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Fig. 3 | Microbiome

Fig. 3

From: Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight

Fig. 3

Differential abundance of microbial taxa and inferred gene content. a A stacked bar plot shows the relative abundance of microbial families uncovered in each sample, sorted by groups. For clarity, families with an overall abundance of less than 0.1% were summed into “Others”. b A heatmap depicts the differential abundance of microbial taxa that varied among RR-1 groups at FDR < 0.05. Rows (microbial taxa at each level) and columns (samples) were ordered by hierarchical clustering. The overall relative abundance of the taxa at a given taxonomic level is also noted as a sidebar of the heatmap. The effect sizes (i.e., the median ratio of between- and within-group differences) of differential taxon abundance comparing Flight samples to Ground samples were estimated using ALDEx2 and are plotted as a sidebar to highlight the differences between the two groups. Taxa that were significantly different (FDR < 0.05) between Flight and Ground samples are labeled in orange, and those suggestively different (P < 0.05 but FDR > 0.05) between Flight and Ground samples are labeled in dark grey. The identities of all the taxa in the heatmap and test statistics are provided in Additional file 1. c A boxplot showing the ratios between bacterial phyla Firmicutes and Bacteroidetes among RR-1 groups. d A heatmap showing inferred microbial metabolic pathways that were differentially abundant between Flight and Ground samples. Rows (microbial pathway) and columns (samples) were ordered by hierarchical clustering. Three clusters of microbial pathways were identified, and the dendrogram is color-shaded for each cluster. Microbial pathways are noted by their level-2 superclasses at the right side, and the identity of each pathway and test statistics are provided in Additional file 1. – log10(FDR) values are noted by the color scale on the right sidebars for the differential abundance test of each pathway between Flight and Ground samples (FLT vs. GRD) and between Flight samples and the combined Basal and Vivarium samples (FLT vs. BSL and VIV). e Simplified diagrams summarizing key microbial pathways of each cluster identified, colored accordingly as in d. Sample sizes in a–d: Basal, n = 10; Vivarium, n = 8; Ground, n = 7; Flight, n = 6

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