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. 2015 Apr 8;16(1):73. doi: 10.1186/s13059-015-0639-8

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© Voigt et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Clustering of the complete time series data set. (A) The unperturbed microbiomes of the subjects were stable except for the Alien samples, which showed a decline of the Shannon diversity index upon antibiotics treatment (d_376–392) while the bowel cleanse (d_630–637) had no detectable effect. The separation of the post-antibiotics from the pre-antibiotics samples along the first principal coordinate (PC1) based on Jensen-Shannon divergence distances was significantly correlated with the decline of the Shannon diversity index (dotted line, P-value = 3.9e⁻¹⁴) (A, lower panel) and explained the separate clustering of pre-and post-treatment samples (A, upper panel and (B)). (C) The unperturbed gut microbiome was highly personal and when omitting the post-antibiotics samples, all subjects that collected time series samples over up to two years can be resolved.