This repository holds code, R scripts, data, and information for the published manuscript:
Bierly, S., Van Syoc, E., Westphalen, M., Miles, A., Gaeta, N., Felix, T., Hristov, A., Ganda, E. 2024. "Alterations of rumen and fecal microbiome in growing beef and dairy steers fed rumen-protected Capsicum oleoresin." Journal of Animal Science https://doi.org/10.1093/jas/skae014
Analysis was done using the dada2 pipeline and downstream analysis was performed with R in RStudio. Below is a breakdown of what each file is relevant for related to analysis.
This file contains information about the raw reads. Obtained by running seqkit stats in miniconda3.
This file contains all the metadata for all samples.
This file contains the asv count information for all samples. This is an output file from dada2.
This file contains the taxa information for all samples. This is an output file from dada2.
This is a phyloseq object of only fecal samples for both breeds.
This is a phyloseq object of only rumen samples for both breeds.
This folder contains all scripts necessary for analysis in the dada2 pipeline. This is a combination of bash and R scripts.
This R script is utilized to generate a phyloseq object from the output asv and tax tables from dada2.
This R script is utilized to remove putative contaminants in samples based on taxa identified in positive and negative controls sequenced with samples.
This R script tests for cross over effects of both alpha and beta diversity based on treatment order.
This R script generates the relative abundance figure for fecal samples (Figure 2).
This R script generates the relative abundance figure for rumen samples (Figure 3).
This R script generates percentages of taxa that are changed based on treatment.
This R script generates p-values for beta diversity of fecal samples by treatment and generates the Principal Coordinate Analysis (PCA) plot for fecal samples (Figure 4).
This R script generates p-values for beta diversity of rumen samples by treatment and time and generates the PCA plot for rumen samples for treatment and time (Figure 5).
This R script generates p-values for alpha diversity of fecal samples by treatment and generates the boxplot for fecal samples (Figure 6).
This R script generates p-values for alpha diversity of rumen samples by treatment and generates the boxplot for fecal samples (Figure 7).
This R script generates the lineplot for alpha diversity of rumen samples by time (Supplemental Figure 1).
This R script uses ALDEx2 to compare taxa based on time (H0 vs. H2 and H0 vs. H18) for rumen samples of both breeds.
This R script uses ALDEx2 to compare taxa between a Control Group and a Capsicum Group based on treatment for both fecal and rumen samples.