The specialty of gastroenterology will be affected profoundly by the ability to modify the gastrointestinal microbiota through the use of antibiotics. This study investigated the in vivo effect of roxithromycin on gut bacteria and gene expression of colonic epithelial cells (CECs) using microbial 16S rDNA and colonic epithelial cell RNA sequencing, respectively. The results showed that roxithromycin distinctly lowered the microbial diversity in both the small intestine and cecum and altered the compositions of bacteria at both the phylum and genus levels, including the reduction of some bacteria beneficial to the hosts' health. Eight decreased and 8 increased genera in the small intestine and 17 decreased and 4 increased genera of bacteria in the cecum were most affected by roxithromycin consumption. This consumption further altered the CECs' expression of multiple genes. Thirty-one genes, which were significantly enriched in seven KEGG pathways and related to immune response, wound healing, and fibrosis, were significantly affected. Roxithromycin ingestion in healthy hosts, therefore, might lead to some undesirable consequences via affecting hosts' gut microbiota and CECs. Our work offers a more comprehensive understanding of the impact of consuming roxithromycin on human health.