Choudhury R, Middelkoop A, Bolhuis J E, Kleerebezem M
Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University and Research, Wageningen, Netherlands.
Adaptation Physiology Group, Department of Animal Sciences, Wageningen University and Research, Wageningen, Netherlands.
Front Microbiol. 2019 Aug 14;10:1886. doi: 10.3389/fmicb.2019.01886. eCollection 2019.
A prerequisite for reliable microbiota analysis is having an effective and consistent sampling method. Fecal sampling, commonly used to study the intestinal microbiome, might not be suitable in all situations, especially considering the potential difficulties in obtaining fresh feces from young animals. Indeed, this study shows that the success rate of collecting fecal samples from young piglets (<2 weeks of age) was very low. Therefore, we evaluated rectal swabs as an alternative sample type (to feces) for studying porcine microbiome development and performed a comparative analysis of microbiome composition obtained from fresh fecal samples and rectal swabs in 15 healthy piglets at seven (6 piglets) and 20 (9 piglets) days of age. Three samples (fresh feces, rectal swab before and after defecation) were collected from individual piglets and microbiome composition was assessed by 16S rRNA gene sequencing. The results demonstrated that rectal swabs and fecal samples provide similar microbiome composition profiles, with samples clustering predominantly by individual animal rather than sample type. Furthermore, regardless of the sample type, the biological interpretation with respect to microbiota colonization patterns associated with different ages (7 and 20 days) was found to be comparable. Independent of sample type, we observed age-related changes like increasing microbiota diversity and alterations in relative abundances of the phyla and , which was also reflected in consistent family- and genus-level microbiota changes. This study establishes that rectal swabs are a suitable alternative sample type to study the porcine microbiome development in early life, when fecal sampling is challenging.
可靠的微生物群分析的一个前提条件是拥有一种有效且一致的采样方法。粪便采样常用于研究肠道微生物组，但在所有情况下可能并不都适用，尤其是考虑到从幼小动物获取新鲜粪便可能存在的潜在困难。事实上，本研究表明，从幼龄仔猪（<2周龄）采集粪便样本的成功率非常低。因此，我们评估了直肠拭子作为（替代粪便的）一种样本类型，用于研究猪微生物组的发育，并对15头健康仔猪在7日龄（6头仔猪）和20日龄（9头仔猪）时从新鲜粪便样本和直肠拭子中获得的微生物组组成进行了比较分析。从每头仔猪采集三个样本（新鲜粪便、排便前后的直肠拭子），并通过16S rRNA基因测序评估微生物组组成。结果表明，直肠拭子和粪便样本提供了相似的微生物组组成概况，样本主要按个体动物而非样本类型聚类。此外，无论样本类型如何，发现与不同年龄（7日龄和20日龄）相关的微生物群定殖模式的生物学解释具有可比性。不考虑样本类型，我们观察到与年龄相关的变化，如微生物群多样性增加以及门和的相对丰度改变，这也反映在一致的科和属水平微生物群变化中。本研究确定，在粪便采样具有挑战性的早期生活中，直肠拭子是研究猪微生物组发育的一种合适替代样本类型。
