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We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to in-depth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe. [Display omitted] • Gut microbiome and diet of European salt miners determined using paleofeces • Until the Baroque, the microbiome resembled that of modern non-Westernized people • Food-fermenting fungi in Iron Age feces indicates blue cheese and beer consumption Maixner et al. describe the gut microbiome and diet of European salt miners using paleofeces dating from the Bronze Age to the Baroque period. This analysis provides evidence for recent changes in the gut microbiome due to industrialization and for the consumption of fermented food and beverages in Iron Age Europe. [ABSTRACT FROM AUTHOR]