Group Activity

Example workflows

Asavela’s Demo
Liz’s Demo
Note: The filepaths to the datasets may not match!


Find your group on the instances tab!

Schedule

Wednesday (4/24)

Time Task
1:30-2:00pm
  • Find your groups!
  • Read project description and aims for your project
  • Identify files and create a new quarto project
2:00 - 3:00pm
  • Create phyloseq object
  • Phyloseq cleaning
3:00 - 3:30pm Break
3:30- 5:00pm
  • Explore the data!
  • Visualizing microbiome composition
  • Alpha Diversity

Thursday (4/25)

Time Task
1:30 - 2:00pm
  • Visualizing microbiome composition
  • Alpha Diversity
2:00 - 3:00pm
  • Ordination and Correlations
3:00 - 3:30pm Break
3:30 - 5:00pm
  • Integrating Shotgun Metagenomics

Friday (4/26)

Time Task
AM
  • Review and Presentation preparation
PM Group Presentations
  • Dataset Demo

Projects

Research Project A - Does yogurt consumption change the vaginal microbiome?

Aim
To investigate whether the consumption of yogurt influences microbiome composition after antibiotics treatment.

Study Description
This is a randomized controlled trial to study whether yogurt consumption has an effect on the microbiome post antibiotic treatment. 16S rRNA sequencing was done to characterize patient microbiome composition. Absolute abundance of bacteria (in gene copies / mL) was measured by 3 qPCR assays (for total, L. crispatus, L. iners). Cytokine levels (in ug/mL of vaginal fluid) were also measured by Luminex. Data was collected at two timepoints, pre and post antibiotic treatment.

Research Project B - Does birth control change inflammation during menstruation?

Aim
To investigate whether taking birth control is associated with vaginal inflammation throughout the menstrual cycle.

Study Description
This is an observational study to evaluate the relationship between birth control and vaginal inflammation in response to menstruation. 16S rRNA sequencing was done to characterize patient microbiome composition. Cytokine levels (in ug/mL of vaginal fluid) were also measured by Luminex. We also looked at the number and type of immune cells in the vagina using Flow Cytometry. Data was collected at four timepoints; before, at the start, the end, and after menstruation.