Deciphering Antibiotic-Targeted Metabolic Pathways in Acinetobacter baumannii: Insights from Transcriptomics and Genome-Scale Metabolic Modeling
Abstract
:1. Introduction
2. Materials and Methods
2.1. Transcriptomic Data Collection and Analysis
2.2. Genome-Scale Metabolic Modeling for Transcriptome Mapping
2.3. KEGG-Based Pathway Enrichment Analysis
2.4. Reporter Metabolite Analysis
3. Results
3.1. Sample-Specific iMAT-Based Metabolic Models from RNA-Seq Data
3.2. Enriched Metabolic Pathways across Different Antibiotics
3.3. Key Findings from the Reporter Metabolite Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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GEO Dataset | A. baumannii Strain | Number of Samples Used in This Study |
---|---|---|
GSE56222 | 1207552 | 18 |
GSE56223 | 1428368 | 18 |
GSE56224 | 1457504 | 18 |
GSE56218 | 34654 | 18 |
GSE56219 | 478810 | 18 |
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Sarı, F.Z.; Çakır, T. Deciphering Antibiotic-Targeted Metabolic Pathways in Acinetobacter baumannii: Insights from Transcriptomics and Genome-Scale Metabolic Modeling. Life 2024, 14, 1102. https://doi.org/10.3390/life14091102
Sarı FZ, Çakır T. Deciphering Antibiotic-Targeted Metabolic Pathways in Acinetobacter baumannii: Insights from Transcriptomics and Genome-Scale Metabolic Modeling. Life. 2024; 14(9):1102. https://doi.org/10.3390/life14091102
Chicago/Turabian StyleSarı, Fatma Zehra, and Tunahan Çakır. 2024. "Deciphering Antibiotic-Targeted Metabolic Pathways in Acinetobacter baumannii: Insights from Transcriptomics and Genome-Scale Metabolic Modeling" Life 14, no. 9: 1102. https://doi.org/10.3390/life14091102