shandley/human_volunteer_rotabiome

Analysis of 16S rRNA (dada2 amplicon sequence variants) from human volunteers given various vaccines following two different antibiotics treatments compared to no antibiotics.

Human Volunteer Rotabiome Study

63 healthy volunteers were enrolled to test how antibiotic pre-treatment altered vaccine immunogenicity.

Cohort Break down:

• 21 Control patients
• 21 patients treated with oral vancomycin
• 21 pateinets treated with oral vancomycin, ciprofloxacin and metronidazole

Antibiotics were provided for 7 days (day -3 to -9) prior to vaccination with the following vaccines:

• Pneumo 23
• Rotarix
• Tetanus toxoid

Vaccination outcome was determined by a combination of fecal and serum antibody tests at periods for 28 days. Stool was collected at Day -9 (antibiotic initiation), Day 0 (vaccine administration) and Day 7 (post-vaccination) and subjected to 16S rRNA gene amplicon sequencing. Samples were demultiplexed and preprocessed with dada2 to extract amplicon sequence variants (ASVs). ASVs were analyzed using R with heavy reliance on PhyloSeq.

Reference

Harris VC, Haak BW, Handley SA, Jiang B, Velasquez DE, Hykes BL Jr, Droit L, Berbers GAM, Kemper EM, van Leeuwen EMM, Boele van Hensbroek M, Wiersinga WJ. Effect of Antibiotic-Mediated Microbiome Modulation on Rotavirus Vaccine Immunogenicity: A Human, Randomized-Control Proof-of-Concept Trial. Cell Host Microbe. 2018 Aug 8;24(2):197-207.e4. doi: 10.1016/j.chom.2018.07.005. PMID: 30092197.

Raw data

Raw data is associated with sequence archive PRJEB25634.

Contact Information

Scott Handley: [email protected] Vanessa Harris: [email protected]

human_volunteer_rotabiome's Issues

Pnuemo and tetanus d0 -> d14

Fold change. >= 3 fold change

Try and sort out how the microbiome package analyzes beta-diversity / divergence over time.

http://microbiome.github.io/microbiome/Betadiversity.html

Does microbiome composition correlate with day 7 RV IgA boosting (defined as >= 2 fold-change)?

Volcano plot per randomization arm

Define take/not take category or category

ADONIS testing of each treatment group per day

Send Lindsay list of samples to resequenced

This needs to be the samples that failed dada2 as well as those that didn't pass the QC threshold in the analysis Rmd.

Discuss GitHub with chandni

Testing

[ ] Item 1
[ ] Item 2

Add interpretation to current battery of ADONIS results

Correlate shedding (P/A) w/ Deseq2

Factorize data for metadata plots

The plot_frequencies function in the microbiome package is nice for giving overviews of the metadata. However, the default for importing mapping data into phyloseq is to set all numeric values as numeric, when what we really want for these plots is numeric as factors. Adjust to factors and replete.

Pneumo serotype

Use random forest to define features that explain take not take category

Add interpretation to beta diversity analysis