A workflow to study the microbiota profile of piglet’s umbilical cord blood: from sampling to data analysis

Francesco Palumbo , Marion Girard , Federico Correa , Giuseppe Bee , Paolo Trevisi
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Abstract

The possibility of pre-birth microbiota colonisation remains controversial in the scientific community. Due to the placenta’s characteristics in pigs, the umbilical cord is the sole way for mother-foetus microbial transmission to occur. Studies on this topic have demonstrated conflicting results; some of these discrepancies might be due to differences during sampling, DNA extraction, bioinformatics and data analysis. The aim of this study is to assess a workflow for characterising the umbilical cord blood microbial profile by adjusting for the contaminating sources of bacterial DNA during the extraction procedure. The results show that among 735 amplicon sequence variants (ASVs), 568 ASVs were contaminants, while 165 ASVs were true samples. Using this workflow, we could distinguish the contaminant ASVs introduced during bacterial DNA extraction and amplification. With the results of the present study, however, we cannot confirm the pre-birth bacterial transfer by the umbilical cord blood due to the lack of samples representative of the contaminants in the surrounding sampling environment. Nevertheless, the present study can be used as a reference to address low microbial biomass, particularly with umbilical cord blood.

研究仔猪脐带血微生物群概况的工作流程:从采样到数据分析
出生前微生物群定植的可能性在科学界仍然存在争议。由于猪胎盘的特性,脐带是母婴微生物传播的唯一途径。对这一主题的研究显示出相互矛盾的结果;其中一些差异可能是由于采样、DNA提取、生物信息学和数据分析过程中的差异。本研究的目的是通过调整提取过程中细菌DNA的污染源来评估脐带血微生物特征的工作流程。结果表明,在735个扩增子序列变体(ASV)中,568个ASV是污染物,而165个ASV则是真实样本。使用这个工作流程,我们可以区分在细菌DNA提取和扩增过程中引入的污染物ASV。然而,根据目前的研究结果,由于缺乏代表周围采样环境中污染物的样本,我们无法确认脐带血在出生前的细菌转移。然而,本研究可作为解决低微生物生物量问题的参考,尤其是脐带血。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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