Using broiler lines selected based on fatness traits,we investigated how the gut microbiota is linked to obesity.We combined 16S rRNA-pyrosequencing and whole genome sequencing to analyze the fecal metagenomes of the lean (LL) and fat (FL) line chickens.Significant structural differences were found in both the phylogenic and functional metagenomes between the two chicken lines by multivariate analyses.Although the phylogenic metagenomes of both chicken lines were dominated by Firmicutes and Bacteroidetes,significantly less Bacteroidetes was detected in the FL group.Fourteen differential genera were identified,with some known short-chain fatty acid producers (including Subdoligranulum,Butyricicoccus,Eubacterium,Bacteroides,Blautia) and a potentially pathogenic genus (Enterococcus).Redundancy analysis identified 190 key responsive operational taxonomic units (OTUs) that accounted for the structural differences between the phylogenic metagenome of the two groups.Functional cluster of orthologous Group (COG) annotation revealed an overrepresentation of four COG categories (Amino acid transport and metabolism,E;Nucleotide transport and metabolism,F;Coenzyme transport and metabolism,H;and Lipid transport and metabolism,I) in LL group.By Kyoto encyclopedia of genes and genomes orthologue group (KO) annotation,fifteen differential pathways (Biosynthesis of amino acids,Pyruvate metabolism,Nitrotoluene degradation,Lipopolysaccharide biosynthesis,Peptidoglycan biosynthesis,Pantothenate and CoA biosynthesis,Glycosaminoglycan degradation,Thiamine metabolism,Phosphotransferase system,Two-component system,Bacterial secretion system,Flagellar assembly,Bacterial chemotaxis,Ribosome,Sulfur relay system) were identified.Our data highlighted interesting variations between the gut metagenomes of these two chicken lines and support that the fatness trait selection also divergently selects for metabolically specialized gut microbiota.