Genome-wide sweeps create ecological units in the human gut microbiome

Isolate genome collection A total of 19,837 publicly available isolate genomes were collected and consisted of the entire data in the Unified Human Gastrointestinal Genome (UHGG) catalogue 45 (v.1.0, 10,648 genomes) and 4 large-scale culturomic studies 28 , 46 , 47 , 48 . Furthermore, a group of 186 isolates from Austrian individuals were newly collected and sequenced. A total of 50 patients undergoing CRC screening colonoscopy at the Vienna General Hospital were enrolled in the study, which comprised 24 individuals with irritable bowel syndrome, 5 with UC and 21 healthy participants. None of the participants were found to have carcinomas during the colonoscopy. For bacterial isolation of participants in the Austrian study, brush samples and biopsy samples were collected during colonoscopy from the ileal or caecal mucosa or the ascending colon with or without an endoscopically visible biofilm and were immediately processed 49 . Brush and biopsy samples were vortexed or homogenized in 0.6 ml of 0.9% NaCl, and the suspensions were subsequently plated on one of the following six culturing conditions: Columbia agar with 5% sheep blood, MacConkey agar, Columbia CNA agar with 5% sheep blood or CPS agar (Becton Dickinson) under aerobic conditions at 37 °C; Brucella agar with 5% horse blood or Schaedler KV agar with 5% sheep blood (Becton Dickinson) under anaerobic conditions at 37 °C. …