Establishment of Normal Gut Microbiota Is Compromised under Excessive Hygiene Conditions

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.

研究背景 早期肠道定植事件被认为对个体成年后感染性、炎症性及自身免疫性疾病的发病风险具有显著影响。因此，能够影响这一过程的因素，对人类与动物健康均具备重要的研究价值与实践意义。此前，本团队已证实早期生命环境对成年猪肠道菌群组成具有显著调控作用。本研究旨在进一步探究早期限制微生物暴露对猪肠道菌群发育的影响。

研究方法与主要结果 将出生头两日暴露于自然饲养环境微生物群的户外饲养与室内饲养动物，转移至隔离器设施中，并通过16S rRNA基因测序分析其成年后的肠道微生物多样性。从总计2196条高质量16S rRNA基因序列中，户外组共鉴定出440个系统型（phylotype），室内组共鉴定出431个系统型。大部分克隆序列被归类为厚壁菌门（Firmicutes，占所有序列的67.5%）、变形菌门（Proteobacteria，17.7%）、拟杆菌门（Bacteroidetes，13.5%），以及占比极低的放线菌门（Actinobacteria，0.1%）。尽管隔离饲养动物的初始母体与环境微生物接种源与其自然饲养的同窝幼崽完全一致，但此前在自然户外饲养动物中观察到的微生物演替与稳定过程并未出现。与之相反，隔离饲养动物的肠道菌群始终保持高度多样性，包含大量不同的系统型。

研究结论与意义 本研究结果表明，正常肠道菌群的建立与发育需要生命早期阶段的持续微生物暴露，而过度洁净的饲养环境会损害这一关键过程。