Fecal microbiomes from screening sampling tubes are stable despite varying sampling and storage conditions

Area of Science:

• Microbiome research
• Genomics
• Molecular biology

Background:

• Fecal immunochemical test (FIT) kits are widely used for colorectal cancer screening.
• Residual FIT samples offer a potential resource for large-scale gut microbiome studies.
• Advances in sequencing allow for full-length bacterial 16S ribosomal gene analysis.

Purpose of the Study:

• To evaluate the impact of pre-analytical handling and storage conditions on microbiome profiling from FIT samples.
• To assess the robustness and representativeness of gut microbiomes preserved in FIT tubes.

Main Methods:

• Stool samples from eight healthy adults were stored under various conditions (+20°C, -18°C, -80°C) for different durations.
• DNA was extracted, and full-length 16S rRNA gene amplicons were sequenced using Oxford Nanopore Technology.
• Microbiome composition was analyzed, considering sampling variation and buffer presence.

Main Results:

• Microbiome richness, Shannon diversity, and individual characteristics were largely preserved across different conditions.
• Minor variations observed, including an increase in collagenase-producing bacteria in samples stored at +20°C for 4-10 days.
• Despite unsupervised sampling and storage, fecal microbiomes remained representative and robust.

Conclusions:

• FIT samples are a viable and robust resource for large-scale gut microbiome research.
• Pre-analytical handling variations in FIT samples minimally impact overall microbiome profiling.
• These findings support the use of FIT-collected samples in population-level microbiome studies.