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- Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization
- Jung Wook Kim, Eun Chae Choi, Kwang Jun Lee
- Received November 14, 2024 Accepted March 6, 2025 Published online April 11, 2025
- DOI: https://doi.org/10.24171/j.phrp.2024.0319 [Epub ahead of print]
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Abstract
PDF - Objectives
This study presents the standardized protocols developed by the Clinical-Based Human Microbiome Research and Development Project (cHMP) in the Republic of Korea.
Methods
It addresses clinical metadata collection, specimen handling, DNA extraction, sequencing methods, and quality control measures for microbiome research.
Results
The cHMP involves collecting samples from healthy individuals and patients across various body sites, including the gastrointestinal tract, oral cavity, respiratory system, urogenital tract, and skin. These standardized procedures ensure consistent data quality through controlled specimen collection, storage, transportation, DNA extraction, and sequencing. Sequencing encompasses both amplicon and whole metagenome methods, followed by stringent quality checks. The protocols conform to international guidelines, ensuring that the data generated are both reliable and comparable across microbiome studies.
Conclusion
The cHMP underscores the importance of methodological standardization in enhancing data integrity, reproducibility, and advancing microbiome-based research with potential applications for improving human health outcomes.
Original Article
- A retrospective study on blood microbiota as a marker for cognitive decline: implications for detecting Alzheimer’s disease and amnestic mild cognitive impairment in Republic of Korea
- Youngchan Park, Jong-Young Lee, Eek-Sung Lee
- Osong Public Health Res Perspect. 2025;16(2):141-151. Published online March 24, 2025
- DOI: https://doi.org/10.24171/j.phrp.2024.0329
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Graphical Abstract
Abstract
PDF 
- Objectives
This study aimed to investigate the relationship between blood microbiota, specifically bacterial DNA, and cognitive decline in individuals with subjective cognitive decline (SCD) and amnestic mild cognitive impairment (aMCI). The objective was to identify potential microbial signatures that could serve as biomarkers for cognitive deterioration. Methods: Forty-seven participants were recruited, including 13 with aMCI, 20 with SCD, and 14 normal cognition (NC). Blood samples were collected, and microbial DNA was analyzed using 16S rRNA sequencing on the Illumina MiSeq platform. Bioinformatics analyses—including α- and β-diversity measures and differential abundance testing (using edgeR)—were employed to assess microbial diversity and differences in bacterial composition among groups. Logistic regression models were used to evaluate the predictive impact of the microbiota on cognitive decline. Results: Microbial diversity differed significantly between groups, with NC exhibiting the highest α-diversity. Both the aMCI and SCD groups showed reduced diversity. Taxa such as Bacteroidia, Alphaproteobacteria, and Clostridia were significantly decreased in the aMCI group compared to NC (p< 0.05). In contrast, Gammaproteobacteria increased significantly in the aMCI group compared to both NC and SCD, indicating progressive microbial changes from SCD to aMCI. No significant differences were found between the NC and SCD groups. Conclusion: Distinct bacterial taxa—particularly the increase in Gammaproteobacteria along with decreases in Bacteroidia, Alphaproteobacteria, and Clostridia—are associated with the progression of cognitive decline. These findings suggest that blood microbiota could serve as potential biomarkers for the early detection of aMCI. However, the small sample size and the lack of control for confounding factors such as diet and medication limit the findings. Larger studies are needed to validate these results and further explore the role of microbiota in neurodegeneration.
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