Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
Jones et al.
The finding, in our words
Spot sampling of stool produces variable detection of microbes and short-chain fatty acid levels, so homogenisation before analysis is recommended. Microbial composition shifts between consecutive stools collected less than 25 hours apart, and OMNIgene·Gut or NORGEN tubes alter bacterial composition compared with immediate freezing. For decentralised microbiome studies, participants should collect the first full bowel movement of the day and freeze immediately.
A paraphrase to the Library’s standard, never the abstract. The source is one link away and is always the authority.
Taxonomic and diversity profiles differed between unstabilised swabs and stabilised OmniGene kits, with transport time disproportionately affecting swab samples; the collection method had a greater impact on taxa and diversity than transport time, highlighting the need for standardised stool collection in decentralised microbiome studies.
A study found that stool stabilised in 95% ethanol or OMNImet•GUT and OMNIgene•GUT kits maintained metabolome and microbiome profiles comparable to flash freezing for up to seven days at room temperature. Non-stabilised samples showed temperature-dependent changes in bile and short-chain fatty acids, supporting decentralised, patient-centric ambient collection.
An ambient-temperature DNA Genotek device recovered 94.5% of the metabolites seen in flash-frozen aliquots with strong agreement: room-temperature stabilisation can stand in for immediate freezing.
A study found that fecal samples on FOBT cards and RNAlater, and oral samples in Scope mouthwash, remained stable for four days at room temperature, with fecal comparability ICCs ranging from 0.63 to 0.93. These methods support decentralised sampling, though consistent method choice is required as each may introduce modest differences.
OMNIgene·GUT stabilised stool gave detectable total bile acid concentrations but differed significantly from snap frozen samples; however, relative concentrations of cholanic, chenodeoxycholic, deoxycholic and lithocholic acids correlated well with a 30 per cent acceptability bias, supporting its use for decentralised bile acid profiling.
Neuberger-Castillo et al., Scientific reports · source ↗