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Standardized self-collection of microbiome samples can improve accessibility and data output.
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Microbiome Self-Collection Can Improve Accessibility and Data

Better quality data accessed from a wider range of individuals provides more robust results for treatments and clinical trials

DNA Genotek
Published:Jul 25, 2023
|3 min read
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Tara Crawford Parks, PhD, is a Sr. R&D Manager at DNA Genotek. She received her undergraduate degree in Biomedical Science with a minor in Chemistry and her PhD in Cellular and Molecular Medicine from the University of Ottawa. Her expertise is in cellular and molecular biology. 

Michael Valentine (not pictured) is the Lab Operations Manager for Diversigen. Prior to joining the team, he worked with the Translational Genomics Research Institute in Arizona, focused on NGS in public health. He received his Master of Science in Biology from Northern Arizona University. His expertise is in microbiology, molecular biology, genomic epidemiology, laboratory construction, management and biosafety.  

What are microbiome studies, and how can they inform patient care? 

The gut microbiota is one of the key elements that contributes to the regulation of human health, and has a critical role in several diseases such as intestinal bowel diseases, celiac disease, colorectal cancer, chronic liver diseases and pancreatic disorders. We have only begun to understand how complex interactions between a host and the different microorganisms colonizing their gut can influence health, positively and negatively. The information learned from the microbiome can be a powerful tool for public health discoveries.

What are some of the challenges presented by the sequencing analysis required for microbiome research?

One of the biggest challenges with patient samples needing sequencing analyses is standardizing microbiome workflows. Biological sampling methodology is a primary concern to ensure proper stabilization of the analyte of interest (nucleic acids) for storage and shipping. The first step to generating good quality microbiome sequencing data is stabilizing the sample and protecting that snapshot in time from environmental changes, because the microorganisms within a sample are quite sensitive to environmental changes. This can lead to shifts in the sample profiles and negatively impact study conclusions. That is why it’s important to ensure that microbiome samples arrive at the lab highly representative of the sample at the time of collection.

Given that sample integrity is essential for microbiome research, how can a self-collected sample meet this high standard?

Patient education is key for self-collection. For example, a collection device that is intended for self-collection should have simple easy to follow instructions to facilitate the proper collection of the sample, without much burden on the study participant. Some studies have a clinical research coordinator provide instructions to patients to increase compliance during sample collection. Taking steps to simplify the process for patients as much as possible while also ensuring standardized methodology is beneficial to the success in the downstream sequencing of the samples.  

What are some of the unique features of the OMNIgene•GUT Dx for self collection?

This fecal sample collection and stabilization kit provides a solution for optimizing the collection step in a microbiome workflow. The OMNIgene•GUT Dx device is the first and only FDA authorized device for gut microbiome profiling and can reduce experimental bias and support successful sample collection. It is designed to have a volumetric sample input while also ensuring sufficient sample homogenization, which standardizes the collection and stabilization process to ultimately provide a reliable and reproducible fecal sample to fit within various downstream microbiome applications. The OMNIgene•GUT Dx device was also robustly validated to ensure sample stability during storage and transport at ambient temperatures for up to 30 days and is truly a collection device positioned to increase accessibility. During the development of this product, we conducted usability and human factor testing to ensure that the user instructions were easy to understand by the general adult population. We also validated that the collection device was suitable for self-collection in an at home setting where study participants then shipped their collected samples back to a processing laboratory via general postal services. This enables more people to have access to microbiome solutions that incorporate the OMNIgene•GUT Dx device, for example, they would be able to collect and provide a high-quality fecal sample regardless of their proximity to a clinical site, access to transportation or comfort level to visit a clinical site.

This is a great example of citizen science, with anyone being able to participate in the process of clinical research or testing from the comfort of their home. Increasing accessibility with this type of collection can help get more people interested in participating in microbiome based screening programs, and that can play an important role in public health advances.

Overall, from patient to laboratory, fecal self-collection kits such as the OMNIgene•GUT Dx device make microbiome testing more accessible and streamline the process from collection to laboratory, with the potential to increase the chance of success and future-proof the quality of data output from the microbiome workflow.