One potential idea would be a gut microbiome experiment studying DNA sequences of healthy mice, mice with inflammation affiliated colorectal cancer, and cancel cell bearing mice with a chemotherapeutic drug. Below is a diagram of how that experimental procedure would look as a flow chart.
Another idea would be to design a a research project to learn more about a specific phyla of bacteria. An area of research that is lacking in the scientific community right now has to do with the specific purpose and function of some of the bacteria found in the gut microbiome. If more is learned about the purpose and reason the bacteria is there and why chemotherapy or cancer makes it change, those findings could hopefully be used to make cancer treatments more successful.
I would also be interested in trying out an evolution based study on gut microbes. A lot of theories and research suggest that our gut microbiomes evolved alongside use through co-evolution. Because of this, it would be cool to start a study where fecal samples are taken every few years from the same person and throughout their family. This would maybe allow us to see how changes in differently daily lifestyles can affect the gut microbiome.