Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping
Amir et al.
The finding, in our words
Gammaproteobacteria proliferate in stool samples shipped at room temperature, distorting microbiome profiles. A computational correction method that removes sequences from these blooming taxa enables reliable microbiome analysis from self-collected samples sent without cold chain, producing results comparable to frozen specimens.
A paraphrase to the Library’s standard, never the abstract. The source is one link away and is always the authority.
This study compared four stool collection methods for infant gut microbiome analysis via post and found that the OMNIgene•GUT kit showed the closest agreement with the frozen standard compared to swabs or plain tubes. The findings suggest that stabilised collection offers a viable decentralised solution for parents to sample infant stool at home with minimal DNA degradation.
The OMNIgene•GUT kit proved reliable for stool microsampling and ambient storage, with samples stored at room temperature for seven days showing comparable bacterial DNA quantity and diversity to fresh samples; transient phylum-level differences were seen at 24 hours but not at seven days. This supports decentralised, patient-centric microbiome research by enabling home self-collection and postal transport, while emphasising that DNA extraction method has greater impact on microbiome profiles than storage conditions.
Saliva samples collected using the OMNIgene ORAL device and oral wash samples remain stable for microbiome diversity and relative abundance analyses for up to five years when stored at -80°C. This supports the use of these self-collection methods for long-term prospective biobanking and decentralised clinical studies.
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.
This study compared OMNIgene Gut tubes and FTA cards for stool collection in a deployed setting, finding that OMNIgene yielded higher nucleic acid concentrations while both methods detected the majority of microbial genera. The authors conclude that distinct microbial abundance profiles between the two methods necessitate standardised protocols for field research.