Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping

摘要: The use of sterile swabs is a convenient and common way to collect microbiome samples, many studies have shown that the effects room-temperature storage are smaller than physiologically relevant differences between subjects. However, several bacterial taxa, notably members class Gammaproteobacteria, grow at room temperature, sometimes confusing results, particularly when stability assumed. Although comparative benchmarking has preservation methods, including 95% ethanol, fecal occult blood test (FOBT) FTA cards, Omnigene-GUT kits, reduce changes in taxon abundance during storage, these techniques all drawbacks cannot be applied retrospectively samples already been collected. Here we performed meta-analysis using different sample condition studies, showing consistent trends which specific bacteria grew (i.e., "bloomed") introduce procedure for removing sequences most distort analyses. In contrast similarity-based clustering operational taxonomic units (OTUs), new technique called "Deblur" identify exact corresponding blooming greatly reducing false positives also dramatically decreasing runtime. We show applying this collected American Gut Project (AGP), participants simply mail back without ice packs or other preservatives, yields results with published frozen otherwise preserved samples. IMPORTANCE necessity store temperature remote fieldwork) ability ship hazardous materials require special handling training, such as ethanol citizen science efforts), paramount. although few days not obscure comparison groups, there still notably, can make profiles difficult interpret. problematic taxa from just fast-growing sufficient correct profiles.