Correlations between the relative abundance of bacteria with cytokine expression. Bacterial family, order, genus, and species are organized into phyla- each phylum is designated by a color. Lactobacillus species organisms belong to the phylum Firmicutes (red). Mycobacterium species belong to the phylum Actinobacteria (pink). There were positive correlations with the described phyla and the presence of IL-17 and IL-6, negative correlation with IL-1α, and both positive and negative correlations with IFN-Υ. IFN-Υ, IL-1α and IL-6 are associated with MAP infections and Th-1 response [1, 11]. IL-17 is associated with Th-17 cells, but is associated with IL-12 family cytokines which are produced during MAP infections . Those cytokines not listed did not demonstrate any correlation with changes in the microbiota. Organisms belonging to the phylum Bacteriodetes were found to be mostly associated with IFN- Υ regulation. Organisms associated to Proteobacteria were mostly linked to IL-6. Additionally, organisms belonging to Actinobacteria (which include MAP) were associated with IL-6 and IFN-Υ regulation with one species also associated with IL-1α. Lactobacillus species and others belonging to the phylum Firmicutes were associated with IL-17. Similar to serum cytokine and transcript data, these data demonstrate regulation of host cytokine activity based on host-microbe interaction, both by pathogenic and beneficial microbes. Data analysis methods are further described in the data analysis section.