Promises and pitfalls of using high-throughput sequencing for diet analysis

Area of Science:

• Ecology
• Genomics
• Bioinformatics

Background:

• High-throughput sequencing (HTS) of environmental DNA (eDNA) from samples like feces is revolutionizing animal diet studies.
• Metabarcoding and shotgun sequencing provide high resolution for detecting prey and addressing ecological questions about trophic interactions.

Purpose of the Study:

• To review studies on HTS-based diet analyses and identify factors distorting taxonomic composition and diversity.
• To provide guidance on study design, limitations, and biases for reliable DNA-based diet assessments.
• To suggest strategies for minimizing distortions, enhancing reproducibility, and scaling up eDNA diet analyses.

Main Methods:

• Review of existing literature on HTS-based diet analyses in ecological studies.
• Analysis of biological and technical factors influencing DNA-based dietary data.
• Synthesis of strategies to improve reliability, reproducibility, and comparability of eDNA diet studies.

Main Results:

• Numerous biological and technical factors can significantly distort taxonomic data derived from HTS diet analyses.
• Effective study design is crucial for mitigating these distortions and ensuring accurate interpretation of dietary information.
• Acknowledging inherent limitations and biases is essential for drawing reliable conclusions from sequencing-based diet assessments.

Conclusions:

• Careful consideration of study design and potential biases is paramount for robust DNA-based animal diet research.
• Standardized methods and improved tools are needed to advance the field of eDNA diet analysis to maturity.
• This review aims to equip researchers with the knowledge to conduct reliable diet studies using HTS approaches.