The relationship of epigenetic processes and the intestinal microbiota may serve as an essential role in elevating the bisulfite sequencing potentials in discovering host-microbiota interactions in germfree (GF) and conventional mice. The previous studies have established that the microbiota regulates a large proportion of the intestinal epithelial transcriptome in the adult host. However, microbial effects on DNA methylation and gene expression during early postnatal development are still poorly understood. In recent years, the number of studies investigating the impact of the gut microbiome in colorectal cancer (CRC) has risen sharply. As a result, we now know that various microbes (and microbial communities) are found more frequently in the stool and mucosa of individuals with CRC than healthy controls, including in the primary tumors themselves and even in distant metastases. We took albino mice and reared them under laboratory conditions. After 16 weeks of rearing, mice were slaughtered, and DNA extraction was performed later on. Bisulfite sequencing was done under controlled environmental conditions to unveil the role of sequencing in determining the host-microbiota interactions. The study results showed a strong host-microbiota interaction in GF mice as it significantly affects lipid metabolism, inflammation, carcinogenic, and postnatal development.