The gut microbiome is a complex microbial community that plays an important role in shaping host biology. Despite immense academic interest surrounding the microbiome and its relation to the host, the ecological processes governing the gut community remain poorly understood. This dissertation investigates the ecological processes influencing gut microbiome assembly and its effects on host behavior using a simplified Drosophila melanogaster model. Chapter 1 examines niche-based and neutral processes driving microbial coexistence, focusing on the interactions between closely related Acetobacter species. The results highlight how niche overlap influences competition and colonization success. Chapter 2 explores the role of variation in habitat quality in shaping co-abundances of colonizing microbiota. This study reveals that even subtle differences in habitat can significantly impact species abundance and community composition, especially among taxa with overlapping niches. Chapter 3 shifts the focus from the ecology of the gut microbiome to the consequences of microbiome composition on host behavior, specifically female mating behavior in D. melanogaster. We demonstrate that distinct microbial communities can alter mating preferences and latency, suggesting a potential influence of the microbiome on host evolutionary trajectories. Together, these chapters provide insights into the factors driving gut microbiome assembly and the broader implications for host biology, highlighting the importance of ecological context in understanding host-microbe interactions.