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. 2019 Apr 1;9:5398. doi: 10.1038/s41598-019-41738-5

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© The Author(s) 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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Microbiota analysis. Alpha diversity (Chao1 estimators and Shannon indices) was analyzed using a repeated measures two-way ANOVA on the D0 and D13 values, and a one-way ANOVA on the D13-adjusted D23 values (A). OTU data were examined using a principal coordinate analysis of weighted and unweighted UniFrac distances, and group effects were evaluated at each time point using a permutational ANOVA (adonis function in R). Post-hoc tests used Bonferroni corrections (C). Data were also analyzed at the genus level. They were filtered (retained if more than 60% non-zeros in at least one group and mean above 0.01% in at least one group). A PLS-DA was performed on the log ratios of abundance between D23 and D13 to discriminate among the three groups (two components). Individual plots with 95% confidence ellipses and a correlation plot are presented. Log ratios are plotted for the genera Streptococcus and Desulfovibrio. Mice groups are as in Fig. 3, with untreated mice in red, CNCM I-23690-treated mice in green, and DspaF–treatedmice in orange; crosses and stars indicate D13 and D23 values, respectively (n = 8) (C).