title: Insights into the biodiversity of the gut microbiota of broiler chickens.
abstract: The gastrointestinal tract of poultry is densely populated with microorganisms, which are presumed to interact with the host and ingested feed. Comparison of the gut microbiota of chickens used for large-scale commercial production (Broiler Chicken, BC) and those grown in semi-wild conditions (Free-Range Chicken, FRC) revealed that at phylum level Firmicutes was the dominant phylum of the gut community in BC, while the gut microbiota of FRC contained higher levels of Bacteroidetes and Proteobacteria. Such differences may be due to the diet and/or the intensive use of antibiotics in BC. Indeed, analysis of the resistome of the cecal microbiomes showed a marked richness in BC datasets, with a modulation of the cecal microbiota toward antibiotic resistant bacteria. Functional characterization of the microbiome of FRC samples revealed an increase in gene pathways involved in degradation of complex carbohydrates. Furthermore, in silico analyses of the microbiomes of FRC and BC revealed a higher presence in genes involved in formate production in BC samples. Notably, compared to the BC microbiomes the FRC microbiomes were shown to contain a higher abundance of genes involved in the pathway for acetate production.
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Mancabelli
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Ferrario
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.affiliation: GenProbio srl, Parma, Italy.
authors.forename: Marta
authors.initials: M
authors.lastname: Mangifesta
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Turroni
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Duranti
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
authors.forename: Gabriele Andrea
authors.initials: GA
authors.lastname: Lugli
authors.affiliation: GenProbio srl, Parma, Italy.
authors.forename: Alice
authors.initials: A
authors.lastname: Viappiani
authors.affiliation: Department of Medical-Veterinary Science, University of Parma, Parma, Italy.
authors.forename: Maria Cristina
authors.initials: MC
authors.lastname: Ossiprandi
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 Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics; D041963:Bacteroidetes / Q000235:genetics; D044822:Biodiversity; D002432:Cecum / Q000382:microbiology; D002645:Chickens / Q000382:microbiology*; D004032:Diet; D000069196:Gastrointestinal Microbiome; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S