A comparison of nonlethal sampling methods for amphibian gut microbiome analyses

Area of Science:

• Amphibian biology
• Microbiome research
• Conservation science

Background:

• Noninvasive sampling is crucial for studying endangered species and experimental monitoring.
• Previous studies show variable accuracy of noninvasive methods across taxa.
• No studies have compared nonlethal sampling methods in adult amphibians.

Purpose of the Study:

• To compare fecal and cloacal swab microbiomes to the large intestine in adult cane toads (Rhinella marina).
• To investigate microbial community shifts along the digestive tract.
• To determine which nonlethal method best represents the large intestinal microbiota.

Main Methods:

• 16S rRNA gene sequencing of fecal, cloacal swab, small intestine, and large intestine samples.
• Analysis of microbial community composition and diversity.
• Comparison of microbial profiles between sample types.

Main Results:

• Cane toad intestinal microbiota is dominated by Bacteroidetes, Proteobacteria, Firmicutes, and Fusobacteria.
• Large and small intestines share microbial similarities, but the large intestine has higher diversity.
• Cloacal swabs more accurately represent the large intestine microbiota than fecal samples.

Conclusions:

• Cloacal swabs are a validated nonlethal method for studying the cane toad large intestine microbiome.
• This research provides essential data for future amphibian gut microbiome investigations.
• Findings support the use of cloacal swabs in nonlethal amphibian microbiome studies.