1. Metagenomics: A viable tool for reconstructing herbivore diet
- Author
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Physilia Ying Shi Chua, Inger Greve Alsos, Kristine Bohmann, Youri Lammers, Sanne Boessenkool, and Alex Crampton-Platt
- Subjects
0106 biological sciences ,0301 basic medicine ,In silico ,Computational biology ,Biology ,shotgun sequencing ,010603 evolutionary biology ,01 natural sciences ,Plant identification ,03 medical and health sciences ,VDP::Mathematics and natural science: 400::Zoology and botany: 480 ,Genetics ,DNA Barcoding, Taxonomic ,Environmental DNA ,Resource Article ,Herbivory ,Ecology, Evolution, Behavior and Systematics ,2. Zero hunger ,Herbivore ,plants ,Shotgun sequencing ,Environmental DNA, Faeces, Grouse, Plants, Shotgun sequencing ,RESOURCE ARTICLES ,Significant difference ,Molecular and Statistical Advance ,environmental DNA ,Diet ,030104 developmental biology ,Metagenomics ,Metagenome ,grouse ,Identification (biology) ,faeces ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 ,Biotechnology - Abstract
Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.
- Published
- 2021