Supplementary Table Captions: Supplementary Table S9. Evaluation and parameter determination of host and microbiome RNA read classification using simulation datasets Supplementary Table S10. 40 pathways significantly upregulated in the cecum as compared to the transverse colon Supplementary Table S11. Host-microbiome gene co-expression network edges Supplementary Table S12. Host-host gene co-expression network edges Supplementary Table S13. Microbiome-microbiome gene co-expression network edges Supplementary Table S14. List of genes included in each gene module identified from the gene co-expression network Supplementary Table S15. Results of enrichment analysis for each gene module identified from the gene co-expression network Supplementary Table S16. The top 32 bacterial species in terms of expression abundance based on metatranscriptome profiles Supplementary Table S17. Number of microbiome RNA reads annotated by the KEGG database Supplementary Table S18. Results of enrichment analysis of gene modules for each parameter Supplementary Table S19. Evaluation of modules in each parameter of Newman algorithm Supplementary Table S20. Evaluation of modules in each parameter of Louvain algorithm Supplementary Table S21. Evaluation of modules in each parameter of Leiden algorithm Supplementary Table S22. Evaluation of modules in each parameter of WGCNA