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Metagenomics: A viable tool for reconstructing herbivore diet
- Source :
- Molecular Ecology Resources, Chua, P Y S, Crampton-Platt, A, Lammers, Y, Alsos, I G, Boessenkool, S & Bohmann, K 2021, ' Metagenomics : A viable tool for reconstructing herbivore diet ', Molecular Ecology Resources, vol. 21, no. 7, pp. 2249-2263 . https://doi.org/10.1111/1755-0998.13425
- Publication Year :
- 2021
- Publisher :
- Wiley, 2021.
-
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.
- 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
Subjects
Details
- ISSN :
- 17550998 and 1755098X
- Volume :
- 21
- Database :
- OpenAIRE
- Journal :
- Molecular Ecology Resources
- Accession number :
- edsair.doi.dedup.....3843faea72bcd6d6712fdf167287e90f