Fig. 3

Case studies: analyzing datasets with Pathonoia. A–D Fronto Temporal Dementia. A The dataset contains 30 cases of FTD (sub-groups shown in C) and 15 controls. Pathonoia reported 431 organisms over all samples. B The volcano plot shows 12 differentially abundant organisms, ten of them up-regulated in FTD samples. The color scale shows the number of samples containing the organism. C B. stabilis was chosen as OoI. \(A_O\) is given across samples. D Three gene sets from a differential expression analysis between patients with and without B. stabilis (34 up-regulated genes, 109 down-regulated genes, in total 143) were compared in an over-representation analysis with gene sets related to Molecular Functions and Biological Processes. (By B. stabilis) up-regulated genes hint towards an immune reaction in the FTD patients. The Biological Processes relate to neural pathways. E–F Fibrosis in Liver Diseases. E A dataset with 51 human liver samples from patients with different liver diseases and fibrosis levels comprises 653 reported species by Pathonoia. F A differential abundance analysis of samples with and without fibrosis lead to 41 organisms of which only one was up-regulated in two non-fibrotic samples. Seven organisms were present in more than nine fibrotic samples