Association between Parkinson’s disease and the faecal eukaryotic microbiota Original paper

What was studied?

This original research article investigated the composition of the faecal eukaryotic microbiota in patients with Parkinson’s disease (PD) compared to age-matched healthy controls. The study specifically focused on analysing the diversity and relative abundance of eukaryotic organisms—particularly fungi and protists—in the gut, using next-generation sequencing of the V6 and V7 regions of the eukaryotic 18S rRNA gene. The authors aimed to determine whether there are distinct eukaryotic microbiome signatures associated with PD, expanding on previous research that had primarily focused on bacterial dysbiosis. The research employed targeted amplicon sequencing on an Illumina MiSeq platform, followed by robust bioinformatics and statistical analyses to identify compositional differences and potential associations that may contribute to the pathobiology of PD.

Who was studied?

The study cohort comprised 34 German patients with idiopathic Parkinson’s disease (10 females, 24 males) and 25 age-matched healthy controls (14 females, 11 males). All participants followed an omnivorous European diet and had not taken antibiotics, probiotics, or prebiotics for at least three months before sampling. Subjects with acute or chronic gastrointestinal disorders were excluded. Faecal samples were collected using standardised protocols, ensuring the reliability of downstream molecular analyses. Ultimately, 18 PD samples (6 females, 12 males) and 18 control samples (10 females, 8 males) yielded sufficient DNA for successful eukaryotic amplicon sequencing, and these were included in the final analyses. The PD patients were diagnosed according to the UK PD Society Brain Bank Clinical Diagnostic Criteria, and relevant clinical metadata, including medication use (e.g., L-DOPA, entacapone), were available for subgroup analyses.

Most important findings

The study revealed that PD patients exhibited significantly reduced alpha diversity (Observed, Shannon, and Simpson indices) and altered beta diversity (weighted and unweighted UniFrac metrics) in their faecal eukaryotic microbiota compared to controls. The most striking microbiome signature was a markedly increased relative abundance of the fungal genus Geotrichum (mean 39.7% in PD vs. 0.05% in controls), identified predominantly as Geotrichum candidum. This difference persisted even after rigorous compositional data analysis (ANCOM-II), highlighting Geotrichum as a robust microbial marker associated with PD. In contrast, several taxa—including Aspergillus/Penicillium, Charophyta/Linum, Opisthokonta, Cercomonas, Heteromita, and certain zooflagellates—were found at significantly lower relative abundances in PD patients than in controls. Notably, no significant correlations were observed between Geotrichum abundance and bacterial genera from the same samples, suggesting a unique, fungus-specific signature rather than a coordinated shift with bacterial taxa. Medication subgroup analyses indicated that PD patients treated with L-DOPA or entacapone had particularly high levels of Geotrichum, although dietary and host factors could not be entirely excluded as contributors.

Table: Key Eukaryotic Taxa Differing Between Groups

Key implications

This study provides compelling evidence that the faecal eukaryotic microbiota—especially the fungal component—differs markedly in PD patients compared to healthy controls. The strong association of Geotrichum candidum with PD, along with reduced diversity and depletion of other eukaryotic taxa, suggests that eukaryotic gut dysbiosis may play a role in the pathogenesis or progression of PD. These findings highlight the potential utility of eukaryotic microbiome signatures (particularly fungal markers) in the development of diagnostic tools or as targets for future therapeutic interventions. Importantly, the results underscore the need to broaden microbiome research in neurodegenerative diseases beyond bacteria to include eukaryotic organisms. Further large-scale, multi-omics studies are warranted to elucidate causality, functional implications, and clinical relevance, as well as to account for confounding factors such as diet and medication.

Citation

Weis S, Meisner A, Schwiertz A, Unger MM, Becker A, Faßbender K, Schnell S, Schäfer K-H, Egert M. Association between Parkinson’s disease and the faecal eukaryotic microbiota. npj Parkinson’s Disease. 2021;7:101. doi:10.1038/s41531-021-00244-0