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. 2021 Feb 18;12:1141. doi: 10.1038/s41467-021-21475-y

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — A Schematic of the clinical trial comparing bactericidal effect of HRZE and NTZ. B Paired M. tuberculosis sputum time to positivity (TTP) at day 0 and day 14 for the NTZ treatment arm and HRZE treatment arm. Data are displayed as range (minimum and maximum) of two-three technical replicates; n = 16 biologically independent individuals for the HRZE arm and n = 19 biologically independent individuals for the NTZ arm. Linear mixed effect modeling was used to determine significance of difference in post/pre treatment in each arm as $T T P ~ 1 + S e x + A g e + T r e a t m e n t + T i m e + T r e a t m e n t : T i m e + 1 ∣ I D$ , where Treatment indicates the arm (NTZ or HRZE), Time indicates Pre or Post antibiotic administration, and : indicates the interaction term. For each individual we use as TTP measurement the average of the relative technical measurements. NTZ treatment is associated with no difference in TTP between day 0 and day 14 (p > 0.05 for the coefficient of variable Time, see Supplementary Data 2), whereas HRZE significantly reduces bacterial load (p < 0.05 for the coefficient of variable Treatment : Time see Supplementary Data 2). Data for TTP were obtained from Walsh et al.²⁶. C Principal Coordinate analysis (PCoA) with Bray–Curtis distance showing differences in microbiome community structure between individuals before and after 14 days of either HRZE or NTZ treatment. The gray line connects baseline and day 14 treatment paired samples. PCoA1 clearly discriminates samples post NTZ treatment (pink triangles) from those at baseline or after HRZE treatment. PERMANOVA analysis was used to reject (p = 0.001, see Supplementary Data 4) the null hypothesis that the centroids and dispersion of the groups (pretreatment, after NTZ and after HRZE) are equivalent for all groups (see Supplementary Data 4). D Microbiota alpha diversity plotted using the Inverse Simpson Diversity index; n = 16 biologically independent individuals for the HRZE arm and n = 19 biologically independent individuals for the NTZ arm. Linear mixed effect modeling was used to determine the significance of difference of treatment on diversity. We fitted the model $D i v e r s i t y ~ 1 + S e x + A g e + T r e a t m e n t : T i m e + 1 ∣ I D$ . The symbol: indicates the interaction term. HRZE was used as the reference level. No significant difference between the two treatment at baseline was observed. Both groups (p < 0.05 for the coefficient of variable Time corresponding to HRZE treatment and p < 0.05 for the coefficient of variable Treatment:Time corresponding to NTZ treatment in this model) display significantly reduced Inverse Simpson diversity after 14 days of treatment (see Supplementary Data 3). Source data are provided as a Source Data file.