Mulder IE, Schmidt B, Stokes CR et al. BMC Biol 2009;7:79.
Early environmental factors including childhood domestic hygiene can influence the risk of future development of IBD. Mulder et al. conducted an investigation using genetically related piglets housed in either indoor or outdoor environments, or in experimental isolators, in order to assess microbial colonization in adult animals. Pigs that had been housed in a natural outdoor environment showed a dominance of the Firmicutes phylum, especially Lactobacillus spp., whereas pigs housed indoors had higher numbers of potentially pathogenic phylotypes. This highlights the importance of the environment in shaping the gut microbiota.
In this study, Mulder and colleagues showed that early life environmental exposure has a significant and long-lasting impact on the microbiota composition of the adult gut and on the immune transcriptome. Using genetically related piglets housed in either indoor or outdoor environments, or in experimental isolators, major differences in mucosa-adherent microbial diversity in the ileum of the adult pigs were observed. Pigs housed in a natural outdoor environment showed a dominance of the Firmicutes phylum, in particular the Lactobacillus spp., whereas animals housed in a hygienic indoor environment had reduced numbers of Lactobacillus and higher numbers of potentially pathogenic phylotypes. A strong inverse correlation between the abundance of Firmicutes and pathogenic bacteria populations in the gut was observed. These differences were exaggerated in animals housed in experimental isolators. Microarray gene expression analyses revealed significant gut-specific gene expression responses that were also related to early-life environment. In particular, indoor-housed pigs displayed increased expression of type 1 interferon genes, major histocompatibility complex class I genes, and several chemokine genes. Rural, outdoor environments appeared to support the establishment of a natural microbiota dominated by lactobacilli and containing low numbers of potentially pathogenic bacteria; this may be an important factor in maintaining mucosal immune homeostasis and limiting excessive inflammatory responses in the gut.