© BRYAN SATALINOIn the last decade or so, researchers have spent billions of dollars categorizing the microbes that populate sites as disparate as the human body, soil, and the oceans. Much of what we know about these different microbiomes has been determined using increasingly sophisticated next-generation sequencing technologies. For instance, scientists typically gauge a sample’s microbial diversity by performing high-throughput sequencing on the gene coding for 16S rRNA, a component of the small subunit of bacterial ribosomes. Shotgun metagenomics is a complementary technique used for microbiome studies when a researcher aims to sample all the genes in all organisms in a sample. These DNA sequencing technologies are quite sensitive, and can pick up fine-scale changes caused by contamination or by the hazards of sample processing.
Because variations in handling and storage of samples can impact a study’s results, maintaining the integrity of samples collected in the field is a major challenge in microbiome research. Vanessa Hale, a microbial ecologist and postdoctoral fellow at the Mayo Clinic in Rochester, Minnesota, says the gold-standard procedure is to extract DNA or RNA from a fresh sample immediately. When immediate processing is not feasible, it’s best to store samples at −80 °C. The microbial composition of a fecal sample starts to shift after one to two days at room temperature (PLOS ONE, 7:e4695, 2012; Open Microbiol J, 3:40-46, 2009); other samples, such as soils, are similarly temperature-sensitive. However, having access to an ultra-low-temperature freezer may not always be possible. Study subjects may collect fecal ...
