Comparison of Different Methods for the Analysis of Gut Microbiome Composition

Healthy Clinical Trial

— COLLECT  

Official title:

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

Clinical Trial Details — Status: Completed

Administrative data

• NCT number: NCT04082221
• Other study ID #: ChariteU-ECRC-COLLECT
• Status: Completed
• Start date: March 11, 2019
• Est. completion date: September 5, 2019

Study information

• Verified date: September 2019
• Source: Charite University, Berlin, Germany
• Contact: n/a
• Is FDA regulated: No
• Study type: Observational

Clinical Trial Summary

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.

Description:

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.).

Recruitment information / eligibility

• Status: Completed
• Enrollment: 28
• Est. completion date: September 5, 2019
• Est. primary completion date: June 30, 2019
• Accepts healthy volunteers: Accepts Healthy Volunteers
• Gender: All
• Age group: 18 Years to 60 Years

Eligibility

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.

Related Conditions & MeSH terms

• Healthy

Intervention

Other:
• no intervention
no intervention

Locations

Country	Name	City	State
Germany	Experimental and Clinical Research Center, Clinical Research Unit	Berlin

Sponsors (1)

Lead Sponsor	Collaborator
Charite University, Berlin, Germany

Country where clinical trial is conducted

Germany, 

References & Publications (2)

Hart ML, Meyer A, Johnson PJ, Ericsson AC. Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing. PLoS One. 2015 Nov 24;10(11):e0143334. doi: 10.1371/journal.pone.0143334. eCollection 2015. — View Citation

Wesolowska-Andersen A, Bahl MI, Carvalho V, Kristiansen K, Sicheritz-Pontén T, Gupta R, Licht TR. Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome. 2014 Jun 5;2:19. doi: 10.1186/2049-2618-2-19. eCollection 2014. — View Citation

Outcome

Type	Measure	Description	Time frame	Safety issue
Primary	Collection of stool samples	Collection of 2 stool samples in one week using different conditions; DNA extraction from all samples will be performed using QIAamp Power Fecal (Qiagen, N. V) and ZymoBIOMICS (Zymo Research, CA.) to assess how different commercially available stool sampling kits and fecal DNA extraction kits influence the apparent composition of the gut microbiome	one week