Researchers at Qingdao University have developed a novel algorithm, Microbiome Elastic Feature Extraction (MEFE), that significantly improves the identification of microbiome biomarkers by incorporating phylogenetic, taxonomic, and functional relationships among microbes.

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This advancement addresses longstanding challenges in microbiome research, such as data sparsity and sequencing errors, potentially leading to more accurate disease diagnostics and personalized medicine. The findings were published on 15 January 2026 in Frontiers of Computer Science.

Traditional methods for identifying microbiome biomarkers often struggle with high false positive and negative rates due to the complex nature of microbial communities and technical limitations in sequencing.

MEFE tackles these issues by elastically integrating the abundance information of a microbe with that of its closely related neighbors, based on evolutionary and functional similarities. This approach allows for a more robust and biologically meaningful identification of biomarkers, enhancing the understanding of microbe-disease associations.

Diverse datasets 

The research team evaluated MEFE using both synthetic and real-world 16S rRNA gene sequencing datasets, including samples related to Autism Spectrum Disorder and Type-2 Diabetes. Results showed that MEFE outperformed existing methods in accurately identifying relevant microbial signatures, reducing both false positives and negatives. Analyses such as Principal Coordinate Analysis and Random Forest classification further confirmed MEFE’s superior discriminative power.

By effectively capturing the complex relationships within microbial communities, MEFE offers a powerful tool for advancing microbiome research. Its ability to provide more accurate biomarker identification holds promise for improving disease diagnostics, informing personalized treatment strategies, and contributing to ecological conservation efforts.

The MEFE algorithm is implemented in Python and is freely available at: https://github.com/qdu-bioinfo/MEFE.

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