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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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Experimental design on Nod2−/− and Nod2+/+ mice to investigate the effect of genetic background and housing conditions on microbiota-immune-system interactions. Black arrows indicate faecal sample collection for microbiota analysis at different time points: (i) at 4 weeks of age, (ii) at 8 weeks of age, and (iii) at day 3 after TNBS-colitis induction in cohoused and reared separately mice groups, respectively. At the three time points, mice were sacrificed to collect colon and test the proportion of LP CD4+ LAP+ Foxp3− T cells and tissue cytokines content.