Fig. 1: Fecal microbiotas are different in CA and non-CA cohorts.
From: Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma
a Organization of microbiome species in non-CA and CA cohorts. Co-occurrence network analyses were performed at the species level, as determined by metagenomic shotgun sequencing data analysis (n = 27 non-CA, n = 122 CA, keystone species are labeled in red). b Multi-variate differential abundance analyses of metagenomic shotgun data at species level. Species with significantly different abundance (ANCOM analysis, followed by two-sided Mann–Whitney U test with Benjamini–Hochberg false discovery rate (FDR) correction for multiple testing, pFDR < 0.01) and medium relative abundance ≥0.25% in either group are presented as box-whisker plots (blue boxes: non-CA cohort; red boxes: CA cohort). c Identification of key species (medium relative abundance ≥0.1% in either group) by random forest analysis. Species identified in both multi-variate and random forest analyses are shown in green. d ROC curve was identified based on best-weighted combination of common bacterial species identified by multi-variate and random forest analyses (AUC = 0.826, specificity = 0.667, sensitivity = 0.925). e α-Diversity analyses of fecal samples by Shannon and Simpson indices based on 16 S rRNA gene amplicon sequencing data, presented as box-whisker plots (n = 250 non-CA, n = 115 CA, Kruskal–Wallis one-way analysis of variance test; blue boxes: non-CA cohort; red boxes: CA cohort). f Relative abundance of Gram-negative and Gram-positive bacteria in non-CA and CA cohorts (n = 250 non-CA, n = 115 CA, ANCOM analysis, followed by two-sided Mann–Whitney U test, blue boxes: non-CA cohort, red boxes: CA cohort). g Multi-variate differential abundance taxonomic analyses of 16S rRNA gene amplicon sequencing data. ESVs with significantly different relative abundances (pFDR ≤ 0.01) and medium relative abundance of ≥1% in either group are presented as box-whisker plots (n = 250 non-CA, n = 115 CA, ANCOM analysis, followed by two-sided Mann–Whitney U test with Benjamini–Hochberg FDR correction; blue boxes: non-CA cohort; red boxes: CA cohort). In box plots, bounds of boxes show interquartile range (IQR), top and bottom whiskers demonstrate maximum and minimum, lines in the middle of the box indicate median, and stars show mean of the data. + signs indicate outliers.
