Freshwater harmful algal blooms (HABs) are a major environmental health problem worldwide caused by water eutrophication. HABs are triggered by predominance of cyanobacteria, some of which produce toxins. The most ubiquitous cyanotoxin is microcystin (MC) and the congener MC-LR is the most studied due to its toxicity. Short-term exposure to toxins can cause liver function failure and disturbances to the gut microbiome, but this has not been well described with MC-LR exposure. This study investigated the gut microbial communities of mice from our liver toxicity study from daily ingestion of MC-LR for 8 days. CD-1 mice were divided into three dosage groups, control, low exposure (sub-lethal MC-LR concentration), and high exposure (near-lethal MC-LR concentration). Fecal samples were analyzed using 16S rRNA sequencing, and bioinformatic analysis was done on the QIIME2 platform. Prediction of microbial functions were examined via PICRUSt2, and differentially abundant taxa and metabolic pathways were determined using Linear discriminant analysis Effect Size (LEfSe). Results revealed that at population level, there were significant differences by sex in microbial community diversity and structure. However, there were no significant shifts in bacterial diversity or the microbial community structure over the study duration with MC-LR exposure, even when analyzed separately by sex. Predictive functional gene analysis indicated that several metabolic pathways were significantly different in the high dose group when comparing fecal samples before exposure and on the last day of the study, as well as the control and high dose groups on Day 8. Significant differentially abundant taxa were also identified contributing to these pathways. Several pathways and taxa were related to liver disease, gut inflammation, and cancer. The outcome of this study suggests a need for in-depth investigation of metabolic activity and other functions in the gut in future toxicity studies of MC, as well as potential consideration of the role of sex in MC-LR toxicity.