Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study
Williams et al.
The finding, in our words
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.
A paraphrase to the Library’s standard, never the abstract. The source is one link away and is always the authority.
In children, stool preserved in OMNIgene-GUT kept its microbial community structure better than unpreserved stool, with alpha and beta diversity similar to direct freezing, which supports the kit for decentralised stool collection from children.
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.
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.
OMNIgene GUT vials improved stool DNA quality by reducing shearing, but storage for one week altered microbiota composition in pooled infant and elderly data, with infant samples more affected. For decentralised collection, extraction within the first week and a consistent storage regime are advisable.
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.