Fig. 4

Relationships between inferred gene abundance of gut microbial pathways and gene expression in the host liver. a The number of host genes whose hepatic expression was significantly correlated (lighter color shades and numbers noted at end of the bars) and partially correlated (darker color shades and numbers noted in parenthesis) with the gene abundance of each of the microbial pathways. Top 10 pathways with the most numbers of correlated genes are shown. b Biological functions and pathways that were enriched with genes correlated with the gene abundance of each of the microbial pathways. c An example of correlations between the expression of a host gene in the liver and the inferred gene abundance of a microbial pathway in the gut. In this example, the overall correlation pattern between the expression of Rpl3 (ribosomal protein L3) in the liver and the inferred gene abundance of microbial putrescine degradation I pathway were consistently observed within each experimental group, giving rise to a significant partial correlation. Only a subset of RR-1 animals has been profiled for both gut microbiome and liver transcriptome, and thus correlation analysis was performed with reduced sample sizes: Basal, n = 5; Vivarium, n = 4; Ground, n = 3; Flight, n = 4