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. 2018 Mar 6;8:4065. doi: 10.1038/s41598-018-21986-7

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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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Caging, bedding, and diet have minimal effect on fecal microbiota. (a) Stacked bar chart showing relative abundance of all operational taxonomic units (OTUs) detected in the feces of 16.5 week-old mice housed in static or ventilated (IVC) microisolator caging, with paper or aspen bedding, and fed one of three standard rodent chows (5008, 5053, or 5058), thirteen weeks after arrival; (b,c) principal coordinate analysis (PCoA) of the samples shown in (a) demonstrating the compositional heterogeneity of the end-point fecal microbiota as determined using both Bray-Curtis (b) and Jaccard (c) distances, legend above. P values indicate main effect, results of pairwise comparisons shown in Supplementary Tables S3 and S4 respectively; (d,e) combined PCoA of the baseline and endpoint fecal samples demonstrating the overall shift in microbial composition of all treatment groups over time based on Bray-Curtis (d) and Jaccard (e) distances, with no apparent clustering by treatment. Combinations of colors and symbols are used to identify factors: red = 5008; blue = 5053; yellow = 5058; squares = static microisolators with paper bedding; diamonds = static microisolators with aspen bedding; circles = IVCs with paper bedding; triangles = IVCs with aspen bedding.