Research Article: The oral microbiome of early stage Parkinson’s disease and its relationship with functional measures of motor and non-motor function

Date Published: June 27, 2019

Publisher: Public Library of Science

Author(s): Dragos Mihaila, Jordan Donegan, Sarah Barns, Daria LaRocca, Qian Du, Danny Zheng, Michael Vidal, Christopher Neville, Richard Uhlig, Frank A. Middleton, Brenda A Wilson.


Changes in the function and microbiome of the upper and lower gastrointestinal tract have been documented in Parkinson’s disease (PD), although most studies have examined merely fecal microbiome profiles and patients with advanced disease states. In the present study we sought to identify sensitive and specific biomarkers of changes in the oral microbiome of early stage PD through shotgun metatranscriptomic profiling. We recruited 48 PD subjects and 36 age- and gender-matched healthy controls. Subjects completed detailed assessments of motor, cognitive, balance, autonomic and chemosensory (smell and taste) functions to determine their disease stage. We also obtained a saliva sample for profiling of microbial RNA and host mRNA using next generation sequencing. We found no differences in overall alpha and beta diversity between subject groups. However, changes in specific microbial taxa were observed, including primarily bacteria, but also yeast and phage. Nearly half of our findings were consistent with prior studies in the field obtained through profiling of fecal samples, with others representing highly novel candidates for detection of early stage PD. Testing of the diagnostic utility of the microbiome data revealed potentially robust performance with as few as 11 taxonomic features achieving a cross-validated area under the ROC curve of 0.90 and overall accuracy of 84.5%. Bioinformatic analysis of 167 different metabolic pathways supported shifts in a small set of distinct pathways involved in amino acid and energy metabolism among the organisms comprising the oral microbiome. In parallel with the microbial analysis, we also examined the evidence for changes in human salivary mRNAs in the same subjects. This revealed significant changes in a set of 9 host mRNAs, several of which mapped to various brain functions and showed correlations with some of the significantly changed microbial taxa. Unexpectedly, we also observed robust correlations between many of the microbiota and functional measures, including those reflecting cognition, balance, and disease duration. These results suggest that the oral microbiome may represent a highly-accessible and informative microenvironment that offers new insights in the pathophysiology of early stage PD.

Partial Text

The etiology of Parkinson’s Disease (PD) is complex. Many factors, including genes, lifestyle, age, sex and even epigenetic factors are all known to affect the risk of PD and its progression [1–3]. Historically, most studies on the etiology of PD have focused on factors that influence midbrain dopaminergic neurons and their projections to the striatum (reviewed in [4]). Over the past decade, however, it has become increasingly clear that disturbances and pathology within the upper and lower gastrointestinal (GI) system in PD actually precede the pathology in the central nervous system (CNS)[1, 4–6]. Specifically, according to Braak and colleagues [5, 7] the submandibular salivary gland and lower esophagus appear to have a high frequency of alpha-synuclein associated Lewy Body (LB) pathology, followed by the stomach, small intestine and colon. Moreover, submandibular biopsy specimens from living PD subjects have also been recently reported to contain LBs [8, 9]. Notably, the appearance of LBs in these sites is thought to coincide with symptoms of GI dysfunction before the onset of motor symptoms in a large proportion of PD subjects, a feature that has also been seen in mouse and non-human primate models of PD [10].

The present study was focused on defining differences in the oral microbiome in early stage PD as determined from shotgun RNA sequencing of saliva samples combined with detailed phenotypic characterization of subjects. We have eight principal findings. First, even in early stage PD, with most subjects on some form of anti-parkinsonian medication, we found evidence of significant (and often highly robust) decreases in balance, sensory, motor and cognitive function. Second, there was no evidence of overall changes in alpha or beta diversity in early stage PD compared with controls. Third, a distinct set of microbial taxa demonstrated consistent changes in sequence abundance at the genus or species level after appropriate correction for multiple testing. Moreover, approximately half of these observed changes fell into clusters of species within the same genera. Fourth, when considered as potential classifiers in a multivariate logistic regression analysis, as few as 11 taxa were found to be capable of distinguishing early stage PD subjects from controls with a 10-fold cross-validated AUC of 0.90 and overall accuracy of 84.5%. Fifth, metabolic pathway analysis of the microbial transcript abundance revealed changes in a distinct subset of biological networks, several of which were highly-related to each other. Sixth, a dual transcriptome analysis revealed strong evidence for changes in abundance of a small set of human mRNAs in PD subjects, many of which are involved in brain or neural functions. Seventh, some of the changes in human mRNAs are significantly correlated with the observed microbial changes. And eighth, exploratory analyses indicated the presence of highly significant correlations between specific microbiota and specific subsets of functional measures, including a robust correlation between one of the significantly changed taxons and one of the changed functional measures. In the space that follows, we briefly discuss the importance of these observations.

There are several limitations worth noting in the present study. First, although the study was moderate in size relative to prior studies in the field, and was focused on early stage PD, it still did not have adequate representation of unmedicated subjects to fully evaluate the consequences of different medications on the outcomes. Second, the results that are described are based on shotgun metatranscriptomic profiling of the oral microbiome which makes direct comparisons with previously published data derived from 16S PCR based approaches somewhat difficult, since 16S reads comprise only a fraction of the available reads for genetic diversity analysis. Third, although the study appears to identify a distinct subset of microbiota that can accurately distinguish early stage PD and control subjects, the true utility of an oral microbiome profile will require establishing the validity of microbiome comparisons between early stage PD subjects and subjects with diagnoses that are commonly confused with or overlap the symptoms of PD, including progressive supranuclear palsy, essential tremor, and multiple system atrophy. Finally, we only quantified the oral microbiome on a single occasion, and it would be very interesting to learn the extent to which dietary and lifestyle factors influence the stability of the outcome. Plans for future studies to address these concerns are currently underway.