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Fig. 3 | Microbiome

Fig. 3

From: Gut-derived metabolites influence neurodevelopmental gene expression and Wnt signaling events in a germ-free zebrafish model

Fig. 3

Metabolites are sufficient to rescue neural gene expression in GF larva. A Venn-diagram comparing gene expression levels between CV and GF and those rescued by the addition of zebrafish metabolites to GF embryos (ZM-GF) (p < 0.05; GF-CV FDR < 0.05, ZM-GF FDR < 0.1). B DAVID generated plot of 31 of the 39 rescued genes and their associated enrichment terms (note: 8 genes did not contribute to significant over representation in DAVID output). Enrichment terms largely fall within seven major biological processes noted on the right. C Normalized counts of all 42 genes (39 downregulated plus 3 upregulated, noted by ‡ ) whose expression was rescued with metabolite treatment. Count comparison and RT-qPCR validation (D–G) of four rescued genes (marked with † in C from the RNA-seq dataset. RT-qPCR validation of hnrnpr (D), ctnnb2 (E), mcm4 (F), and taf15 (G) (one-way ANOVA of all 3 groups’ standard weighted mean analysis, 3 independent samples, 2 degrees of freedom, total p value is as stated, error bars represent SEM). H Boxplot of normalized counts of 39 downregulated and rescued genes between treatment groups with outliers removed. Top and bottom of box represents the 75th and 25th percentile respectively. The 50th percentile and solid horizontal line in the box represents the median. Whiskers represent the largest and smallest value within 1.5 times interquartile range above 75th percentile and below 25th percentile, respectively

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