Correlation between gut bacterial community and host transcriptional profile
To investigate the direct effect of variation in the gut microbiome BC composition on host gene expression patterns, regression analyses were performed using the function lm in R (R version 4.1.1). We selected common bacterial taxa (bacteria families with more than 5% contribution to total sequence reads counts within each treatment; (7 taxonomic families) and individual genes with evidence for possible treatment effects (P value <0.1 (9 genes)) from the gene-level analysis described above. We included treatment and family ID as covariates to account for specific treatment and family effects on the relationship between host gut microbiome BC composition and gene transcription. Moreover, a sequential Bonferroni P value correction was applied for multiple testing correction (Rice, 1989). We visualized the pattern of correlation across all genes and bacterial taxa using a heatmap generated in the pheatmap function in R.