Abstract
Microbiomes affect many aspects of host biology, but the eco‐evolutionary forces that shape their diversity in natural populations remain poorly understood. Geographical gradients, such as latitudinal clines, generate predictable patterns in biodiversity at macroecological scales, but whether these macroscale processes apply to host–microbiome interactions is an open question. To address this question, we sampled the microbiomes of 13 natural populations of Drosophila melanogaster along a latitudinal cline in the eastern United States. The microbiomes were surprisingly consistent across the cline, as latitude did not predict either alpha or beta diversity. Only a narrow taxonomic range of bacteria were present in all microbiomes, indicating that strict taxonomic filtering by the host and neutral ecological dynamics are the primary factors shaping the fly microbiome. Our findings reveal the complexity of eco‐evolutionary interactions shaping microbial variation in D. melanogaster and highlight the need for additional sampling of the microbiomes in natural populations along environmental gradients.