Optimized sampling method for fecal microbiome and metabolome preservation under room temperature

BackgroundThe relationship among the human gut microbiome, microbially produced metabolites, and health outcomes remains of great interest. To decrease participant burden, room-temperature storage methods for fecal samples have become increasingly important. However, kits for storing the fecal microbiome and metabolome have not been well explored. We hypothesized that storing fecal samples by drying them with silica gel may be suitable. ObjectivesThe objective was to evaluate the performance of storage at room temperature by drying feces for subsequent examination of the microbiome, microbial pathways, and the metabolome. MethodsFeces from ten healthy adults (6 male and 4 female) were sampled and immediately processed, as controls, and stored at room temperature in an incubator, on an FTA card, in RNAlater, or dried by silica gel. Storage at room temperature continued for 7 days. Drying by the silica gel method was assessed for 14 days. The fecal microbiome was assessed by sequencing the bacterial 16S ribosomal RNA-encoding gene (V1-V2 region), fecal microbial pathway profiles were analyzed by whole-genome shotgun metagenomics, and fecal metabolome profiles were analyzed using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). ResultsQualitative and {beta}-diversity analyses of the microbiome, microbial pathways, and the metabolome showed that drying by silica gel were closest to those immediately after processing. When focusing on the abundances of individual microbes, microbial pathways, and metabolites, some were found to be significantly different. However, the intra-method ranking of individual items showed that 100%, 87-97%, and 63-76% of microbes, microbial pathways, and metabolites, respectively, were significantly correlated between silica gel preserving and immediately processing method. ConclusionsThe results showed that fecal sample drying could be effectively used for the preservation of the fecal microbiome and metabolome.