{"title":"Microbiological methodologies: Comparative evaluation of microbial community and enhanced antibiotic susceptibility testing","authors":"Sinethemba H. Yakobi, Uchechukwu U. Nwodo","doi":"10.1016/j.ejbt.2025.01.001","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><div>This study provides a comparative analysis of microbial community profiling and antibiotic susceptibility testing (AST) methodologies.</div></div><div><h3>Microbial community profiling</h3><div>Methods such as Shotgun Metagenomics and 16S rRNA sequencing were evaluated based on criteria including resolution, throughput, cost, and reproducibility. Shotgun Metagenomics was found to offer the highest resolution and detailed insights into microbial diversity, though at a higher cost and complexity. In contrast, 16S rRNA Sequencing provided a more cost-effective and high-throughput alternative, suitable for large-scale studies despite lower taxonomic resolution. Culturomics, while offering unique phenotypic data, showed variability in reproducibility and required more labor-intensive processes.</div></div><div><h3>Antibiotic susceptibility testing (AST)</h3><div>Traditional methods such as disk diffusion and broth microdilution were compared to emerging molecular and automated AST technologies. Traditional methods were noted for their precision in determining minimum inhibitory concentrations (MICs), crucial for guiding effective antimicrobial therapy. However, the emerging methods provided faster turnaround times and higher throughput, which are increasingly important in clinical settings focused on antimicrobial stewardship.</div></div><div><h3>Conclusions</h3><div>The study underscores the importance of selecting appropriate methodologies based on specific research or clinical needs, balancing factors such as cost, sensitivity, and throughput. The integration of multiple methodologies is recommended to overcome the limitations of individual techniques, providing a more comprehensive understanding of microbial ecosystems and resistance profiles. These findings are crucial for enhancing both research and clinical practices, particularly in the context of the global challenge posed by antimicrobial resistance.</div><div><strong>How to cite:</strong> Yakobi SH, Nwodo UU. Microbiological methodologies: Comparative evaluation of microbial community and enhanced antibiotic susceptibility testing. Electron J Biotechnol 2025;74. <span><span>https://doi.org/10.1016/j.ejbt.2025.01.001</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":11529,"journal":{"name":"Electronic Journal of Biotechnology","volume":"74 ","pages":"Pages 29-40"},"PeriodicalIF":2.3000,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Electronic Journal of Biotechnology","FirstCategoryId":"5","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0717345825000053","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Background
This study provides a comparative analysis of microbial community profiling and antibiotic susceptibility testing (AST) methodologies.
Microbial community profiling
Methods such as Shotgun Metagenomics and 16S rRNA sequencing were evaluated based on criteria including resolution, throughput, cost, and reproducibility. Shotgun Metagenomics was found to offer the highest resolution and detailed insights into microbial diversity, though at a higher cost and complexity. In contrast, 16S rRNA Sequencing provided a more cost-effective and high-throughput alternative, suitable for large-scale studies despite lower taxonomic resolution. Culturomics, while offering unique phenotypic data, showed variability in reproducibility and required more labor-intensive processes.
Antibiotic susceptibility testing (AST)
Traditional methods such as disk diffusion and broth microdilution were compared to emerging molecular and automated AST technologies. Traditional methods were noted for their precision in determining minimum inhibitory concentrations (MICs), crucial for guiding effective antimicrobial therapy. However, the emerging methods provided faster turnaround times and higher throughput, which are increasingly important in clinical settings focused on antimicrobial stewardship.
Conclusions
The study underscores the importance of selecting appropriate methodologies based on specific research or clinical needs, balancing factors such as cost, sensitivity, and throughput. The integration of multiple methodologies is recommended to overcome the limitations of individual techniques, providing a more comprehensive understanding of microbial ecosystems and resistance profiles. These findings are crucial for enhancing both research and clinical practices, particularly in the context of the global challenge posed by antimicrobial resistance.
How to cite: Yakobi SH, Nwodo UU. Microbiological methodologies: Comparative evaluation of microbial community and enhanced antibiotic susceptibility testing. Electron J Biotechnol 2025;74. https://doi.org/10.1016/j.ejbt.2025.01.001.
期刊介绍:
Electronic Journal of Biotechnology is an international scientific electronic journal, which publishes papers from all areas related to Biotechnology. It covers from molecular biology and the chemistry of biological processes to aquatic and earth environmental aspects, computational applications, policy and ethical issues directly related to Biotechnology.
The journal provides an effective way to publish research and review articles and short communications, video material, animation sequences and 3D are also accepted to support and enhance articles. The articles will be examined by a scientific committee and anonymous evaluators and published every two months in HTML and PDF formats (January 15th , March 15th, May 15th, July 15th, September 15th, November 15th).
The following areas are covered in the Journal:
• Animal Biotechnology
• Biofilms
• Bioinformatics
• Biomedicine
• Biopolicies of International Cooperation
• Biosafety
• Biotechnology Industry
• Biotechnology of Human Disorders
• Chemical Engineering
• Environmental Biotechnology
• Food Biotechnology
• Marine Biotechnology
• Microbial Biotechnology
• Molecular Biology and Genetics
•Nanobiotechnology
• Omics
• Plant Biotechnology
• Process Biotechnology
• Process Chemistry and Technology
• Tissue Engineering