Fecal storage condition induces variations of microbial composition and differential interpretation of metagenomic analysis

Abstract

Advances in metagenomics have facilitated population studies of associations between microbial compositions and host properties, but strategies to minimize biases in these population analyses are needed. However, the effects of storage conditions, including freezing and preservation buffer, on microbial populations in fecal samples have not been studied sufficiently. In this study, we investigated metagenomic differences between fecal samples stored in different conditions. We collected 46 fecal samples from patients with lung cancer. DNA quality and microbial composition within different storage Methods were compared throughout 16S rRNA sequencing and post analysis. DNA quality and sequencing results for two storage conditions (freezing and preservation in buffer) did not differ significantly, whereas microbial information was better preserved in buffer than by freezing. In a metagenomic analysis, we observed that the microbial compositional distance was small within the same storage condition. Taxonomic annotation revealed that many microbes differed in abundance between frozen and buffer-preserved feces. In particular, the abundances of Firmicutes and Bacteroidetes varied depending on storage conditions. Microbes belonging to these phyla differed, resulting in biases in population metagenomic analysis. We suggest that a unified storage Methods is requisite for accurate population metagenomic studies.

New Faecal Calprotectin Assay by IDS: Validation and Comparison to DiaSorin Method

“…FC extracts stored in the fridge (2–8 °C) were only stable for up to 2 days, while they could be stored at −20 °C for up to 4 weeks without significant variation. These results are indeed in accordance with other studies regarding the good conservation at −20 °C [ 13 , 29 ] as well as the lack of stability in the fridge [ 30 , 31 ].…”