Abstract
Using metagenomics to determine animal diet offers a new and promising alternative to current methods. Here we show that rapid and inexpensive diet quantification is possible through metagenomic sequencing with the portable Oxford Nanopore MinION. Using a simple amplification-free approach, we profiled the stomach contents from wild-caught rats. We conservatively identified diet items from over 50 taxonomic orders, ranging across nine phyla that include plants, vertebrates, invertebrates, and fungi. This highlights the wide range of taxa that can be identified using this simple approach. We calibrate the accuracy of this method by comparing the characteristics of reads matching the ground-truth host genome (rat) to those matching diet items. We also suggest a means to correct for biases in metagenomic approaches that arise due to the paucity of genomic sequence in databases as compared to mitochondrial DNA or rDNA. Finally, we implement a constrained ordination analysis to show that it is possible to identify the sampling location of an individual rat within tens of kilometres based on diet content alone. This work establishes long-read metagenomic methods as a straightforward and robust approach for diet quantification. It considerably simplifies the workflow and avoids many inherent biases as compared to metabarcoding. Continued increases in the accuracy and throughput of Nanopore sequencing, along with improved genomic databases, means that this approach will continue to improve in accuracy.
Footnotes
Communicating authors: Olin K. Silander, Institute of Natural and Mathematical Sciences, Massey University, Auckland 0745, New Zealand, olinsilander{at}gmail.com, +64 9 213 6618; Nikki E. Freed, Institute of Natural and Mathematical Sciences, Massey University, Auckland 0745, New Zealand, freednikki{at}gmail.com, +64 9 213 6639