FAST method. Homo sapiens

Convenient, reproducible, and rapid preservation of unique biological samples is pivotal to their use in microbiome analyses. As an increasing number of human longitudinal studies are looking to incorporate human microbiome data, the need for such sample collection and storage methods is high. Here, we describe the Fecal Aliquot Straw Technique (FAST) of fecal sample processing for long-term storage. In comparison to previous methods, FAST requires minimal supplies making it convenient to utilize both in the lab and in the field. FAST yields easily obtainable, reproducible subsamples that capture community diversity and allow for effective humanization of germ-free mice. Using high-throughput sequencing of the bacterial 16S V4 region, the majority of reasonably abundant OTUs found in the initial scoop sampling of feces were present in FAST aliquots. Overall sample diversity did not change across FAST subsamples. OTUs that were lost, or gained, represented low abundance taxa. In contrast, diversity decreased and some OTUs failed to colonize in humanization of germ-free mice with FAST samples. However, colonized mice retained their donor subject’s identity when compared to other subjects in this study. Using choline consumption/TMAO accumulation as a proxy for microbial metabolic activity, we further confirmed reproducible humanization across FAST samples as well as two mouse strains. Specifically, we find that TMAO accumulation is inversely correlated with choline bioavailability, both of which are significantly influenced by microbial community composition. These metabolome findings validated previously reported synthetic community conclusions. Overall, FAST represents a considerable improvement in fecal processing methods and has the potential to advance human, as well as other host, microbiome research through easy, convenient, and reproducible sample processing.