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This study aimed to evaluate the disruption of the swine gut microbiota and histopathological changes caused by infection with enterotoxigenic <i>E. coli</i>. Fecal samples were collected from piglets suffering from diarrhea post-recovery and healthy animals. Intestinal tissues were collected for histopathological changes. The results revealed histopathological changes mainly in the ileum of the infected animals compared to those in the ileum of the control and recovered animals. The operational taxonomic units (OTUs) revealed that the <i>E. coli</i> diarrheal group exhibited the highest bacterial richness. Principal coordinate analysis (PCoA) corroborated the presence of dysbiosis in the gut microbiota following <i>E. coli</i>-induced diarrhea. While the normal control and infected groups displayed slight clustering, the recovery group formed a distinct cluster with a distinct flora. <i>Bacteroidetes</i>, <i>Firmicutes</i>, and <i>Fusobacteria</i> were the dominant phyla in both the healthy and recovered piglets and in the diarrheal group. LEfSe and the associated LDA score analysis revealed that the recovered group exhibited dominance of the phyla <i>Euryarchaeota</i> and <i>Bacteroidota</i>, while groups N and I showed dominance of the phyla <i>Firmicutes</i> and <i>Fusobacteriota</i>, respectively. The LDA scores highlighted a significant expression of the <i>Muribaculacea</i> family in group R. The obtained findings will help in understanding the microbiome during swine colibacillosis, which will support control of the outbreaks.