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.