Problem
Deep brain stimulation is known to benefit patients with Parkinson's disease, but the underlying mechanisms are still not fully understood. Researchers at the Department of Clinical Medicine designed a longitudinal study using mini-pigs as a Parkinson's disease model to investigate how deep brain stimulation affects synaptic changes in the brain. One important objective was to assess the possible role of the gut microbiome, making microbiome insight a relevant part of the broader research project.
Question
How does the gut microbiome respond to deep brain stimulation or placebo in control animals versus Parkinson's disease model animals?
What we did
The research team collected fecal samples from the mini-pigs at three stages of the study and sent them to Biomcare for analysis. We carried out DNA extraction and sequencing, followed by bioinformatic and statistical analysis of the microbiome data in combination with metadata on study design and sample details. Biomcare provided full wet-lab and dry-lab support for the project and delivered a total of three reports, together with all raw and processed data. The project also included online meetings to review the results, as well as follow-up email dialogue while the client worked with the data for interpretation and publication. At project start, Biomcare also advised on how to set up the microbiome part of the study and on sample storage prior to analysis.
Insight
The microbiome analysis generated diversity metrics that were used first to explore potential confounders and then to assess how the microbiome responded to the intervention. Differential abundance analysis was subsequently performed to evaluate whether specific taxa were driving the observed response. During result review, the client requested additional analyses, which Biomcare carried out. These provided valuable input for designing a follow-up study to further investigate the role of the microbiome.
Value
Biomcare's full-support project setup enabled the research team to generate a microbiome data layer that could be integrated directly into the wider Parkinson's disease study. This supported analysis of microbiome diversity changes in relation to disease induction and brain stimulation, while making the microbiome component practical to include in a complex longitudinal animal model project. The work also gave the team a stronger basis for investigating gut-brain interactions and for defining relevant follow-up analyses in the broader research programme.
"We relied heavily on the experience of Biomcare for help and advice on setting up the project and storing the samples. After the rapid analysis at Biomcare, the team provided extensive data analysis and insightful interpretation."
