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. 2019 May 29;25(6):1012–1021. doi: 10.1038/s41591-019-0450-2

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© The Author(s), under exclusive licence to Springer Nature America, Inc. 2019

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. 4 — Analysis was performed by mapping reads from PTB (n = 41) and TB (n = 81) samples to a custom database of genomes representing 56 taxa. Comparative analysis was performed with DESeq2 using a global scaling approach. Genes in candidate PTB taxa identified in 16S rRNA analyses that differ significantly at P_adj< 0.05 with a two-sided Wald test, as implemented in DESeq2 with a Benjamini–Hochberg FDR correction, are shown in red and those that were not statistically significant are shown in pink. Genes are also shown for the L. crispatus cluster (associated with TB in the 16S rRNA analyses), with genes that differ significantly (P_adj < 0.05) in transcript levels shown in dark blue and those that do not in light blue. Four other common and abundant taxa (L. jensenii, L. gasseri cluster, L. iners and G. vaginalis) are shown, with dark green dots denoting genes that differ significantly (P_adj < 0.05) between cohorts and light green dots denoting those that were not statistically significant.