© 2019Background: The intestinal bacterial community has an important role in maintaining human health. Dysbiosis is a key inducer of many chronic diseases including obesity and diabetes. Kunming mice are frequently used as a model of human disease and yet little is known about the bacterial microbiome resident to the gastrointestinal tract. Results: We undertook metagenomic sequencing of the luminal contents of the stomach, duodenum, jejunum, ileum, cecum, colon, and rectum of Kunming mice. Firmicutes was the dominant bacterial phylum of each intestinal tract and Lactobacillus the dominant genus. However, the bacterial composition differed among the seven intestinal tracts of Kunming mice. Compared with the small intestine, the large intestine bacterial community of Kunming mice is more stable and diverse. Conclusions: To our knowledge, ours is the first study to systematically describe the gastrointestinal bacterial composition of Kunming mice. Our findings provide a better understanding of the bacterial composition of Kunming mice and serves as a foundation for the study of precision medicine. How to cite: Han X, Shao H, Wang Y, et al. Composition of the bacterial community in the gastrointestinal tract of Kunming mice. Electron J Biotechnol 2020;43. https://doi.org/10.1016/j.ejbt.2019.11.003