applications in the food, pharmaceutical, and cosmetic industries.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100579"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145265932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A metagenomic exploration of microbial distribution among the pond sediment, shrimp (Penaeus monodon) tissue and pond water: A special focus on nutrient cycling and shrimp viral pathogens","authors":"Avik Sarkar ,&nbsp;Rakesh Kr. Patra ,&nbsp;Mathavan Muthaiyan ,&nbsp;Ajoy Mallik","doi":"10.1016/j.jgeb.2025.100568","DOIUrl":"10.1016/j.jgeb.2025.100568","url":null,"abstract":"<div><div><em>Penaeus monodon</em>, a major shrimp species cultivated in Eastern Asia, has faced setbacks in aquaculture due to disease outbreaks. Metagenomic studies offer insights into the pond microbiome, revealing its critical roles in nutrient cycling, water quality, and disease control. This study investigated microbial communities in sediment, water, and shrimp samples from an aquaculture pond in Chaital, West Bengal, India. Shotgun metagenomic sequencing and bioinformatics analyses were used to assess taxonomic and functional profiles, focusing on nutrient cycling genes and viral populations. Sediments showed the highest microbial diversity, contributing to organic matter decomposition and ecological stability. Water microbes played roles in oxygenation and pathogen suppression, while shrimp tissues hosted microbes aiding digestion and immunity. Pathogenic viruses, especially Whispovirus (White Spot Syndrome Virus), dominated shrimp tissues. Functional gene analysis identified key pathways in carbon, nitrogen, and sulfur cycling. Integrating water quality data with microbiome profiles could help identify bioindicators and predict pathogen risks.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100568"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145019471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}