New tools for diet analysis: nanopore sequencing of metagenomic DNA from rat stomach contents to quantify diet

Abstract

14Introduced species of mammals in New Zealand have had catastrophic effects on 15 populations of diverse native species. Quantifying the diets of these omnivorous and 16 predatory species is critical for understanding which native species are most impacted, 17 and to prioritize which mammal species and locations should be targeted with control 2009). These metabarcoding methods require a PCR step using primers that bind to 24 highly conserved genomic regions (e.g. mitochondrial COI) to amplify specific regions 25 for sequencing. This step introduces significant bias, primarily due to the lack of a 26 universal primer set (King et al. 2008). Here we show that direct metagenomic 27 sequencing using the Oxford Nanopore Minion allows rapid quantification of rat diets. 28Using a sample of rats collected from within 100km of Auckland, NZ, we show that 29 these rats consume a wide variety of plant, invertebrate, vertebrate, and fungal taxa, 30 with substantial differences in diet content between locales. We then show that, based 31 on diet content alone, it is possible to pinpoint the sampling location of an individual rat 32 within tens of kilometres. We expect that the rapidly increasing accuracy and 33 throughput of nanopore-based sequencing, as well as increases in the species 34 diversity of genomic databases, will soon allow rapid and unbiased assessments of 35 animal diets in field settings.

DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

“…Finally, genomic approaches, describing complete organelle genomes and nuclear ribosomal DNA, encompassing many potential barcoding loci, have been suggested as a more accurate and powerful alternative (Coissac et al, ). Notwithstanding, this has been applied only to study the diet of two terrestrial mammalian model species: in a methodological study focusing on the house rat Rattus rattus (Pearman et al, ) and for disclosing diets of humans (Søe et al, ).…”

“…Notwithstanding, this has been applied only to study the diet of two terrestrial mammalian model species: in a methodological study focusing on the house rat Rattus rattus (Pearman et al, 2018) and for disclosing diets of humans (Søe et al, 2018).…”