By Angus Ball

Introduction

Fungaltraits is a program that attaches metabolism information to the taxons of fungi produced by metabarcoding. To use the below tutorial you are expected to have finished the DADA2 pipeline, but have yet to create a phyloseq object, BUT because I'm lazy I don't explain the phyloseq code within this documentation, see Making-a-Phyloseq-Object to understand what the phyloseq code is doing

Required Reading

haha get rekt go read this paper. It's large but it does a very good job overviewing both fungal and bacterial functional annotation

Inferring microbiota functions from taxonomic genes: a review

Link

Fungaltraits importing data

Citations

Citations in R are hard, here are all the packages you use and how to cite them, but you don't necessarily need to cite all of them? Depends on the ethical considerations regarding data management packages (always cite statistical packages). For this section please cite:

Phyloseq:

phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. Paul J. McMurdie and Susan Holmes (2013) PLoS ONE 8(4):e61217.

dplyr:

Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.3, https://CRAN.R-project.org/package=dplyr.

tidyverse:

Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). “Welcome to the tidyverse.” Journal of Open Source Software, 4(43), 1686. doi:10.21105/joss.01686 https://doi.org/10.21105/joss.01686.

Fungaltraits:

Põlme, S., Abarenkov, K., Henrik Nilsson, R., Lindahl, B. D., Clemmensen, K. E., Kauserud, H., Nguyen, N., Kjøller, R., Bates, S. T., Baldrian, P., Frøslev, T. G., Adojaan, K., Vizzini, A., Suija, A., Pfister, D., Baral, H.-O., Järv, H., Madrid, H., Nordén, J., … Tedersoo, L. (2020). FungalTraits: A user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity, 105(1), 1–16. https://doi.org/10.1007/s13225-020-00466-2