How should we store avian faecal samples for microbiota analyses? Comparing efficacy and cost-effectiveness

Area of Science:

• Microbiology
• Avian Ecology
• Molecular Biology

Background:

• Bird microbiome research is expanding, but understanding avian fecal sample preservation is limited.
• Sample storage methods significantly impact DNA preservation and subsequent microbiome composition analysis.
• Limited information exists on optimal preservation techniques for avian feces.

Purpose of the Study:

• To evaluate the efficacy, cost, and practicality of five common nucleic acid preservation methods for avian fecal samples.
• To determine how different storage conditions affect bacterial DNA preservation and inferred microbiota profiles.
• To provide guidance on selecting appropriate sample storage methods for avian microbiome studies.

Main Methods:

• Five preservation methods were tested: in-situ bead-beating (TerraLyzer), silica-bead desiccation, ethanol, refrigeration, and RNAlater buffer.
• Fifty fresh House sparrow (Passer domesticus) fecal samples were analyzed.
• Bacterial DNA preservation and microbiota profiles were compared across methods.

Main Results:

• Storage method significantly altered bacterial community composition and the relative abundance of major phyla (Firmicutes, Proteobacteria).
• Refrigerated and ethanol-stored samples showed the most significant changes, affecting aerobic/facultative anaerobic taxa.
• In-situ bead-beating (TerraLyzer) recovered higher microbial levels but is less practical and more expensive for field use.

Conclusions:

• Sample storage method is a critical factor influencing avian fecal microbiome analysis.
• Refrigeration and ethanol are not ideal for preserving bacterial profiles accurately.
• The TerraLyzer method offers high recovery but presents practical challenges in field settings; method choice depends on research needs and constraints.