The stability of the populations in the human gastrointestinal tract is not fully appreciated, and represents a significant knowledge gap regarding gastrointestinal community structure, as well as resistance to incoming pathogenic bacterial species and antibiotic treatment. The current study examines the genomic content of 240 isolates from 30 children, aged 2 to 35 months old, in Tanzania. The strains were isolated from three time points spanning a six-month time period, with and without antibiotic treatment. The resulting isolates were sequenced, and the genomes compared. The findings in this study highlight the transient nature of strains in the gastrointestinal tract of these children, as during a six-month interval, no one individual contained phylogenomically related isolates at all three time points. While the majority of the isolates at any one time point were phylogenomically similar, most individuals did not contain phylogenomically similar isolates at more than two time points. Examination of global genome content, canonical virulence factors, multilocus sequence type, serotype, and antimicrobial resistance genes identified diversity even among phylogenomically similar strains. There was no apparent increase in the antimicrobial resistance gene content after antibiotic treatment. The examination of the from longitudinal samples from multiple children in Tanzania provides insight into the genomic diversity and population variability of resident within the rapidly changing environment of the gastrointestinal tract of these children. This study increases the number of resident genome sequences, and explores diversity through longitudinal sampling. We investigate the genomes of isolated from human gastrointestinal tracts as part of an antibiotic treatment program among rural Tanzanian children. Phylogenomics demonstrates that resident are diverse, even within a single host. Though the isolates of the gastrointestinal community tend to be phylogenomically similar at a given time, they differed across the interrogated time points, demonstrating the variability of the members of the community in these subjects. Exposure to antibiotic treatment did not have an apparent impact on the community or the presence of resistance and virulence genes within genomes. The findings of this study highlight the variable nature of specific bacterial members of the human gastrointestinal tract.