Comparison of Different Methods for the Analysis of Gut Microbiome Composition

The Influence of Different Sample Collection and DNA Extraction Methods on the Bacterial Composition of the Gut of Healthy Subjects

The human gastrointestinal tract shelters a complex and dynamic population of microorganisms, the gut microbiota, which plays an important role in immune and metabolic homeostasis. In recent years several major diseases were linked with alterations in the gut microbiome composition.

There are known factors which can influence gut microbiata composition. For example diet is known to play a fundamental role in determining the composition of the intestinal microbiota over time. However, there are very few studies evaluating how collection and DNA isolation methods affect microbiome composition.

An observational clinical study with 28 healthy subjects is planned to assess how different commercially available stool sampling kits and fecal DNA extraction kits influence the apparent composition of the gut microbiome. Participants will be instructed to collect stool samples at two time points separated by one week using six different methods (naïve and Zymo DNA/RNA Shield kit on dry ice as well as OMNIgene GUT, RNALater, 95% EtOH, Zymo DNA/RNA Shield at room temperature). DNA extraction from all samples will be performed using QIAamp Power Fecal (Qiagen, N. V) and ZymoBIOMICS (Zymo Research, CA.).

Inclusion Criteria:

• Age between 18-60
• Body mass index (BMI) 18,5- 29,9 kg/m2
• Willingness to participate in the study examination and fecal sample collection process

Exclusion Criteria:

• Subjects currently on medication (with the exception of contraceptives)
• Subjects with acute or chronic disease
• Pregnant or lactating women
• Subjects with a history of drug or alcohol abuse
• Subjects on a vegan diet
• Subjects who are legal incapacitated or their circumstances do not enable the patient to fully understand the nature, significance and scope of this study.