This repository comprises Jupyter notebooks used for the analysis in the research article:
Youngblut, Nicholas D., Georg H. Reischer, William Walters, Nathalie Schuster, Chris Walzer, Gabrielle Stalder, Ruth E. Ley, and Andreas H. Farnleitner. 2019. “Host Diet and Evolutionary History Explain Different Aspects of Gut Microbiome Diversity among Vertebrate Clades.” Nature Communications 10 (1): 2200. https://doi.org/10.1038/s41467-019-10191
These notebooks provide a detailed account of the methods (eg., code) used for the analyses in the publication.
The directories and notebook files are numbered in the general order in which they were run (although sometimes the analysis was not fully linear!).
- 16S rRNA Illumina sequence data
- The raw sequence data are available from the European Nucleotide Archive under the study accession number PRJEB29403
- Host metadata (diet, habitat, geography, phylogeny, etc.)
- See Supplemental Table 1 of the manuscript