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However, to date, no study has comprehensively assessed the relationships between the esophageal microbiome and the host.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Here, we examine the esophageal microenvironment in gastro-esophageal reflux disease and metaplasia using multi-omics strategies targeting the microbiome and host transcriptome, followed by targeted culture, comparative genomics, and host-microbial interaction studies of bacterial signatures of interest.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Profiling of the host transcriptome from esophageal mucosal biopsies revealed profound changes during metaplasia. Importantly, five biomarkers showed consistent longitudinal changes with disease progression from reflux disease to metaplasia. We showed for the first time that the esophageal microbiome is distinct from the salivary microbiome and the enrichment of<jats:italic>Campylobacter<\/jats:italic>species as a consistent signature in disease across two independent cohorts. Shape fitting and matrix correlation identified associations between the microbiome and host transcriptome profiles, with a novel co-exclusion relationship found between<jats:italic>Campylobacter<\/jats:italic>and napsin B aspartic peptidase. Targeted culture of<jats:italic>Campylobacter<\/jats:italic>species from the same cohort revealed a subset of isolates to have a higher capacity to survive within primary human macrophages. Comparative genomic analyses showed these isolates could be differentiated by specific genomic features, one of which was validated to be associated with intracellular fitness. Screening for these<jats:italic>Campylobacter<\/jats:italic>strain-specific signatures in shotgun metagenomics data from another cohort showed an increase in prevalence with disease progression. Comparative transcriptomic analyses of primary esophageal epithelial cells exposed to the<jats:italic>Campylobacter<\/jats:italic>isolates revealed expression changes within those infected with strains with high intracellular fitness that could explain the increased likelihood of disease progression.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>We provide a comprehensive assessment of the esophageal microenvironment, identifying bacterial strain-specific signatures with high relevance to progression of metaplasia.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s13073-021-00951-6","type":"journal-article","created":{"date-parts":[[2021,8,19]],"date-time":"2021-08-19T10:18:41Z","timestamp":1629368321000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett\u2019s esophagus"],"prefix":"10.1186","volume":"13","author":[{"given":"Nandan P.","family":"Deshpande","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen M.","family":"Riordan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire J.","family":"Gorman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaun","family":"Nielsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tonia L.","family":"Russell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolina","family":"Correa-Ospina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bentotage S. 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