Distinct microbial taxa and antimicrobial resistance classes were, in some situations, similarly affected across samples, while others were not, suggesting an impact of individual inherent sample characteristics. Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes. We examined two different pig feces and sewage samples, unspiked and spiked with a mock community, in triplicate, respectively, amounting to a total of 438 samples (777 Gbp 5.1 billion reads). Here, we assess the effect of common storage temperatures (deep freezer, -80☌ freezer, -20☌ refrigerator, 5☌ room temperature, 22☌) and storage times (immediate sample processing, 0 h next day, 16 h over weekend, 64 h longer term, 4, 8, and 12 months) as well as repeated sample freezing and thawing (2 to 4 freeze-thaw cycles). Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. Storage of biological specimens is crucial in the life and medical sciences.
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