Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian...

Area of Science:

• Microbiology
• Human Health
• Epidemiology

Background:

• Prospective analyses of human gut microbiome are crucial for understanding disease development.
• Variation in the gut microbiome plays a significant role in various health conditions.

Purpose of the Study:

• To assess the feasibility of home fecal sample collection for microbiome analysis in a large cohort study.
• To evaluate the impact of different collection methods and questionnaire components on participant compliance and sample quality.

Main Methods:

• A pilot study randomized participants into groups based on fecal sample collection method (fecal occult blood test card vs. ethanol tube) and questionnaire type.
• Participant opt-in rates, sample return rates, and DNA quality/quantity for metagenomic analysis were assessed.
• Whole-genome sequencing and metagenomic analysis were performed on paired samples to compare collection methods.

Main Results:

• 610 out of 1,093 invited participants (56%) opted-in, with 88% returning a sample.
• Sample return rates were comparable across different collection methods and questionnaire additions (48-51%).
• Both fecal occult blood test cards and ethanol tubes provided sufficient DNA quality and quantity, yielding highly concordant microbiome profiles.

Conclusions:

• Home fecal sample collection is a feasible method for large prospective microbiome studies.
• Incorporating additional questionnaires or collection methods did not significantly decrease participant compliance.
• This approach supports future large-scale metagenomic and host-microbiome analyses in cohort studies.