Additional file 1 of Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study
Creators: name: Langdon, Amy
name: Schwartz, Drew J.
name: Bulow, Christopher
name: Xiaoqing Sun
name: Hink, Tiffany
name: Reske, Kimberly A.
name: Jones, Courtney
name: Carey-Ann D. Burnham
name: Dubberke, Erik R.
name: Dantas, Gautam
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 1: Fig. S1. Study protocol for Phase II clinical trial NCT01925417 adapted from reference [25]. Samples specifically used for this study depicted in Fig. 1. Fig. S2. The relative abundance of bacterial phyla in all patients are shown at day 0 (panel A) and in all donor samples from the 4 donors (panel B). The patient IDs are marked in gray if symptoms resolved in a single dose of the study drug and in red if they required repeat intervention. A) Patient ID is listed after the letter A on the x axis with relative abundance of each phylum in stacked bar chart format on the y-axis. B) Donor samples are named as donor number.samplenumber followed by DS for donor substance. Fig. S3. linear discriminant analysis compares functional pathway abundance, as annotated by HUMAnN2 and visualized with LEfSe, at day 7 between the two outcome groups. In red are pathways more enriched in the reintervention (RI) group, while those patients who recovered after a single treatment had a significantly higher abundance of the pathways in green. Fig. S4. Shown are the HUMAnN2 functional pathway abundances for all patients with both day 0 and day 7 samples. Fig. S5. The relative abundance of Akkermansia muciniphila ASV 2 is shown over time stratified by outcome. A) The patient IDs are marked in gray if symptoms resolved in a single dose of the study drug, in red if they required repeat intervention, and black if they come from the donor. B) Akkermansia muciniphila ASV2 abundance after re-intervention. Fig. S6. The PCA analysis from Main Fig. 2 is reproduced here via the dual principal component function of phyloseq, which uses Euclidean distances. The overall taxonomic composition is graphed in Panel A, while Panel B shows the directionality of the influence of individual taxa upon those samples. Fig. S7. A) The relative abundance of Clostridioides difficile is tracked here using species-specific toxin genes detected in metagenomic sequences via ShortBRED. The gene count was normalized to the number of metagenomic reads and expressed in terms of copies per metagenome. B) The relative abundance for the ASV corresponding to C. difficile is shown in the bottom panel. The patient IDs are marked in gray if symptoms resolved in a single dose of the study drug and in red if they required repeat intervention.