Metagenomics: A viable tool for reconstructing herbivore diet

Area of Science:

• Ecology
• Bioinformatics
• Genomics

Background:

• Metagenomics presents an alternative to metabarcoding for herbivore diet analysis, bypassing PCR and primer selection.
• However, metagenomic diet studies require bioinformatic validation, and few have integrated both chloroplast and nuclear markers for enhanced plant identification.
• This study addresses the need for validated bioinformatic parameters in metagenomic herbivore diet research.

Purpose of the Study:

• To validate bioinformatic parameters for metagenomic diet analysis using in silico simulations.
• To compare the efficacy of metagenomics and metabarcoding for characterizing herbivore diet.
• To assess the impact of sample age on metagenomic and metabarcoding diet analyses.

Main Methods:

• In silico simulation of metagenomic data sets from known plant sequences to establish reliable taxonomic assignment parameters.
• Application of these parameters to characterize the diet of western capercaillies (Tetrao urogallus) using fecal samples.
• Comparison of metagenomic results with metabarcoding (trnL P6 loop) data from the same samples.

Main Results:

• Metagenomics and metabarcoding identified a similar number of plant taxa (42 vs. 43) with comparable species resolution (24% vs. 23%).
• Metagenomic analysis was significantly influenced by fecal sample age, with fresh samples yielding better results than older ones.
• Metabarcoding was unaffected by sample age, but metagenomics enabled simultaneous recovery of the host's mitochondrial genome.

Conclusions:

• Metagenomics shows significant potential for herbivore diet reconstruction, offering advantages over metabarcoding.
• Key considerations, such as sample age and the integration of diverse marker types, are crucial for optimizing metagenomic diet studies.
• The ability to obtain host genomic data simultaneously enhances the ecological information derived from metagenomic approaches.