Opioid use disorder is a public health crisis that leads to tremendous suffering for patients as well as substantial social and economic cost for society. There are currently available treatments for patients with opioid use disorder, but they remain intolerable or ineffective for many. The need to develop new avenues for therapeutics development in this space is great. There is a tremendous amount of work that has been done in models of substance use disorders, including opioid use disorder, demonstrating that prolonged exposure to drugs of abuse leads to marked dysregulation of the transcriptional and epigenetic landscape of important limbic substructures. It is widely believed that these changes in the regulation of gene expression in response to drugs may be a key driving factor in the perpetuation of drug taking and seeking behaviors. Thus, development of interventions that could shape transcriptional regulation in response to drugs of abuse would be of high value. Over the past decade there has been a surge in research demonstrating that the resident bacteria of the gastrointestinal tract, collectively the gut microbiome, can have tremendous influence on neurobiological and behavioral plasticity. Previous work from our group and others has demonstrated that alterations in the gut microbiome can alter behavioral responses to opioids in multiple different paradigms. Additionally, we have previously reported that depletion of the gut microbiome with antibiotics markedly shifts the transcriptome of the nucleus accumbens following prolonged morphine exposure. In this manuscript we present a comprehensive analysis of the effects of the gut microbiome on transcriptional regulation of the nucleus accumbens following morphine by utilizing germ-free, antibiotic treated, and control mice. This allows for detailed understanding of the role of the microbiome in regulating baseline transcriptomic control, as well as response to morphine. We find that germ-free status leads to a marked gene dysregulation in a manner distinct to adult mice treated with antibiotics, and that altered gene pathways are highly related to cellular metabolic processes. These data provide additional insight into the role of the gut microbiome in modulating brain function and lay a foundation for further study in this area.