Fig. 5 Clustering of the distal gut microbiome, the C

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Fig. 5 Clustering of the distal gut microbiome, the C Fig. 5 Clustering of the distal gut microbiome, the C. innocuum SB23 transcriptome, and the community meta transcriptome in the ceca of humanized mice. Clustering of the distal gut microbiome, the C. innocuum SB23 transcriptome, and the community meta transcriptome in the ceca of humanized mice. Microbiome or transcriptome profiles were normalized by z score, used to construct a correlation distance matrix, clustered with UPGMA (unweighted pair group method with arithmetic mean), and visualized (see Supplementary Material; Matlab version 7.7.0). (A) Clustering of fecal microbial gene content in the human donor’s microbiome and two groups of humanized mice starting at day 1 after colonization (n = 3 to 5 mice per group; fecal DNA was pooled before sequencing). All mice were maintained on the LF/PP diet (red) for 28 days, at which point group 2 was transferred to the Western diet (blue). (B) Clustering of C. innocuum SB23 gene expression in humanized mice fed the LF/PP (red) or Western (blue) diet. (C) Clustering of the gut microbiome’s meta transcriptome in humanized mice fed a LF/PP (red) or a Western (blue) diet. Black circles represent validated clusters (inconsistency threshold = 0.75, “cluster” function in Matlab version 7.7.0). (D) qRT-PCR validation of C. innocuum SB23 gene expression in humanized mice (n = 3 to 5 samples per group; see Supplementary Material). Mean values ± SEM are plotted (*P < 0.05, Student’s t test). Peter J. Turnbaugh et al., Sci Transl Med 2009;1:6ra14 Copyright © 2009, American Association for the Advancement of Science