Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients

Abstract

Background: Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker.

Methods: We performed metagenomic shotgun analyses and compared the fecal microbiomes of 31 early stage, L-DOPA-naïve PD patients to 28 age-matched controls.

Results: We found increased Verrucomicrobiaceae (Akkermansia muciniphila) and unclassified Firmicutes, whereas Prevotellaceae (Prevotella copri) and Erysipelotrichaceae (Eubacterium biforme) were markedly lowered in PD samples. The observed differences could reliably separate PD from control with a ROC-AUC of 0.84. Functional analyses of the metagenomes revealed differences in microbiota metabolism in PD involving the ẞ-glucuronate and tryptophan metabolism. While the abundances of prophages and plasmids did not differ between PD and controls, total virus abundance was decreased in PD participants. Based on our analyses, the intake of either a MAO inhibitor, amantadine, or a dopamine agonist (which in summary relates to 90% of PD patients) had no overall influence on taxa abundance or microbial functions.

Conclusions: Our data revealed differences of colonic microbiota and of microbiota metabolism between PD patients and controls at an unprecedented detail not achievable through 16S sequencing. The findings point to a yet unappreciated aspect of PD, possibly involving the intestinal barrier function and immune function in PD patients. The influence of the parkinsonian medication should be further investigated in the future in larger cohorts.

Keywords: Archaea; Bacteria; Enteric nervous system; Gut-brain axis; Microbiome; Parkinson; Viruses.

Fig. 1

Genus and species level differences in PD participants and controls. a NMDS ordination of all samples used in this study, using a Bray–Curtis between-sample distance at genus level. This shows the composition relatedness of samples and that PD samples form a subgroup. Outliers denoted with # took antibiotics in a period of 28–34 days prior to feces sampling. See also Additional file 2 for taxonomic analysis while taking these samples into account. b Genus-level sample composition. c The most significant species or groups of taxa that could not be further classified. Unclassified Prevotella is not significant after multiple testing, but was implied in PD in several studies (see “Discussion”). d Species correlating strongest to PD disease severity (as measured by UPDRS III). Note that after multiple testing correction, these are all q > 0.1

Fig. 2

Functional differences in PD patients based on selected metabolic pathways. a Phylum and (b) genus level composition of six modules that were increased/decreased in PD patients. c All genera were contributing to these modules as expected by random chance, with the exception of MF0065 and MF0118, where a higher than expected proportion of reads contributing could be traced to Eubacterium in PD patients

Fig. 3

Classification of PD participants based on their microbiome. Here the classifier selected a very similar set of features as were determined by univariate testing (Fig. 1). With only six genera, PD could be separated from control patients with an AUC of 0.84. The exact mOTU composition of each feature is given in Additional file 15

Fig. 4

Structural equation modeling (SEM). SEM analysis of PD in relation to key correlating bacterial functions and taxa (MSEA = 0, PCLOSE = 0.79, AIC = 59.385). Values on paths and boxes are standardized regression and determination coefficients (R2), respectively. Dashed lines and red colors denote negative relationships. The thickness of lines is proportional to regression coefficients. All relationships are statistically significant (P < 0.05, Additional file 5). AIC Akaike information criterion, MSEA mean square error of approximation, PCLOSE probability of close fit