The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus

Area of Science:

• Ecology
• Molecular Biology
• Bioinformatics

Background:

• Fecal metabarcoding offers high-resolution insights into animal diets.
• Methodological variations in metabarcoding can influence ecological interpretations.

Purpose of the Study:

• To critically evaluate data treatments for inferring the diet of the bat *Plecotus auritus*.
• To assess the impact of different analytical approaches on ecological conclusions from fecal metabarcoding data.

Main Methods:

• Analysis of bat guano collected across colonies and seasons.
• Comparison of DNA extraction yields based on fecal material quantity.
• Trophic niche analyses using prey occurrence and relative read abundance data.
• Evaluation of different taxonomic depths and removal of rare prey items.

Main Results:

• Larger fecal sample volumes yield broader prey taxonomic diversity.
• Trophic niche analysis reveals strong dietary seasonality and inter-colony variation.
• Removing rare prey items can introduce biases, especially in species-rich samples.
• Presence-absence data capture biologically meaningful patterns, unlike relative read abundances.

Conclusions:

• Methodological choices in metabarcoding significantly affect ecological conclusions regarding bat diets.
• Presence-absence approaches are more reliable than relative abundance for inferring prey consumption.
• Previous methodological recommendations may not be universally applicable for diverse diets.