title: Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations.
abstract: Metagenomic studies of the human gut microbiome have only recently begun to explore the differences in taxonomic composition between subjects from diverse geographical origins. Here, we compared taxonomy, resistome and functional metabolic properties of publicly available shotgun datasets of human fecal samples collected from different geographical regions (Europe, North America, Asia and Oceania). Such datasets encompassed gut microbiota information corresponding to 13 developed/industrialized societies, as well as two traditional hunter-gatherer, pre-agricultural communities (Tanzanian and Peruvian individuals). Assessment of the retrieved taxonomic profiles allowed the most updated reconstruction of the global core-microbiome as based on currently available data, as well as the identification and targeted genome reconstruction of bacterial taxa that appear to have been lost and/or acquired during urbanization/industrialization. Functional characterization of these metagenomic datasets indicates that the urbanization/industrialization process which occurred in recent human history has shaped the gut microbiota through the acquisition and/or loss of specific gut microbes, thereby potentially impacting on the overall functionality of the gut microbiome.
authors.affiliation: Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Mancabelli
authors.affiliation: Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.affiliation: Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
authors.forename: Gabriele Andrea
authors.initials: GA
authors.lastname: Lugli
authors.affiliation: Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Turroni
authors.affiliation: Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Ferrario
authors.affiliation: APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
authors.affiliation: Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
mesh_terms: D000383:Agriculture; D001208:Asia; D005060:Europe; D005243:Feces; D000069196:Gastrointestinal Microbiome; D014644:Genetic Variation; D006801:Humans; D056186:Metagenomics; D009656:North America; D012424:Rural Population; D014505:Urban Population