Ptarmi-GUTT: Cecal Microbiomes in Ptarmigan

Long-term patterns in cecal microbial communities in Icelandic Rock Ptarmigan

This repository contains open-source code, data, & text files for the project exploring microbial communities in the cecal microbiome of Icelandic rock ptarmigan

Project Goals

• Aim 1) Characterize the cecal microbiome of Icelandic rock ptarmigan over a 12-year study period (2007-2018)

• Aim 2) Determine if the cecal microbiome predicts metrics of foraging behavior, diet digestibility, and body condition over time

Repo Contents

• Analyses:

• Ptarmi-GUTT_processing.r: R script for analyzing microbiome data
• Ptarmi-GUTT_figures.R: R script for generating figures

• Data:

  1. Raw metadata:
  • Only_ceca_subsampling_2022.csv -- Ptarmigan metadata
  • PtarmiganHealthData_Dec_2023.csv -- Ptarmigan health data
  • 2018GizzardFFDM.csv -- Gizzard fat free dry mass from 2018
  • Diet_diversity.csv -- Crop contents (diversity of diet)
  • IcelandPtarmiganID_GoodPoorFoodPercent_BCI.csv -- Crop contents (% food type)
  2. Raw mothur output data:
  • GUTT.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.pick.ASV.abund.asv.shared.gz - ASV table. Note: needs to be uncompressed
  • GUTT.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.pick.ASV.abund.nr_v138_1.wang.taxonomy -- taxonomy file
  3. Processed data:
  • asv_rel.csv.gz* - Processed ASV relative abundance table. Note: needs to be uncompressed
  • diversity.csv - Microbiome alpha diversity metrics
  • metadata_diet.csv - Crop contents paired to metadata metadata_health - Health data paired to metadata
  • tax_top30.csv - Top 30 ASVs (Table 1)
  • asv_reps_rel.csv - Processed ASV relative abundance table for replicates (QC)
  • metadata_reps - Processed metadata for replicates (QC)

• Figures: Fig 1A Fig 1B Fig 2A Fig 2B Fig 3A Fig 3B Fig 3C Fig 4 Fig S1 Fig S2

• Bin:

• DiversityFunctions.R: R functions for calculating alpha diversity
• MothurTools.R: R tools to analyze data output from the mothur software pipeline

Software Versions and Dependencies

Contributors

Amanda Stromecki: PhD Student, Department of Biology and Wildlife, University of Alaska Fairbanks

Dr. Mario Muscarella:Principle Investigator, Assistant Professor, Institute of Arctic Biology, University of Alaska Fairbanks. Head of the Muscarella Lab.