Stool Microbial DNA Isolation: Studying the Effect of Environmental Enrichment on Microbiome Diversity in Murine Tumor Model

- Environmental enrichment, or EE, refers to the modifications in the housing parameters to obtain beneficial effects on various diseases such as cancer. In a tumor bearing mouse, EE activates the immune system and reduces inflammation, which ultimately improves the gut microbiota and improves survival rate. To study the changes in gut microbiota, add the desired amount of stool lysis buffer in a tube containing the mouse stool.

Centrifuge the sample and transfer the supernatant to a fresh microcentrifuge tube. Add guanidinium chloride lysis buffer that denatures DNase and RNase. Next, add ethanol and transfer the sample to a silica spin column.

Ethanol helps DNA bind to silica. Centrifuge the sample. Now, transfer the column to a fresh microcentrifuge tube and add an elution buffer to the column to elute DNA.

Centrifuge the sample and discard the column. Transfer the sample into a PCR tube and run PCR to amplify the DNA. Load the DNA on agarose gel and perform electrophoresis to quantify the size of microbial DNA. In the following protocol, we will isolate DNA from stools to analyze the EE effect on colon microbiota in the tumorigenic mouse.

- Utilize a commercial kit to isolate m