The gut microbiota is a potentially modifiable risk factor for various health complications. Therefore, advanced techniques are warranted to understand the relationship between gut microbiota, disease, and clinical relevance. This chapter focuses on the emerging application of artificial intelligence (AI) techniques in the studies of gut microbiota. It opens with a discussion on the role of gut microbiota in health, mentions an overview of AI techniques, and provides information on the application of AI in the study of the gut microbiome and its role in the diagnosis and treatment of diseases. It also gives a glimpse into the challenges and future direction of artificial intelligence in gut microbiome research. The chapter provides new insights into the extraordinary applications of AI in the study of the gut microbiome.