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. 2018 Sep 24;8:14241. doi: 10.1038/s41598-018-32583-z

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© The Author(s) 2018

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 comparison between Nod2−/− and Nod2+/+ mice at 8 weeks of age in different housing conditions. (A,C) Alpha diversity measures in mice (A) reared separately and (C) in cohousing. Box plots of number of observed OTUs and Shannon entropy in Nod2−/− and Nod2+/+ mice (A) reared separately at 4 and 8 weeks of age and (C) in cohousing at 8 weeks of age. Statistically significant differences were performed by pairwise comparisons using Student t test with FDR correction. For each significant pairwise comparison p-value < 0.05 are indicated by different letters (“a”, “b”, “c”, and “d”). (B–D) Microbiota profile comparison in Nod2−/− and Nod2+/+ mice at 8 weeks (B) reared separately and (D) in cohousing. Cladogram showed the most discriminative bacterial clades identified by LEfSe analysis. Coloured regions/branches indicate differences in the bacterial population structure between Nod2−/− and Nod2+/+ mice at 8 weeks. Regions in red indicate clades that were enriched in Nod2−/− mice, while regions in green indicate clades that were enriched in Nod2+/+ mice. LEfSe results indicate a sequentially significant ranking between the two groups (Alpha value = 0.05 for the factorial Kruskal-Wallis test among classes; the threshold for the logarithmic LDA score was 2.0).