Unknown

Dataset Information

0

Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing.


ABSTRACT: DNA metabarcoding of faecal samples is being successfully used to study the foraging niche of species. We assessed the ability of two benchtop high-throughput sequencing (HTS) platforms, to identify a large taxonomic array of food items from domestic cats Felis silvestris catus, including prey and human-related food taxa (pet food and leftovers leaving undetectable solid remains in faeces). Scats from a captive feeding trial (n?=?41) and from free-ranging individuals (n?=?326) were collected and analysed using a cytb mini-barcode in independent PCR replicates on the Ion PGM and the MiSeq platforms. Outputs from MiSeq were more sensitive and reproducible than those from Ion PGM due to a higher sequencing depth and sequence quality on MiSeq. DNA from intact prey taxa was detected more often (82% of the expected occurrences) than DNA from pet food (54%) and raw fish and meat (31%). We assumed that this variability was linked to different degree of DNA degradation: The Ion PGM detected significantly less human-linked food, birds, field voles, murids and shrews in the field-collected samples than the MiSeq platform. Pooling the replicates from both platforms and filtering the data allowed identification of at least one food item in 87.4% of the field-collected samples. Our DNA metabarcoding approach identified 29 prey taxa, of which 25 to species level (90% of items) including 9 rodents, 3 insectivores, 12 birds and 1 reptile and 33 human-related food taxa of which 23 were identified to genus level (75% of items). Our results demonstrate that using HTS platforms such as MiSeq, which provide reads of sufficiently high quantity and quality, with sufficient numbers of technical replicates, is a robust and non-invasive approach for further dietary studies on animals foraging on a wide range of food items in anthropogenic landscapes.

SUBMITTER: Forin-Wiart MA 

PROVIDER: S-EPMC6244006 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

altmetric image

Publications

Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing.

Forin-Wiart Marie-Amélie MA   Poulle Marie-Lazarine ML   Piry Sylvain S   Cosson Jean-François JF   Larose Claire C   Galan Maxime M  

Scientific reports 20181120 1


DNA metabarcoding of faecal samples is being successfully used to study the foraging niche of species. We assessed the ability of two benchtop high-throughput sequencing (HTS) platforms, to identify a large taxonomic array of food items from domestic cats Felis silvestris catus, including prey and human-related food taxa (pet food and leftovers leaving undetectable solid remains in faeces). Scats from a captive feeding trial (n = 41) and from free-ranging individuals (n = 326) were collected and  ...[more]

Similar Datasets

| S-EPMC5553782 | biostudies-literature
| S-EPMC4249215 | biostudies-literature
| S-EPMC3431227 | biostudies-literature
| S-EPMC4113289 | biostudies-literature
2017-08-04 | GSE98562 | GEO
| PRJEB11475 | ENA
| S-EPMC5319672 | biostudies-literature
| S-EPMC8601232 | biostudies-literature
| S-EPMC4315398 | biostudies-literature
| S-EPMC4550469 | biostudies-literature