Fig. 1

Mtb infection causes minimal alterations in the diversity and composition of the intestinal microbiota. a Alpha diversity estimates calculated from the sequenced data using Chao1 (left panel) and Shannon (right panel) indices for each time point (W1–W20) of stool sample collection in the naïve and TB group. Fecal collection time points are shown along the x-axis. Error bars indicate minimum and maximum values. Statistical significance was calculated between the corresponding time points of the two groups. *p < 0.05 (Wilcoxon rank-sum test). b Principal coordinate (PC) analysis of unweighted (left) and weighted (right) UniFrac distances of the microbial sequence data in the two animal groups. Each sphere represents a single animal with the size of the sphere referring to the sample collection time point (early to late time points indicated as a gradient in the size of the spheres from small to large). One sample each from W16 and W20 time points of the naïve group was not included in the analysis since these two samples formed an independent cluster highly separated from and inconsistent with the other clusters (For comparison, these samples are included, nevertheless, in Additional file 13: Figure S13). c Heat map comparing average abundances of species level classification of the 16S sequences from the naïve and TB animal groups. Data are clustered according to sample collection time point and animal group along the x-axis. The species indicated on the y-axis are grouped according to family level classification as noted on the right of the map and were filtered for those with an overall relative variance >3 (see “Methods”). n = 4–5 except TB group W20 time point where n = 3