Extended Data Fig. 1: Overview of the study.

Fecal metagenomes (n = 264 animals), caecal lipidomes (n = 381 animals) and distal small intestine transcriptomes (n = 234 animals) were generated from Diversity Outbred mice. Quantitative trait loci (QTL) analysis identified genomic regions associated with variations in bacterial taxa, bacterial functions, levels of bacterial- and host-derived lipids and small intestine transcript levels. Mediation analysis and co-mapping comparisons were used to identify causal links between traits.