PMC

ATT induces temporal changes in the community structure of the intestinal flora. a Principal coordinate (PC) values along the second ordinate of unweighted (top) and weighted (bottom) UniFrac analyses shown in Fig.  for each sample of the three animals groups are plotted. The x-axes indicate the sample collection time points and the y-axes indicate the PC values. The dotted lines represent the linear regression analysis trends. Error bars indicate mean ± SEM. b Relative abundances from W4 to W20 of select bacterial families for the three animal groups are plotted. *p < 0.05; **p < 0.01 (Wilcoxon rank-sum test). Error bars indicate mean ± SEM. n = 4–5 except TB group W20 time point where n = 3

ATT causes a rapid and persistent alteration in the composition of the intestinal microbiota. a Average relative abundance of bacterial families in each group and experimental time point identified from the sequenced data of the stool samples. Time points are indicated along the x-axis and arranged by the experimental groups. The bacterial families are grouped under their respective phylum and class in the color key. b Heat map showing the average species level abundance. Data are filtered for overall relative variance >5 and clustered as described in Fig. . c, d LEfSe analyses depicting genera that are differentially abundant between the naïve and TB + HRZ groups (c) and TB and TB + HRZ groups (d). Analyses were performed on data from W4 to W20 time points (see ). Taxa significantly enriched in naïve, TB, and TB + HRZ groups are shown with blue, red, and orange bars, respectively. Data are filtered for p < 0.01 and linear discriminant analysis (LDA) score >2. n = 4–5 except TB group W20 time point where n = 3

ATT changes the intestinal bacterial community structure. a Community diversity in the naïve, TB, and TB + HRZ animal groups calculated from 16S sequences (W4–W20) using Chao1 (left) and Shannon (right) indices. Fecal collection time points are shown along the x-axis. Error bars indicate minimum and maximum values. Significance tests were performed between the corresponding time points in the naive and each experimental group (TB or TB + HRZ) and in a separate comparison between the TB and the TB + HRZ groups. Significant differences with respect to naive or TB are marked with a blue or red asterisks. *p < 0.05 (Wilcoxon rank-sum test). b Principal coordinate (PC) analysis of unweighted (top) and weighted (bottom) UniFrac distances of the sequences from the three groups. Sizes of spheres depict the time of sample collection as described in Fig. . 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 separated from and inconsistent with the other clusters (For comparison, these samples are included, nevertheless, in Additional file : Figure S13)

The intestinal dysbiosis triggered by ATT is long-lasting and persists following cessation of treatment. a Community diversity in the naïve and post HRZ animal groups calculated from 16S sequences (W24–W32) using Chao1 (left) and Shannon (right) indices. Error bars indicate maximum and minimum values. b Principal coordinate (PC) analysis of unweighted (top) and weighted (bottom) UniFrac distances of the sequences from the two groups. Sizes of spheres depict the time of sample collection as described in Fig . One sample each from W24, W28, and W32 time points of the naïve group was not included in the analysis since these three samples formed a separate independent cluster inconsistent with the other clusters. (For comparison, these samples are included, nevertheless, in Additional file : Figure S13). c Average relative abundance of bacterial families identified from the sequenced data of the naïve and post HRZ stool samples (W24–W32). The bacterial families are grouped under their respective phylum and class in the color key. d Heat map showing the average species level relative abundance. Data are filtered for overall relative variance >5 and clustered as described in Fig. . e LEfSe comparisons showing the differentially abundant genera between the naïve and post HRZ groups (W24–W32). Taxa significantly enriched in naïve or post HRZ groups are depicted with blue or yellow bars, respectively. Data are filtered for p < 0.05 and LDA score >2. n = 4–5

Differential effects of the components in the HRZ cocktail on the intestinal microbiota. a Nine groups of mice with 3–4 animals in each group were employed. One group was left untreated as the naïve age-matched control. Seven of the groups were each treated with one or a combination of H (Isoniazid), R (Rifampin), and/or Z (Pyrazinamide) as indicated and separated by a ‘/’. The last group was treated with a cocktail of vancomycin, ampicillin, neomycin, and metronidazole (VANM). b Bacterial community diversity of all the samples in each group was estimated using alpha diversity indices Chao1 (left) and Shannon (right). Error bars indicate maximum and minimum values. *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001, Welch’s t test. Blue and pink asterisks indicate significance in comparison to Naïve and VANM, respectively. c Principal coordinate (PC) analysis of unweighted UniFrac distances of sequences from all nine groups. d Average relative abundance of bacterial families in each group identified from the sequenced data. The bacterial families are grouped under their respective phylum and class in the color key. e Heat map showing the average species level abundance. Data shown are filtered for an overall relative variance >10 and depicted as described in Fig.  except along the x-axis which show the different treatment groups. Naïve, VANM, HRZ, n = 3; remaining groups n = 4

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 : 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 ). n = 4–5 except TB group W20 time point where n = 3