![]() ![]() ( A) Schematic representation of the hydrogenase-1 and hydrogenase-2 encoding gene loci in E. See also Figure 1-figure supplement 1, a Figure 1-source data 1, Figure 1-source data 2, and Figure 1-source data 3. Statistical significance was determined by Bonferroni-corrected Mann–Whitney U-test (*p<0.05 **p<0.01, ***p<0.001 ns: not statistically significant). Medians are labeled with a red solid line, and error bars correspond to interquartile ranges. Averages equal to zero were assigned a value of 0.0005. Each symbol corresponds to the average number of normalized reads that map to a specific hydrogenase sequence. Reads from non-IBD controls (55 samples) and patients with Crohn’s disease (87 samples) ( B) or ulcerative colitis (76 samples) ( C) were aligned to the HydDB hydrogenase database of predicted hydrogenase activities ( Søndergaard et al., 2016). ( B, C) Analysis of a previously published metagenomic sequencing dataset from stool samples collected from non-inflammatory bowel disease (IBD) controls and patients with Crohn’s disease or ulcerative colitis (SRA BioProject number PRJNA400072 Franzosa, 2019). Averages equal to zero were assigned a value of 0.05. Each symbol corresponds to the average number of normalized reads that map to a specific sequence in the mock or DSS-treated animals (six mice per group). Reads were aligned to the HydDB hydrogenase database ( Søndergaard et al., 2016) and segregated based on predicted hydrogenase activity. ( A) Shotgun metagenomic sequencing of mock or dextran sulfate sodium (DSS)-treated mice with endogenous Enterobacteriaceae (obtained from Charles River) was previously performed to generate the analyzed dataset (ENA accession number PRJEB15095 Hughes, 2017). ![]()
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