Background: Early microbial colonization of the gut reduces the incidence of infectious,udinflammatory and autoimmune diseases. Recent population studies reveal that childhood hygiene isuda significant risk factor for development of inflammatory bowel disease, thereby reinforcing theudhygiene hypothesis and the potential importance of microbial colonization during early life. Theudextent to which early-life environment impacts on microbial diversity of the adult gut andudsubsequent immune processes has not been comprehensively investigated thus far. We addressedudthis important question using the pig as a model to evaluate the impact of early-life environmentudon microbe/host gut interactions during development.udResults: Genetically-related piglets were housed in either indoor or outdoor environments or inudexperimental isolators. Analysis of over 3,000 16S rRNA sequences revealed major differences inudmucosa-adherent microbial diversity in the ileum of adult pigs attributable to differences in earlylifeudenvironment. Pigs housed in a natural outdoor environment showed a dominance of Firmicutes,udin particular Lactobacillus, whereas animals housed in a hygienic indoor environment had reducedudLactobacillus and higher numbers of potentially pathogenic phylotypes. Our analysis revealed audstrong negative correlation between the abundance of Firmicutes and pathogenic bacterialudpopulations in the gut. These differences were exaggerated in animals housed in experimentaludisolators. Affymetrix microarray technology and Real-time Polymerase Chain Reaction revealedudsignificant gut-specific gene responses also related to early-life environment. Significantly, indoorhousedudpigs displayed increased expression of Type 1 interferon genes, Major HistocompatibilityudComplex class I and several chemokines. Gene Ontology and pathway analysis further confirmedudthese results.
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