Microbial Community Analysis

About

This respository contains R workflows used to analyze microbial communities rRNA count data. Individual taxa comarisons were performed using the package DESeq2 while community comparisons were performed via the microbiome package. All analyses utlized phylogenetic, taxonomic, and meta data sets to inform comparisons.

Repository Overview

• data_raw/         Original data recieved for analysis.
• data_prepared/ Formatted data prepared for analysis using the script format_data_raw.R.
• scripts/           All R scripts used in this publication analysis.

Analysis Overview

Four analyses were performed to analyze how the fungal genus Fusarium and its associated microbial communities respond to various agricultural crop rotation schemes.

• EF, uses elogation factor oligotype OTU rRNA count data to explore species-level comparisons between treatments.
• ITS, uses interal transcribed spacer rRNA count data to explore genus-level comparisons between treatments.
• comb-wsfs, uses EF rRNA OTU counts to compare the effects of two tillage and two cover cropping treatments.
• RK-T52, uses estimates of actual soil microbe EF rRNA OTU abundances to compare species between treatments.

For each analysis, raw data (found in data_raw/) was formatted via the script format_data_raw.R and exported into the directory data_prepared/ to be analyzed by its corresponding analysis script.

Dependencies

• phyloseq for stacked bar chart and NMDS vizualizations.
• DESeq2 for individual taxa comarisons.
• microbiome for community-level comparisons.
• vegan is used with microbiome to perform PERMANOVA community comparisons.
• xlsx for manipulating excel files.