Abstract

BackgroundEarly gut colonization events are purported to have a major impact on the incidence of infectious, inflammatory and autoimmune diseases in later life. Hence, factors which influence this process may have important implications for both human and animal health. Previously, we demonstrated strong influences of early-life environment on gut microbiota composition in adult pigs. Here, we sought to further investigate the impact of limiting microbial exposure during early life on the development of the pig gut microbiota.Methodology/Principal FindingsOutdoor- and indoor-reared animals, exposed to the microbiota in their natural rearing environment for the first two days of life, were transferred to an isolator facility and adult gut microbial diversity was analyzed by 16S rRNA gene sequencing. From a total of 2,196 high-quality 16S rRNA gene sequences, 440 phylotypes were identified in the outdoor group and 431 phylotypes in the indoor group. The majority of clones were assigned to the four phyla Firmicutes (67.5% of all sequences), Proteobacteria (17.7%), Bacteroidetes (13.5%) and to a lesser extent, Actinobacteria (0.1%). Although the initial maternal and environmental microbial inoculum of isolator-reared animals was identical to that of their naturally-reared littermates, the microbial succession and stabilization events reported previously in naturally-reared outdoor animals did not occur. In contrast, the gut microbiota of isolator-reared animals remained highly diverse containing a large number of distinct phylotypes.Conclusions/SignificanceThe results documented here indicate that establishment and development of the normal gut microbiota requires continuous microbial exposure during the early stages of life and this process is compromised under conditions of excessive hygiene.

Highlights

  • The mammalian gut is colonized by a highly complex, diverse and dynamic microbiota

  • Analysis of 16S rRNA gene sequences has revealed major differences in mucosa-adherent microbial diversity in the ileum of adult pigs reared in different environments [18]

  • Bacterial diversity is elevated in pigs naturally colonized but reared in isolators Rarefaction curves (Fig. 1), which estimates species richness as a function of the number of clones sampled, were generated by plotting the number of phylotypes against the number of newly identified sequences

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Summary

Introduction

The mammalian gut is colonized by a highly complex, diverse and dynamic microbiota. considered sterile during gestation, at delivery the gut is exposed to microbes during passage through the birth canal. Experimental evidence has highlighted its crucial role in regulating complex mechanisms of host development, lipid metabolism, pathogen response, tissue repair and immune homeostasis [7,8,9,10,11,12,13]. Both hostdependent and host-independent factors affect microbial composition and include host genetics, nutrition, mode of delivery, gestational age, rearing environment and antibiotic exposure [14,15,16]. We sought to further investigate the impact of limiting microbial exposure during early life on the development of the pig gut microbiota

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