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Taherkhani H, KavianFar A, Aminnezhad S, Lanjanian H, Ahmadi A, Azimzadeh S, Masoudi-Nejad A. Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome. Heliyon 2024; 10:e24775. [PMID: 38370212 PMCID: PMC10869780 DOI: 10.1016/j.heliyon.2024.e24775] [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: 06/27/2023] [Revised: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 02/20/2024] Open
Abstract
In microbiome studies, the diversity and types of microbes have been extensively explored; however, the significance of microbial ecology is equally paramount. The comprehension of metabolic interactions among the wide array of microorganisms in the lung microbiota is indispensable for understanding chronic pulmonary disease and for the development of potent treatments. In this investigation, metabolic networks were simulated, and ecological theory was employed to assess the diagnosis of COPD, subsequently suggesting innovative treatment strategies for COPD exacerbation. Lung sputum 16S rRNA paired-end data from 112 COPD patients were utilized, and a supervised machine-learning algorithm was applied to identify taxa associated with sex and mortality. Subsequently, an OTU table with Greengenes 99 % dataset was generated. Finally, the interactions between bacterial species were analyzed using a simulated metabolic network. A total of 1781 OTUs and 1740 bacteria at the genus level were identified. We employed an additional dataset to validate our analyses. Notably, among the more abundant genera, Pseudomonas was detected in females, while Lactobacillus was detected in males. Additionally, a decrease in bacterial diversity was observed during COPD exacerbation, and mortality was associated with the high abundance of the Staphylococcus and Pseudomonas genera. Moreover, an increase in Proteobacteria abundance was observed during COPD exacerbations. In contrast, COPD patients exhibited decreased levels of Firmicutes and Bacteroidetes. Significant connections between microbial ecology and bacterial diversity in COPD patients were discovered, highlighting the critical role of microbial ecology in the understanding of COPD. Through the simulation of metabolic interactions among bacteria, the observed dysbiosis in COPD was elucidated. Furthermore, the prominence of anaerobic bacteria in COPD patients was revealed to be influenced by parasitic relationships. These findings have the potential to contribute to improved clinical management strategies for COPD patients.
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Affiliation(s)
- Hamidreza Taherkhani
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Azadeh KavianFar
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Sargol Aminnezhad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hossein Lanjanian
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Tehran, Iran
| | - Sadegh Azimzadeh
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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