This project contains code for: Pfenning-Butterworth A.C, Cooper R.O., and Cressler C.E. Diel rhythm influences microbiota composition in two zooplankton species.

Here, we examine the microbiota of two zooplankton species, Daphnia magna and Daphnia dentifera. Though both species are freshwater zooplankton, they differ drastically in life history traits, including feeding preferences and migratory patterns. We looked at 16S rRNA sequences from both day and night samples from both species to see if we could find any taxa that may influence or be influenced by these life history differences.

Code for figure creation and data analysis is stored in the scripts directory. To run these R scripts, the following packages are required (sorted by install method):

CRAN

• here
• phangorn
• ggpubr
• tidyverse
• cowplot
• rstatix
• vegan
• stringi
• plyr
• parallel
• gt

Bioconductor

• dada2
• DECIPHER
• phyloseq
• microbiome

Developer Github

• speedyseq
• DivNet

Data is stored in the data directory. A pre-processed .rds object that is the phyloseq output of the process_16s.Rmd script is included as processed_16s_all.rds, if you want to skip that entire step. Otherwise, you will need to download the dada2-formatted GTDB database, located here to appropriately identify ASV taxonomy.

Raw 16S data is available on NCBI under BioProject PRJNA715454.