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Antimicrobial resistance (AMR) is a major global public health problem. Human gut microbiome plays an important role in modulating AMR. On one hand, the microbiome itself can serve as a reservoir of AMR genes, i.e. resistome. On the other hand, the microbiome performs colonization resistance, preventing invasive microbes from colonizing the gastrointestinal tract. In this study, we investigated how antibiotic treatment affects the resistome and colonization resistance of the gut microbiome in children receiving amoxicillin, amoxicillin-clavulanate, or no treatment for acute otitis media in a randomized clinical trial. Fecal samples from children receiving an antibiotic or no treatment before and after the treatment were analyzed using deep metagenomic sequencing. We used a flow cytometry-based approach to quantify the bacterial load in the fecal samples. Both metagenomic sequencing-based relative abundance and flow cytometry-based absolute abundance of the microbial species were analyzed. We found that the resistome fluctuated over time and in a small fraction (∼10%) of subjects, AMR genes increased rapidly due to colonization by AMR species, even in the control group without any antibiotic treatment. Amoxicillin significantly increased the risk for invasive species, especially pathogenic species carrying AMR genes, to colonize the gut. We also found that children lacking Blautia, Ruminococcus, Faecalibacterium, Roseburia, or Faecalitalea were more vulnerable to colonization by invasive AMR species in their gut microbiome.