We read with great interest the meta’omic study by Kong et al 1 which reported on metagenomic sequencing of faecal samples to discover microbiome-derived biomarkers for colorectal cancer (CRC). Faecal immunochemical test (FIT) samples provide consistent microbiome profiling based on 16S rRNA gene (ie, amplicon-based) sequencing when compared with immediately frozen samples from whole stool2 and are stable during storage for up to 20 days.3 However, it is important to understand whether FIT samples are stable for longer periods and to ascertain if metagenomic (ie, non-amplicon) sequencing is feasible using these samples, given the relatively low biomass of FIT samples compared with whole stool. Metagenomics provides better taxonomic resolution and information on functional capacity and may detect rarer taxa compared with amplicon-based sequencing.4 We aimed to (1) investigate the stability of the faecal microbiome in FIT samples that had been stored for up to 6 months at −80°C using both amplicon-based and metagenomic sequencing and (2) compare microbiome profiles obtained with both amplicon-based and metagenomic sequencing. Samples from 10 healthy volunteers were stored at −80°C and analysed at 5 time points (0, 1, 2, 3, 6 months). All samples underwent amplicon-based sequencing (V4 region). Metagenomic …

中文翻译：

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粪便免疫化学测试 (FIT) 样本中粪便微生物组谱的长期稳定性


我们饶有兴趣地阅读了 Kong 等人的元组学研究 1，该研究报告了粪便样本的宏基因组测序，以发现源自微生物组的结直肠癌 (CRC) 生物标志物。与立即冷冻的整个粪便样本相比，粪便免疫化学测试 (FIT) 样本可基于 16S rRNA 基因（即基于扩增子）测序提供一致的微生物组分析2，并且可在长达 20 天的储存过程中保持稳定。3 然而，重要的是考虑到与全粪便相比，FIT 样品的生物量相对较低，了解 FIT 样品是否能长期稳定，并确定使用这些样品进行宏基因组（即非扩增子）测序是否可行。与基于扩增子的测序相比，宏基因组学提供了更好的分类分辨率和功能能力信息，并且可以检测到更稀有的分类群。4我们的目标是 (1) 研究 FIT 样本中粪便微生物组的稳定性，这些样本已在 - 下保存长达 6 个月。 80°C，使用基于扩增子的测序和宏基因组测序，并且 (2) 比较通过基于扩增子的测序和宏基因组测序获得的微生物组概况。来自 10 名健康志愿者的样本储存在 -80°C 下，并在 5 个时间点（0、1、2、3、6 个月）进行分析。所有样本均经过基于扩增子的测序（V4 区域）。宏基因组…