Reagent contamination human feces

We evaluated DNA extraction method, initial sample biomass and reagent contamination on the assessment of the human gut microbiota. We found significant differences in the total number of reads among samples from different kits and dilutions, but not between donors. The number of reads from technical controls was negligible. DNA extraction kits allowed inferring microbial consortia with similar membership but different abundances. Furthermore, we found differences in the taxonomic profile of the microbial community. Unexpectedly, the effect of sample dilution was moderate and did not introduce severe bias into the microbial inference. Our results indicate that the gut microbiota inference is not much affected by contamination with laboratory reagents, even in highly diluted samples, but largely impacted by the protocol to extract DNA.

我们在人类肠道菌群的评估研究中，考察了DNA提取方法、初始样本生物量以及试剂污染的影响。研究发现，不同试剂盒与稀释梯度处理的样本间，测序读段（reads）总数存在显著差异，但不同供体的样本间无此差异。技术对照（technical controls）的测序读段数量可忽略不计。不同DNA提取试剂盒可推断得到成员组成相似但丰度存在差异的微生物群落（microbial consortia）。此外，我们还观测到微生物群落的分类学特征谱存在差异。出乎意料的是，样本稀释的影响较为温和，并未对微生物群落推断引入显著偏倚。我们的研究结果表明，即便在高度稀释的样本中，肠道菌群推断结果也基本不受实验室试剂污染的影响，但会在很大程度上受DNA提取实验方案的影响。