Chicks are ideal to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Taxonomic/metagenomic analyses captured the development of the chick microbiota in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm) during development. Taxonomic analysis suggests that colonization by the chicken microbiota takes place in several waves. The cecal microbiota stabilizes at day 12 post-hatch with prominent Gammaproteobacteria and Clostridiales. Introduction of S. Typhimurium at day 4 post-hatch disrupted the expected waves of intestinal colonization. Taxonomic and metagenomic shotgun sequencing analyses allowed us to identify species present in uninfected chicks. Untargeted metabolomics suggested different metabolic activities in infected chick microbiota. This analysis, and GS-MS on ingesta confirmed that lactic acid in cecal content coincides with the stable presence of Enterococci in STm infected chicks. Unique metabolites including 2-isopropylmalic acid, an intermediate in the biosynthesis of leucine, was present only in the cecal content of STm infected chicks. Metagenomic data suggested that the microbiota in STm infected chicks contained a higher abundance of genes, from STm itself, involved in branched chain amino acid synthesis. We generated a deletion mutant in ilvC (STM3909) encoding ketol-acid-reductoisomerase, a gene required for the production of L-isoleucine and L-valine. ΔilvC mutants are disadvantaged for growth during competitive infection with the wild type. Providing the ilvC gene in trans restored growth of the ΔilvC mutant. Our integrative approach identified biochemical pathways used by STm to establish a colonization niche in the chick intestine during development.IMPORTANCEChicks are an ideal model to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Using taxonomic and metagenomic analyses we captured the development of the chick microbiota to 19 days post-hatch in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm). We show that normal development of the microbiota takes place in waves, and is altered in the presence of a pathogen. Metagenomics and metabolomics suggested that branched chain amino acid biosynthesis is especially important for Salmonella growth in the infected chick intestine. Salmonella mutants unable to make L-isoleucine and L-valine colonize the chick intestine poorly. Restoration of the pathway for biosynthesis of these amino acids restored the colonizing ability of Salmonella. Integration of multiple analyses allowed us to correctly identify biochemical pathways used by Salmonella to establish a niche for colonization in the chick intestine during development.
