Functional & Taxonomic Identification of Microbial Inflammation in COVID-19 & Parkinson’s Disease: A Metagenomic Analysis

Abstract

Past metagenomic research links disruptions in the gut microbiome to various inflammatory and neurological conditions, including Parkinson’s disease (PD). Recent studies show that PD and SARS-CoV-2 (COVID-19) infections are associated with decreased microbial diversity, altered renin-angiotensin system (RAS) signaling, and increased oxidative stress. This thesis hypothesized a shared dysbiotic signature between these conditions and sought to identify overlaps relative to neurologically healthy controls (NHC). A metagenomic analysis of publicly available datasets from Wallen et al., 2022 (PRJNA834801), and Nguyen et al., 2023 (PRJNA976404) was performed to characterize microbial taxonomy (MetaPhlAn2), functional pathways (HUMAnN2), and to identify statistical biomarkers (QIIME2, MaAsLin2). The goal was to compare PD and COVID-19 metagenomes. Contrary to the initial hypothesis, results revealed distinct, independent microbial signatures. The COVID-19 group showed significant taxonomic imbalance, with increased alpha diversity, lower levels of beneficial bacteria, and higher levels of opportunistic bacteria. In contrast, the PD group's microbiome was similar to that of the NHC group, both taxonomically and functionally. Despite notable taxonomic shifts in COVID-19, functional diversity remained stable across all groups, indicating high functional redundancy. Although no standard inflammatory profile was identified, this study provides a robust workflow for the computational analysis of metagenomic data.