Project for looking at prophage induction of MAGs by antibiotics. Using previously published dataset.
List of directories:
- 0_RawData : Downloaded Sequences
- 1_QCReads : Quality controlled reads (Trimmed/Removed Host)
- 2_BacterialAnalysis : Assembly, binning, and taxonomy
- 3_ViralAnalysis : Prophages and Viral Assembled Phages
Kang et al 2021, Gut Microbes DOI
10 healthy human volunteers were recruited and randomized to receive one in four different antibiotic courses or to be a control. Before, during, and after exposure to antibiotics, they provided a total of six stool samples. Four antibiotics were selected based on their clinical relevance and broad-spectrum activity against Gram-positive and/or Gram-negative organisms.
Four antibiotics from different chemical and therapeutic classes were used: ciprofloxacin (quinolone class), cefuroxime (β-lactam class), doxycycline (tetracycline class), and azithromycin (macrolide class). As a control, stool samples from two untreated healthy individuals also were processed.