Esophageal microbiota during homeostasis, dysbiosis and following microbiota transplantation

The esophagus is colonized with bacteria but their interactions with the host esophageal epithelium remain unknown. Here, we describe the basic properties of the esophageal microbiome in mice. We report that the esophagus of specific pathogen free (SPF) mice is colonized with diverse and unique microbial communities within the first month of life. The esophageal microbiota is distinct from other anatomical sites examined, dominated by Firmicutes, and demonstrates spatial heterogeneity as the distal esophagus is enriched in Lactobacilli and has less Streptococci compared with the proximal esophagus. Microbiota transplantation restores the residential esophageal microbiota of germ-free mice, including the spatial heterogeneity, demonstrating that the local environment drives diversity. In addition, microbiota colonization modifies esophageal gene expression and is enriched in pathways associated with epithelial barrier function. Systemic antibiotic exposure reduces the abundance of Firmicutes, expands Actinobacteria and Tenericutes and exaggerates type 2 allergic inflammation in the esophagus. Taken together, these data establish the composition, transplantation potential, antibiotic responsiveness, and host-microbiota interaction in the esophagus, and have implications for both health and disease.