The predator problem and PCR primers in molecular dietary analysis: Swamped or silenced; depth or breadth?

Area of Science:

• Ecology
• Molecular Biology
• Bioinformatics

Background:

• Dietary metabarcoding enhances animal diet analysis.
• A key limitation is the predator problem: disproportionate amplification of predator DNA.
• This issue can reduce prey DNA detection in molecular dietary analyses.

Purpose of the Study:

• To review methods for overcoming the predator problem in DNA-based dietary studies.
• To assess how these methods impact multipredator-taxon analyses.
• To guide researchers in effectively addressing DNA-based diet analysis constraints.

Main Methods:

• Review of existing techniques to mitigate predator DNA amplification.
• Analysis of PCR-based exclusion methods and deeper sequencing.
• Exploration of multiprimer approaches for prey DNA detection.

Main Results:

• Current methods for reducing predator DNA may interfere with multipredator-taxon studies.
• Multiprimer approaches can improve prey detection depth and breadth.
• Alternative methods show promise but require further empirical validation.

Conclusions:

• The predator problem is a significant constraint in molecular diet analysis.
• Multiprimer strategies offer potential solutions for multitaxon studies.
• Further research is needed to validate alternative methods for DNA-based diet analysis.