title: Establishment of normal gut microbiota is compromised under excessive hygiene conditions.
abstract: BACKGROUND
  Early 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.
  
  
  RESULTS
  Outdoor- 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
  The 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.
authors.affiliation: Gut Immunology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.
authors.forename: Bettina
authors.initials: B
authors.lastname: Schmidt
authors.forename: Imke E
authors.initials: IE
authors.lastname: Mulder
authors.forename: Corran C
authors.initials: CC
authors.lastname: Musk
authors.forename: Rustam I
authors.initials: RI
authors.lastname: Aminov
authors.forename: Marie
authors.initials: M
authors.lastname: Lewis
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Stokes
authors.forename: Mick
authors.initials: M
authors.lastname: Bailey
authors.forename: James I
authors.initials: JI
authors.lastname: Prosser
authors.forename: Bhupinder P
authors.initials: BP
authors.lastname: Gill
authors.forename: John R
authors.initials: JR
authors.lastname: Pluske
authors.forename: Denise
authors.initials: D
authors.lastname: Kelly
mesh_terms: D000818:Animals; D044822:Biodiversity; D003433:Crosses, Genetic; D041981:Gastrointestinal Tract / Q000382:microbiology*; D015723:Gene Library; D006920:Hygiene; D007413:Intestinal Mucosa / Q000382:microbiology; D054892:Metagenome / Q000502:physiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013552:Swine
chemical_list: D012336:RNA, Ribosomal, 16S