Gut bacterial tyrosine decarboxylase associates with clinical variables in a longitudinal cohort study of Parkinsons disease

Gut microbiota influences the clinical response of a wide variety of orally administered drugs. However, the underlying mechanisms through which drug–microbiota interactions occur are still obscure. Previously, we reported that tyrosine decarboxylating (TDC) bacteria may restrict the levels of levodopa reaching circulation in patients with Parkinson’s disease (PD). We observed a significant positive association between disease duration and the abundance of the bacterial tdc-gene. The question arises whether increased exposure to anti-PD medication could affect the abundance of bacterial TDC, to ultimately impact drug efficacy. To this end, we investigated the potential association between anti-PD drug exposure and bacterial tdc-gene abundance over a period of 2 years in a longitudinal cohort of PD patients and healthy controls. Our data reveal significant associations between tdc-gene abundance, several anti-PD medications, including entacapone, rasagiline, pramipexole, and ropinirole but not levodopa, and gastrointestinal symptoms, warranting further research on the effect of anti-PD medication on microbial changes and gastrointestinal function.

D D The exact sample size (n) for each experimental group/condition, given as a discrete number and unit of measurement D D A statement on whether measurements were taken from distinct samples or whether the same sample was measured repeatedly D D The statistical test(s) used AND whether they are one-or two-sided Only common tests should be described solely by name; describe more complex techniques in the Methods section.

D D
A description of all covariates tested D D A description of any assumptions or corrections, such as tests of normality and adjustment for multiple comparisons D D A full description of the statistical parameters including central tendency (e.g. means) or other basic estimates (e.g. regression coefficient) AND variation (e.g. standard deviation) or associated estimates of uncertainty (e.g. confidence intervals)

□□ □□ □□ □□
For null hypothesis testing, the test statistic (e.g. F, t, r) with confidence intervals, effect sizes, degrees of freedom and P value noted

Software and code
Policy information about availability of computer code Data collection

Data analysis
For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. We strongly encourage code deposition in a community repository (e.g. GitHub). See the Nature Portfolio guidelines for submitting code & software for further information.

Data
Policy information about availability of data All manuscripts must include a data availability statement. This statement should provide the following information, where applicable: -Accession codes, unique identifiers, or web links for publicly available datasets -A description of any restrictions on data availability -For clinical datasets or third party data, please ensure that the statement adheres to our QQ!ky_ The p-value adjustments were performed in R version 4.0.0 using p.adjust (p-values, "fdr"). The qPCR data were tested for outliers per group and time point using the ROUT method (Q=0.1%) in GraphPad Prism v7 and the identified outliers were removed. Outlier removal was restricted to the qPCR data only. All variables were tested for normality using Kolmogorov-Smirnov and Shapiro-Wilk tests using the Explore function in SPSS. Based on the distribution of data, the differences were tested using the appropriate statistical tests. The group sizes and appropriate statistical tests are indicated in the tables. The general linear models (GLMs) were performed using the Generalized Linear Models function, the main effects were tested using the Wald Chi Square test. Additionally, the variance inflation factor (VIF) was computed to check for potential collinearity between variables Clinical data are not publicly available due to participant privacy and are available from the corresponding authors

Field-specific reporting
Please select the one below that is the best fit for your research. If you are not sure, read the appropriate sections before making your selection.

D Life sciences D Behavioural & social sciences D Ecological, evolutionary & environmental sciences
For a reference copy of the document with all sections, see nature.com/documents/nr-reporting-summary-flat.pdf

Life sciences study design
All studies must disclose on these points even when the disclosure is negative.
Sample size

Data exclusions
Rep I ication

Behavioural & social sciences study design
All studies must disclose on these points even when the disclosure is negative.

Ecological, evolutionary & environmental sciences study design
All studies must disclose on these points even when the disclosure is negative.

Study description
Research sample The samples were originally collected for an observational microbiome study. Since the initial study was exploratory in nature, no formal power calculations were made. The cohort is still among the largest that have been analyzed with respect to microbiota and PD and has proven sensitivity to detect differences between study groups.
The qPCR data were tested for outliers per group and time point using the ROUT method (Q=0.1%) in GraphPad Prism v7 and the identified outliers were removed. Outlier removal was restricted to the qPCR data only.

All attempyts for replication were successful
This was a case-control study without randomiization No blinind was perfmormed due to the nature of a case-control study

I
We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material, system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.

Palaeontology and Archaeology
Specimen provenance

Specimen deposition
Dating methods D Tick this box to confirm that the raw and calibrated dates are available in the paper or in Supplementary Information.

Ethics oversight
Note that full information on the approval of the study protocol must also be provided in the manuscript.

Animals and other organisms
Policy information about studies involving animals: ARRIVE guidelines recommended for reporting animal research

Laboratory animals
Wild animals

Field-collected samples
Ethics oversight Note that full information on the approval of the study protocol must also be provided in the manuscript.

Human research participants
Policy information about studies involving human research participants

Ethics oversight
Note that full information on the approval of the study protocol must also be provided in the manuscript.

Clinical data
Policy information about clinical studies All manuscripts should comply with the ICMJE guidelines for publication of clinical research and a completed CONSORT checklist must be included with all submissions.

Clinical trial registration
Study protocol

Data collection
Outcomes I I Recruitment through hospital inpatient or outpatient department or throgh self-volunteering. All diagnoses verified by physician and medical records.
The original gender, age and sex-matched cohort was recruited for a pilot study in 2015 investigating PD and gut microbiota (Scheperjans et al., 2015). All subjects were invited to a follow-up on average 2.25±0.20 years later to investigate temporal stability in the PD microbiota (Aho et al., 2019).

Visits in study hospitals between 2012 and 2015
Not applicable for case-control study The study was approved by the ethics committee of the Hospital District of Helsinki and Uusimaa.
All participants gave written informed consent and the study was registered at clinicaltrials.gov (NCT01536769).

Dual use research of concern
Policy information about dual use research of concern

Hazards
Could the accidental, deliberate or reckless misuse of agents or technologies generated in the work, or the application of information presented in the manuscript, pose a threat to: No Yes 0 0 Public health D D National security D D Crops and/or livestock D D Ecosystems D D Any other significant area

Experiments of concern
Does the work involve any of these experiments of concern: No Yes D D Demonstrate how to render a vaccine ineffective D D Confer resistance to therapeutically useful antibiotics or antiviral agents D D Enhance the virulence of a pathogen or render a nonpathogen virulent D D Increase transmissibility of a pathogen D D Alter the host range of a pathogen D D Enable evasion of diagnostic/detection modalities D D Enable the weaponization of a biological agent or toxin D D Any other potentially harmful combination of experiments and agents

Ch IP-seq
Data deposition D Confirm that both raw and final processed data have been deposited in a public database such as GEO. D Confirm that you have deposited or provided access to graph files (e.g. BED files) for the called peaks.

Data access links
May remain private before publication.

Files in database submission
Genome browser session