Gut transcriptome response to treatment
The DESeq2 (version ‘1.32.0’) package in R (version 4.1.1) was used to
identify differentially expressed transcripts in the host gut
transcriptome between any of the treatment groups in three pairwise
comparisons (antibiotic vs control, probiotic vs control, antibiotic vs
probiotic). The package uses a Wald test to test the significance of
gene transcription differences. To identify differentially expressed
transcripts, Benjamini–Hochberg corrections for multiple testing was
used (false discovery rate (FDA) < 0.05). We identified
differentially expressed transcripts as those genes with thresholds of
FDR < 0.05 and |log2 FC|
> 1. Volcano plots of differentially expressed genes
between the treatments were generated by using the FC and the log-scaled
adjusted p value using the EnhancedVolcano package (Blighe et
al., 2021) in R.