Quantifying bias introduced by sample collection in relative and absolute microbiome measurements
Maghini et al.
The finding, in our words
This study compared two preservatives for stool samples and found that OMNIgene GUT OMR-200 produced less variation in metagenomic taxonomic data across different storage temperatures, supporting its use in decentralised field studies. The authors recommend absolute quantification to address bias in microbial measurements.
A paraphrase to the Library’s standard, never the abstract. The source is one link away and is always the authority.
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.
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.
Stool samples collected in DNA/RNA Shield tubes showed better preservation of microbiome taxonomic composition and functional stability over 18 months than OMNIgene-Gut tubes. This demonstrates that ambient stabilisation enables reliable decentralised microbiome collection and long-term storage before analysis.
DNA extraction methods explained 5.7% of microbiome variability, nearly as much as interindividual differences (7.4%), while collection methods had minimal impact. The choice of kit significantly skewed recovery of Gram-positive bacteria and enterotype distribution, underscoring the need for standardisation in decentralised stool sampling for clinical research.
Comparison of six stool collection methods in healthy volunteers found OMNIgene Gut, FOBT cards, RNAlater and Microlution were reliable for metagenomics, whereas 95% ethanol best preserved metabolite profiles; the authors recommend using separate collection methods for different analytical aims in large population studies.