Storage and handling of human faecal samples affect the gut microbiome composition: A feasibility study

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Human gut microbiome analysis is crucial for understanding health and disease.
• Faecal DNA extraction and storage are critical, irreversible steps in microbiome analysis.
• Standardized methodologies are needed to ensure reliable microbial profiling.

Purpose of the Study:

• To assess and compare different faecal DNA extraction techniques.
• To evaluate the impact of short-term storage conditions on DNA yield, purity, and microbial profiles.
• To identify optimal methods for human gut microbiome analysis.

Main Methods:

• Compared six DNA extraction techniques (kits and manual protocols) on human faecal samples.
• Assessed DNA yield, purity, and 16S rDNA-based microbial diversity profiles.
• Evaluated seven short-term storage conditions for extracted DNA over 120 hours.

Main Results:

• Significant variance in DNA yield (2.7-164 ng/mg) and microbial diversity profiles observed across extraction methods.
• The MetaHIT technique demonstrated the highest DNA yield.
• Short-term storage conditions showed no statistically significant difference in DNA yield or purity.
• Microbial diversity profiles were largely comparable across storage conditions, with minor genus differences.

Conclusions:

• DNA extraction method choice significantly influences gut microbiome profiles.
• Short-term storage has a lesser impact on microbial diversity compared to DNA extraction.
• The MetaHIT method is recommended for its efficiency and cost-effectiveness in faecal DNA extraction.