Parkinson’s disease (PD) is a debilitating neurodegenerative disorder thought to be caused by a combination of genetic and environmental factors. Although the presence of motor impairments primarily determine the diagnosis of PD (DeMaagd and Philip, 2015), a range of non-motor symptoms including impaired olfaction and gastrointestinal (GI) dysfunction may be present at the time of diagnosis, or even before the onset of motor manifestations. There is some evidence that some GI symptoms such as constipation may appear even decades before the development of the classic motor symptoms resulting from nigrostriatal dopaminergic neuronal death, suggesting the involvement of peripheral systems in the initial development and primary stages of PD. Given the interface between environmental factors and the GI tract, and its potential role in prodromal symptoms of the disease, research has increasingly focused on the gut microbiota as a potential regulator in the origin and pathogenesis of PD.

Evidence is accumulating of a bidirectional communication between the gut microbiome and the nervous system, allowing the modulation of brain activity, immunological function, and behavior based on the gut’s bacterial composition (Martin et al., 2018). Indeed, there is evidence that an unbalanced pro-inflammatory (“dysbiotic”) microbiota may adversely affect the host, resulting in disease (Schippa and Conte, 2014). Disruptions to the balanced ecosystem of the gut microbiota can result in increased inflammation in the GI tract, commonly presenting as GI symptoms. These disruptions may be triggered by factors including poor diet and exercise patterns, and chemical and pesticide exposure, which may increase the risk of developing PD (Nandipati and Litvan, 2016). Furthermore, a positive relationship between inflammatory bowel diseases (such as Ulcerative Colitis and Crohn’s disease) and PD risk has been reported in a number of populations, which are usually accompanied by proinflammatory changes to the gut microbiota (Lai et al., 2019; Villumsen et al., 2019). In response to microbial dysbiosis, disrupted intestinal barrier permeability and signaling may contribute to immune activation the formation of insoluble α-synuclein aggregates, a key pathological feature of PD.

It has been proposed that such α-synuclein aggregation first occurs in the peripheral and enteric nervous systems before spreading to the brain. Such retrograde spread of insoluble α-synuclein aggregates via the gut-brain axis has been previously been demonstrated in rodent models (Challis et al., 2020), and aggregation in these systems has been shown to associate with increased intestinal permeability and inflammation (Braak et al., 2003, 2006; Forsyth et al., 2011; Gorecki et al., 2019). Taken together this evidence raises the possibility that individuals who develop PD may undergo a proinflammatory shift in microbiota composition during the prodromal phases of developing the disease, coinciding with the earliest symptoms and pathological hallmarks appearing in the GI tract.

It is well established that the composition of the gut microbiome varies according to geographic location (Gaulke and Sharpton, 2018). However, as the influence of geographic location on the gut microbiome in PD has not been comprehensively investigated, it remains unknown whether some of the reported differences in the microbiome of affected individuals could be attributable to geographic factors, or are a commonality of the disease itself. To this end, comparative studies of the microbiome in people with Parkinson’s disease (PwP) from different geographical populations are of interest, in order to help solidify the knowledge surrounding the relationship between the gut microbiome and PD. So far, there have been only a few studies from the Southern hemisphere. A previous pilot study in a small PD cohort from our laboratory found that the relative abundance of mucin-degrading Verrucomicrobia and lipopolysaccharide-producing Gammaproteobacteria groups were increased in PwP (Gorecki et al., 2019). Recently, a comparative study of the gut microbiome in small groups of PwP undergoing device-assisted therapies has also been reported (Lubomski et al., 2021). In the Northern hemisphere, studies have documented significantly altered levels of various bacterial taxa, predominantly a decrease in the family Bacteroidetes (Prevotellaceae), and Phyla Firmicutes (Clostridiaceae, clostridium and butyricicoccus spp.; Lachnospiraceae, Blautia, dorea, roseburia, and coprococcus spp.,; Ruminococcaceae, Faecalibacterium spp.) (Keshavarzian et al., 2015; Bedarf et al., 2017; Petrov et al., 2017; Heintz-Buschart et al., 2018; Cirstea et al., 2020). Together, the reduction in these bacterial taxa and shift in microbiome composition are hypothesized to be a cause of increased intestinal permeability and inflammation, leading to the prodromal GI symptoms reported in the majority of PwP.

In this more comprehensive study we have investigated the role of the gut microbiome in PD by combining 16S rRNA sequencing and functional predictions of alterations in host metabolic pathways in a larger multicentre Australian cohort.

In view of the known geographic influences on the composition of the gut microbiome, there is an important need to explore this to further understanding of the role of the gut microbiome in Parkinson’s disease (PD). Previous studies investigating the relationship between the gut microbiome and PD have not comprehensively investigated populations in the southern hemisphere, thus it was unknown whether PwP had differences in their gut microbiome similar to that reported in existing literature. In this study we used 16S rRNA sequencing followed by KEGG analysis to investigate the differences in the gut microbiota and resulting changes in metabolic pathways between PwP and controls. Our findings demonstrate that the gut microbiota, and 26 associated metabolic pathways, are significantly altered in Australian PwP compared to non-affected individuals.

Firstly, alpha diversity analysis indicated a reduced richness and diversity within the PwP cohort in comparison to the control cohort. A reduced alpha diversity has also been reported in Alzheimer’s Disease (Vogt et al., 2017), gastrointestinal disorders (Saffouri et al., 2019), and obesity (Stanislawski et al., 2019). The overall microbiome composition of both PwP and controls were predominated by Firmicutes (Controls: 63.6%, PwP: 56.8%), which is reported frequently in individuals who consume a Western diet (Nandipati and Litvan, 2016) such as that in Australia. As noted in our previous preliminary study, the abundance of the phylum Verrucomicrobia was greater than double in PwP (Controls: 4.25 vs. PwP: 10.5%), which has been reported to populate a healthy individual’s microbiota from 1–5% (Roy, 2017). Importantly, Verrucomicrobia are mucin-degrading bacteria (Gorecki et al., 2019), thus it is plausible that their dominance could contribute to an increase in intestinal permeability and inflammation. Significant bacterial differences were identified more broadly in two phyla, three classes, two orders, three families, and five genera in PwP when compared to non-affected individuals (see Figure 2). In the present study we report comparable findings to previous studies from the Northern hemisphere in regard to changes in gut microbiota composition, with increases in the pro-inflammatory bacterial phyla Proteobacteria (Gammaproteobacteria, Enterobacterales, and Enterobacteriaceae), and decreases in commensal bacteria Clostridia, from the Firmicutes phylum (Keshavarzian et al., 2015; Scheperjans et al., 2015; Sampson et al., 2016; Unger et al., 2016; Hill-Burns et al., 2017; Hopfner et al., 2017; Li et al., 2017; Petrov et al., 2017; Heintz-Buschart et al., 2018; Qian et al., 2018; Aho et al., 2019; Gorecki et al., 2019; Li et al., 2019; Pietrucci et al., 2019; Weis et al., 2019). Within our results, Lachnospiraceae and its related genera were decreased in PwP. This bacterial family is generally considered a significant producer of anti-inflammatory short chain fatty acids (SCFA) and are associated with a healthy functioning gut (Wong et al., 2006). Low levels of the Lachnospiraceae family have also been reported previously in individuals with diarrhea, Crohn’s disease and ulcerative colitis (Flint et al., 2012; Donaldson et al., 2016). Of particular interest are the genera Roseburia and Agathobaculum which were also both significantly reduced in our PwP cohort. Both of these bacterial genera are producers of the SCFA butyrate that has demonstrated protective effects on dopaminergic cell death, and reduced motor impairments and dopamine deficiency when administered in animal models of PD (St Laurent et al., 2013; Paiva et al., 2017; Getachew et al., 2020). Furthermore, butyrate also regulates the permeability of the gut through the stimulation of tight junctions and mucus production (Getachew et al., 2020), and promotes an acidic gut pH which reduces the growth of pathogenic pro-inflammatory bacteria (Walker et al., 2005). The reduction in Agathobaculum, which exhibits effects on gut motility regulating ability, could be a contributory factor to the increased severity and frequency of GI dysmotility symptoms in this particular cohort (Kenna et al., 2021), as well as other PwP cohorts (Kaye et al., 2006; Knudsen et al., 2017; Li et al., 2019; Cirstea et al., 2020). On the other hand, Gammaproteobacteria, a pro-inflammatory bacterium that produces endotoxins and is associated with GI disorders such as Crohn’s disease (Sekido et al., 2020), and Synergistetes (Synergistia) a bacterium involved in GI infections (Vartoukian et al., 2007), were significantly increased in our PwP cohort. Together, these findings support a significantly altered, pro-inflammatory gut microbiome in PwP.

The functional implications of such changes within the gut microbiome between diseased and non-affected control populations have not been adequately investigated and remain a significant challenge within the field of PD and wider microbiome research. To this end, in the present study we combined the compositional 16S microbiota analysis with computational KEGG modeling to gain insight into the functional effects of the changed microbial abundances in PwP, and their significance in understanding the interaction between the gut microbiome and PD. Of the 26 significantly altered pathways (see Figure 3), two downregulated pathways were involved in primary and secondary bile acid biosynthesis. Primary bile acids are synthesized in the liver and secondary bile acids are synthesized in the colon as a result of microbial activity (Ridlon et al., 2016). Bile acids eliminate cholesterol from the body (Ticho et al., 2019), aid GI motility (Ticho et al., 2019), and reduce the bacteria found in the small intestine (Ridlon et al., 2014). This corresponds with previous research indicating constipation as one of the first symptoms in PD and identifying that PwP are more likely to be constipated than the general public (Kenna et al., 2021). Another interesting implication of this finding would help explain the increased prevalence of small intestinal bacterial overgrowth (SIBO) in PwP, as the reduced biosynthesis of bile acids would diminish the capacity to moderate bacterial populations in the small intestine. In relation to the downregulation of secondary bile acid biosynthesis in PwP, it has been suggested that this pathway is dependent on a “microbial community” (Schmidt et al., 2010), thus we postulate that this may be ensuing from the reduced gut microbial diversity demonstrated in this cohort of PwP. Although not conclusive, recent studies suggest a loss of HDL cholesterol is associated with an increased inflammatory response and increased risk of developing neurodegenerative disorders like PD (Pes et al., 2021). Although we did not measure HDL levels within our cohort, it presents as a promising area of interest for future exploration. Furthermore, as previous studies have suggested that bile acids are protective in animal models of neurodegeneration, protecting against mitochondrial damage specifically in PD (Abdelkader et al., 2016), and having other effects in Alzheimer’s disease (Nunes et al., 2012) and amyotrophic lateral sclerosis (Elia et al., 2016) models, this mechanism warrants further investigation in relation to its role in PD pathophysiology.

Seven of the significantly altered metabolic pathways involve amino acid degradation or metabolism, and ones of particular interest were alanine, valine and tryptophan. Overall, amino acid biosynthesis was predicted to decrease and metabolism to increase. Defects in the metabolism of amino acids valine, leucine or isoleucine can produce motor dysfunction and neurodegeneration (Mor et al., 2020), recapitulating major features of PD, and suggesting that normal amino acid metabolism is critical for normal physiological and biological functioning. Environmental alanine exposure has been associated with neurodegenerative disorders, however, this hypothesis does require further verification (Figura et al., 2018). Alanine has also been shown to break down tryptophan, thus the exhibited decrease in metabolism of alanine corresponds with the demonstrated increase in metabolism of tryptophan within our cohort of PwP. Although we did not see an association between PD medication and the gut microbiota in our cohort, it is important to note that literature is currently investigating the possible effect levodopa has on decreasing tryptophan metabolism via the serotonergic system (Stansley and Yamamoto, 2015), therefore highlighting this as something to consider in further studies.

Accelerated tryptophan metabolism has commonly been considered as a feature of clinical ailments such as inflammation, infection and malignant disease (Gostner et al., 2020), especially IBD (Nikolaus et al., 2017), which as we have previously discussed also increases the risk of developing PD (Lai et al., 2019; Villumsen et al., 2019). Metabolites of tryptophan metabolism are hypothesized to extensively influence systemic inflammation as well as blood brain barrier permeability (Szabo et al., 2011). These results align with previous studies reporting increased catabolites of tryptophan in PwP which related to disturbances in mitochondrial function and brain energy metabolism involved in the development of neurodegenerative diseases (Szabo et al., 2011; Luan et al., 2015). Tryptophan metabolism is also involved with the formation of neurotransmitters such as serotonin and melatonin. IDO-1 is a tryptophan degrading enzyme which recognizes serotonin as a substrate, and the predicted increase in tryptophan metabolism may suggest increased IDO-1 activity. Interestingly, increased IDO-1 activity has been reported to contribute to mood-lowering (Gostner et al., 2020), which is a common comorbidity reported in PwP. Fittingly, 95% of serotonin is synthesized and stored in the GI tract, where it modulates GI secretion and motility. Thus, an increase in IDO-1 activity may reduce the amount of serotonin in the gut, possibly underlying the decreased motility previously reported in this cohort of PwP (Kenna et al., 2021). Melatonin is also a by-product of the serotonin pathway, and as it is predicted that serotonin levels are depleted in PwP, the increased prevalence of sleep disorders in PwP (Suzuki et al., 2011) could be due to a decreased level of melatonin. It is also important to mention that as aging is associated with decreased tryptophan concentration (Capuron et al., 2014), it could be a commonality among an older population. However, as our analyses controlled for age, this potential variable has been mitigated in this study. Nevertheless, amino acids and their associated metabolic pathways present as a promising target for future therapeutic research in PD.

For decades, exposure to environmental toxins has been a proposed risk factor for the development of PD (Nandipati and Litvan, 2016). Accordingly, three pathways involved in toxin degradation were predicted to be significantly increased in PwP in this study: Caprolactam degradation, Selenocompound metabolism, and Nitrotoluene degradation. Despite selenium being an essential nutritional element, excessive levels cause toxicity and adverse effects (Rayman, 2020), with previous studies demonstrating links between elevated selenium levels in PwP and increased PD mortality (Ellwanger et al., 2016; Adani et al., 2020). Another compound of interest is nitrotoluene which is primarily used in dyes for cotton, wool, silk, leather and paper, and the synthesis of explosives, organic chemicals, pesticides, petrochemicals and pharmaceuticals [National Toxicology Program (NTP), 2016], exposure to which can detrimentally modify the microbiome into a pro-inflammatory state. Both compounds are indicated as human carcinogens, thus exposure can be very detrimental to health. Interestingly, literature suggests that GI microbial composition plays an obligatory role in toxin degradation and toxicity (Claus et al., 2016), thus it is plausible that individuals who develop PD may be predisposed to a gut microbiome that has reduced capacity to degrade toxins, or one that is predisposed to succumb more rapidly to toxicity.

Finally, three pathways that were predicted to be upregulated in PwP are known to be involved in the virulence of pathogenic bacteria. The biosynthesis of “siderophore group NRPS,” which is involved in ferritin acquisition for growth and proliferation, has been shown to be a crucial factor in determining the virulence of many pathogenic bacterial and fungal species (Carroll and Moore, 2018). In addition, the “bacterial secretion system” pathway is responsible for secreting virulence factors into the host; and the “bacterial invasion of epithelial cells” pathway, whereby pathogenic bacteria induce colonization, followed by dissemination into other cells (Ribet and Cossart, 2015). Together, the upregulation of these pathways is compatible with a cycle in which pathogenic bacteria are undergoing proliferation and dissemination, and thus, may explain the dysbiotic microbiome evident in PwP.

The current study provides the first comprehensive characterization of the gut microbiome in Australian PwP. It is important to note, a limitation of this study is the small proportion of drug-naïve PwP in this cohort, and thus the inability for further group comparisons to exclude the effects of drug treatment. In addition, the temporal changes within the gut microbiota could not be considered in this cross-sectional study, which requires a longitudinal study design allowing for the effects of confounding variables (such as diet and exercise). While it is clear that additional studies are required to elucidate the complex role of the gut microbiota and how they influence host functional pathways in PwP, the results of the present study illuminate a number of areas of interest that present as promising targets to be further explored. Firstly, as many of the pathways which are predicted to be significantly affected in PwP have an involvement with the immune system, such as adverse effects of low lysine levels on the production of immune cells and the role of alanine in strengthening the immune system, it would be of interest to investigate the relationship between changes in the gut microbiome and various immune components at different stages of disease progression in future studies. Secondly, as bacteria are not the only constituents of the gut microbiome, and the fungi, viruses and protozoa in the gut microbiome are known to influence the bacterial composition of the gut microbiota, it will be important to investigate the changes in these other components of the gut microbial “ecosystem” in PD. This is an area of human gut microbiome research that is currently understudied, with only a single study to date looking at 18S fungal sequencing in PD (Heintz-Buschart et al., 2018). Lastly, to better understand the interaction between factors underlying PD pathophysiology, integrating various approaches such as microbiome and dietary analysis, metabolomics and computational biology approaches is likely to help identify key interactions in an unbiased manner. Such approaches could also be individualized to determine the effects of different anti- parkinsonian medications, and possibly to help predict optimal treatment routes and treatment responses. As the prevalence of PD is rapidly rising (Rocca, 2018), investigations into the pathophysiological underpinnings of the disease are increasing in demand, and findings are urgently required.

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://figshare.com/, https://doi.org/10.6084/m9.figshare.14345513.

The studies involving human participants were reviewed and approved by The University of Western Australia Human Research Ethics Committee RA/4/20/4470, and St Vincent’s Hospital Melbourne Human Research Ethics Committee LRR137/18. The patients/participants provided their written informed consent to participate in this study.

JK: conception, organization, and execution of the research project, design, execution, and review and critique of the statistical analysis, and writing of the first draft and review and critique of manuscript preparation. EC: design and execution of statistical analysis and writing of the first draft and review and critique of manuscript preparation. MB: execution of research project, review and critique of statistical analysis, and review and critique of the manuscript preparation. AT: organization and execution of research project and review and critique of manuscript preparation. SM: organization and execution of research project. AG: review and critique of statistical analysis and review and critique of manuscript preparation. MH: organization and execution of research project and review and critique of manuscript preparation. BM: organization and execution of research project. FM: conception of research project, review and critique of statistical analysis, and writing of the first draft and review and critique of manuscript preparation. RA: conception and organization of research project, design, execution, review and critique of statistical analysis, and writing of the first draft and review and critique of manuscript preparation. All authors contributed to the article and approved the submitted version.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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