Natural history of the infant gut microbiome and impact of antibiotic treatments on strain-level diversity and stability. human gut metagenome

Longitudinal study of 39 Finnish children sampled monthly from month 2 to 24-36. Sequencing data includes 16S sequencing for all 1,101 samples and metagenomic sequencing for 240 of these. Children who received multiple antibiotic treatments show a decreased diversity on both species and strains, and also decreased stability overtime, compared to children who never received any antibiotics. In addition, the abundance of resistance genes increases following treatment, and decreases shortly after.