Freezing fecal samples preserves the microbiota

Editors note: Happy St. Patrick's day to all our readers!  We hope you all enjoy some tasty fermented beverages today, (always in moderation based on yesterday's blog), and instead of corned beef and cabbage, how about corned beef and kimchi!

The microbiome field has exploded over the past few years in large part due to the advent of high-throughput sequencing technologies.  These technologies give scientists the ability to sequence the bacteria in a sample at a fraction of the cost with much greater accuracy than prior methods.  With the growth of this new field, there are more research teams conducting microbiome research with each lab doing things slightly differently. It’s important for scientists to understand the multiple factors that influence the results of experiments, and one of those variables is the storage condition of samples prior to DNA extraction. 

A research team from Ireland published a paper in the Proceedings of the National Academy of Sciences (PNAS) that investigated the impact that storage techniques had on the microbial communities within samples using a MiSeq from Illumina. While it is likely that immediately extracting the DNA from a sample is the most ideal method for research, this is often not feasible due to sampling locations as well as collaborations between investigators at various sites. 

In this study, samples were collected from 7 individuals and each sample was separated into three groups, fresh samples that were processed within 4 hours of sampling, samples that were “snap frozen” and immersed in dry ice for 4 minutes before being stored for a week at -80°C, or samples that were frozen immediately at -80°C.  The researchers found that there were no significant differences between the three experimental groups. The samples that were sampled fresh, snap frozen using dry ice, and those frozen only at -80°C had similar numbers of total bacteria as well as bifidobacteria which was sampled due to its sensitivity to freezing as well as its low abundance in fecal microbiomes. 

This study has shown that immediately freezing fecal samples should appropriately preserve them for use in research. This type of study is incredibly valuable in order for the greater scientific community to understand the impact that important variables such as storage techniques can have on microbial sampling.  There are many variables that play a role in microbiome data and it is important for studies like this as well as initiatives like the Microbiome Quality Control Project to lead the way in allowing us to better understand these factors.  

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