Understanding Parkinson's: The microbiome and machine learning approach

Objective: Given that Parkinson's disease is a progressive disorder, with symptoms that worsen over time, our goal is to enhance the diagnosis of Parkinson's disease by utilizing machine learning techniques and microbiome analysis. The primary objective is to identify specific microbiome signatures that can reproducibly differentiate patients with Parkinson's disease from healthy controls.

Methods: We used four Parkinson-related datasets from the NCBI repository, focusing on stool samples. Then, we applied a DADA2-based script for amplicon sequence processing and the Recursive Ensemble Feature Selection (REF) algorithm for biomarker discovery. The discovery dataset was PRJEB14674, while PRJNA742875, PRJEB27564, and PRJNA594156 served as testing datasets. The Extra Trees classifier was used to validate the selected features.

Results: The Recursive Ensemble Feature Selection algorithm identified 84 features (Amplicon Sequence Variants) from the discovery dataset, achieving an accuracy of over 80%. The Extra Trees classifier demonstrated good diagnostic accuracy with an area under the receiver operating characteristic curve of 0.74. In the testing phase, the classifier achieved areas under the receiver operating characteristic curves of 0.64, 0.71, and 0.62 for the respective datasets, indicating sufficient to good diagnostic accuracy. The study identified several bacterial taxa associated with Parkinson's disease, such as Lactobacillus, Bifidobacterium, and Roseburia, which were increased in patients with the disease.

Conclusion: This study successfully identified microbiome signatures that can differentiate patients with Parkinson's disease from healthy controls across different datasets. These findings highlight the potential of integrating machine learning and microbiome analysis for the diagnosis of Parkinson's disease. However, further research is needed to validate these microbiome signatures and to explore their therapeutic implications in developing targeted treatments and diagnostics for Parkinson's disease.