tonyaward / bugbase_manuscript

Analysis for the BugBase Manuscript

Requirements:

• BugBase installed and able to run test dataset
• This git repository

R packages required for BugBase, plus 1 additional package "cowplot"

• Graphlan installed to generate Figure 4
  
  

Data Files:

HMP Body Sites

HMP OTU table was generated using QIIME v.1.8.0 (closed reference) with the GreenGenes 97% representative set v.13.5.8 and was filtered to keep only samples with at least 500 counts and samples from the tongue dorsum, stool and plaque

Reference:

Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).

Files:

• HMP_Map.txt
• HMP_OTUS.biom
  
  

Western vs. Non-western Stool Samples

The OTU table for the western, non-western stool analysis was pulled from the Qitta websiteand was filtered to keep samples from only non-infants (>3 years of age) and samples with a minimum of 500 sequence counts

Reference:

Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).

Files:

• Yats_Adult_Map.txt
• Yats_Adult_OTUs.biom
  
  

Yellowstone Hotsprings Data

The OTU table for the Yellowstone hotspring analysis was pulled from the Qitta website and was filtered to keep only water samples and samples with a minimum of 500 sequence counts

Reference:

This data is not published elsewhere (yet!)

Files:

• Yellow_Stone_Map.txt
• Yellow_Stone_OTUs.biom
  
  

Soil pH

The OTU table for the soil analysis was pulled from the Qitta website and was filtered to keep samples with a minimum of 500 sequence counts

Reference:

Bartram, A. K. et al. Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm. FEMS Microbiol. Ecol. 87, 403–415 (2014).

Files:

• Soil_Map.txt
• Soil_OTUs.biom
  
  

Vaginal Samples

The vagina OTU table was generated using NINJA-OPS (closed reference) with the GreenGenes 97% representative set v13.5.8 all samples had a minimum of 300 sequences

Reference:

Ravel, J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl. Acad. Sci. 108, 4680–4687 (2011).

Files:

• Vagina_Map.txt
• Vagina_OTUs.biom
  
  

Running the Analysis:

To complete the BugBase analysis for all the work presented in the publication, you can run the commands listed in the BugBase_Workflow.txt file.

These commands should be run from within the BugBase_Manuscript main directory.