Establishment of normal gut microbiota is compromised under excessive hygiene conditions

Background: Early gut colonization events are purported to have a major impact on the incidence of inflammatory and autoimmune diseases in later life. Hence, factors which influence this process may have implications for both human and animal health. Previously, we demonstrated strong influences of early-life environment gut microbiota composition in adult pigs. Here, we sought to further investigate the impact of limiting microbial during early life on the development of the pig gut microbiota.

Methodology/Principal Findings: Outdoor-and indoor-reared animals, exposed to the microbiota in their natural environment for the first two days of life, were transferred to an isolator facility and adult gut microbial diversity analyzed by 16S rRNA gene sequencing. From a total of 2,196 high-quality 16S rRNA gene sequences, 440 phylotypes identified in the outdoor group and 431 phylotypes in the indoor group. The majority of clones were assigned to the phyla Firmicutes (67.5% of all sequences), Proteobacteria (17.7%), Bacteroidetes (13.5%) and to a lesser Actinobacteria (0.1%). Although the initial maternal and environmental microbial inoculum of isolator-reared animals identical to that of their naturally-reared littermates, the microbial succession and stabilization events reported previously naturally-reared outdoor animals did not occur. In contrast, the gut microbiota of isolator-reared animals remained diverse containing a large number of distinct phylotypes.

Conclusions/Significance: The results documented here indicate that establishment and development of the normal microbiota requires continuous microbial exposure during the early stages of life and this process is compromised conditions of excessive hygiene.