Estuarine organisms, such as the model cnidarian the starlet sea anemone (Nematostella vectensis), experience daily variation in their marine environment. The adaptability of N. vectensis can be attributed not only to genetic recombination and natural selection, but potentially to DNA methylation, an heritable and reversible change in DNA expression where a methyl group is added to the five-position carbon on a cytosine ring to alternate gene expression in response to environment changes. This study focuses on understanding microbial metabolite interactions from Bacillus thuringiensis with N. vectensis using the solution containing secreted metabolites from bacterial growth known as cell-free supernatant (CFS). We examined larval development and methylation rates of adult polyp genes. For both experiments, larvae or adult N. vectensis were placed into a 0.5% concentration of CFS for a week. The larvae were observed to determine life stage progression at various time points, and adult N. vectensis had their DNA extracted after exposure. Examining larval development, development time was not affected by the presence of CFS. Analyzing the methylation of genes in adult N. vectensis, a total of 23 differentially methylated genes were noted. Multiple genes were identified as having unknown functions, being uncharacterized, or were pseudogenes. Genes that did present a function were functions related to cell wall integrity & stress response, ubiquitin-like-specific protease, and tRNAs. Genome methylation showed similar groupings of methylated genes between sexes rather than treatment types. Overall, our work provides insight into the role of CFS within estuarine environments and its potential effects on marine invertebrate survival.