Diet analysis

If you are considering an application to the facility, we can provide advice and help with the experimental design for any proposed diet study. Please email Dr Deborah Dawson to discuss.

We use an Illumina MiSeq Sequencer for obtaining sequences from mixed samples where multiple species are present - including DNA-based studies of diet from faecal material.

For DNA extraction from faecal samples we typically use the QIAamp Fast DNA Stool Mini Kit (cat. no. 51604).  We have a database of primer sets suitable for detecting different species. We have protocols for most of the standard primer sets (COI, cytb, 12s, 16s, ITS, rbcL, etc). We also custom design primer sets for picking up specific species/ taxa. PCRs are set up in a laminar flow hood in a separate laboratory to avoid contamination.

During the stages of experimental design, we check for primer-species target compatibility in-silico. Prior to sequencing on the MiSeq, we PCR amplify test samples to check the primer sequences amplify products of the expected size. If required, Sanger sequencing is performed, eg if a sequence is required for primer redesign to give more appropriate product sizes for MiSeq sequencing.

We typically use primers with indexes to allow identification of individual samples after pooling and attach these along with the Illumina tag sequences required for the MiSeq sequencing procedure in a second PCR step - however, we are flexible and happy to discuss other methods. We can sequence fragments from 90bp to a maximum of 550bp. Longer sequences are sequenced using a 300bp paired-end sequencing run.

We provide training and support in the processing of Illumina sequences and the subsequent data analyses.

A pipeline is set up for analysing dietary metabarcoding data from the Illumina MiSeq. The pipeline will perform:

• Sample demultiplexing
• Removal of low quality sequences and Illumina adapter sequences
• Alignment of paired reads
• Removal of MID-tag and primer sequences
• Clustering of identical reads and chimeric sequence removal
• Alignment of sequences to established reference database.

Current and recently completed projects

We have supported diet studies of a wide range of species including carnivores, omnivores, insectivores, piscivores and herbivores, listed below.

Mammals

Carnivores:

• African golden wolf, Canis anthus

Piscivores:

• Eurasian otter, Lutra lutra

Omnivores:

• European hedgehog, Erinaceus europaeus
• Eurasian badger, Meles meles

Herbivores:

• Royle's pika, Ochotona roylei

Insectivores:

• Bechstein's bat, Myotis bechsteinii
• Natterer's bat, Myotis nattereri
• Common pipistrelle, Pipistrellus pipistrellus
• Pygmy shrew, Sorex minutus
• Greater white-toothed shrew, Crocidura russula

Nectarivores:

• Lesser long-nosed bat, Leptonycteris yerbabuenae
• Greater long-nosed bat, Leptonycteris nivalis
• Mexican long-tongued bat, Choeronycteris mexicana
• Geoffroy's tailless bat, Anoura geoffroyi

Birds

• Blue tit, Cyanistes caeruleus
• European blackbird, Turdus merula
• Song thrush, Turdus philomenas
• European nightjar, Caprimulgus europaeus

Piscivores:

• Gentoo penguin, Pygoscelis papua
• Red-throated diver, Gavia stellata
• Scopoli's shearwater, Calonectris diomedea

Granivores:

• European Turtle Dove, Streptopelia turtur
• Eurasian Collared Dove, Streptopelia decaocto
• Stock Dove, Columba oenas
• Woodpigeon, Columba palumbus
• Pink pigeon, Nesoenas mayeri
• Eurasian crane, Grus grus

Reptiles

• Aldabra giant tortoise, Aldabrachelys gigantea
• Telfair’s skink, Leiolopisma telfairii

Insects

• Hoverfly

Spiders

• Spider: Erigone atra
• Spider: Tenuiphantes tenuis

Carnivorous plants

• Purple pitcher plant, Sarracenia purpurea
• Cobra lily, Darlingtonia califormica

In 2020, we will support diet studies of several species, including the snow leopard, African golden wolf, nectarivorous bats, hoverflies, pitcher plants and the African elephant: 

NBAF1196 NBAF-S
Richard Davies, University of East Anglia
Effects of florally enhanced field margins on diversity and pollen resource use of hoverfly assemblages

NBAF1185 NBAF-S
Mark Chapman, University of Southampton
Pollination networks of nectarivorous bats in Mexico and dietary dependence upon the cultivated cactus Stenocereus queretaroensis

NBAF1180 NBAF-S
William Symondson, Cardiff University
Nutrient-specific foraging by invertebrate predators in the field

NBAF1147, NBAF-S
Allan McDevitt, University of Salford
Know your enemy: A DNA metabarcoding approach to investigate competitive exclusion during an ongoing invasion

NBAF1143 NBAF-S
Jonathan Millett, Loughborough University
The function of carnivorous pitcher plants in their native and non-native range: extrinsic vs intrinsic drivers of inquiline community composition

NBAF1137 NBAF-S
PI: Richard Yarnell, Nottingham Trent University; Visitor: Katie Lee
Untangling the roles of prey availability, habitat quality and predation as predictors of hedgehog abundance

NBAF1081 NBAF-S
PI: David Macdonald, University of Oxford, Visitor: Liz Campbell
The diet and conservation genetics of the African golden wolf (Canis anthus) in the Moroccan Atlas Mountains.

NBAF1065 NBAF-S
PI: Claire Stevenson-Holt, University of Cumbria
A next-gen approach to relate snow leopard population size and diet to species distribution models.

NBAF1062 NBAF-S
PI: Hannah Mumby, University of Cambridge
Savannah elephant diet in the greater Kruger area: sex differences, seasonality and impact on vegetation.

NBAF1046 NBAF-S
PI: George Turner, Bangor University, Visitor: Alexandra Tyers
Cichlid fish dietary analysis by gut content metabarcoding.

Completed diet studies we have supported (2015-19) and for which publications are in press, submitted or in preparation:

(see our publications page for more information)

*Bhattacharyya S, Dawson DA, Hipperson H, Ishtiaq F (2018) A diet rich in C3 plants reveals the sensitivity of an alpine mammal to climate change. Molecular Ecology, 28, 250-265.

NBAF1141 NBAF-S
PI: Kathryn Arnold, University of York; Visitor: Lucy Ryan
Investigation of diet in the European Nightjar Caprimulgus europaeus

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PI: Elizabeth Chadwick, Cardiff University; Visitor: Lorna Drake
Variation in the diet of the Eurasian otter Lutra lutra, and its implications for parasitology, ecotoxicology and conservation

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PI: Elizabeth Clare, Queen Mary University of London; Visitor: Omar Khalilur Rahman
Response of parasite-bat networks to forest fragmentation in REGUA, Brazil

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PI: Richard Hopkins, University of Greenwich; Visitor: Kate Denton
The potential of insectivorous bats as agents of crop pest control in the UK.

NBAF989 NBAF-S; seabird diet
PI: William Symondson, Cardiff University, Visitor: Birgit Kleinschmidt
Diet analysis of Seabirds (Red-throated Divers and Scopoli's shearwater) in relation to habitat use, human activities and movement ecology.

Kleinschmidt B, Burger C, Dorsch M, Nehls G, Heinänen S, Morkūnas J, Žydelis R, Moorhouse-Gann RJ, Hipperson H, Symondson WOC, Quillfeldt P (2019) The diet of red-throated divers overwintering in the German Bight (North Sea) analysed using molecular diagnostics. Marine Ecology, 166, 77.

NBAF983 NBAF-S; tortoise & skink diet
PI: William Symondson, Cardiff University, Visitor: Rosemary Moorhouse-Gann
Tortoises as analogue species providing the ecosystem service of habitat restoration through grazing.

Moorhouse-Gann RJ, Dunn JC, de Vere N, Goder M, Cole N, Hipperson H, Symondson WOC (2018) New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones. Scientific Reports 8, 8542. (10.1038/s41598-018-26648-2)

NBAF981 NBAF-S; diet of UK thrushes
PI: William Symondson, Cardiff University, Visitor: Jennifer Stockdale
Novel application of high throughput sequencing to track prey exploitation by birds across a patchy landscape.

NBAF979 NBAF-S; crane diet
PI: William Symondson, Cardiff University, Visitor: Jennifer Stockdale
Analysing the diet of reintroduced Eurasian Cranes (Grus grus) on the Somerset Levels UK, using Next Generation Sequencing.

NBAF969 NBAF-S; blue tit diet
PI: Sarah Knowles, The Royal Veterinary College, Visitor: Paula Vargas Pellicer
Understanding the effects of diet on gut microfauna ecology, in blue tit (Cyanistes caeruleus) nestlings.

NBAF967 NBAF-S; penguin diet
PI: William Symondson, Cardiff University, Visitor: Renata Medeiros
Flexible foraging strategies in Gentoo penguins Pygoscelis papua.

NBAF943 NBAF-S; UK dove & pigeon diet
PI: William Symondson, Cardiff University, Visitor: Jenny Dunn
Developing novel methodology for dietary analysis in temperate granivores.

Dunn et al. (2018) The decline of the Turtle Dove: Dietary associations with body condition and competition with other columbids analysed using high‐throughput sequencing. Molecular Ecology, 27, 3386-3407.

NBAF779 NBAF-S/L; hedgehog diet
PI: David Macdonald, University of Oxford, Visitor: Carly Pettet
Assessing hedgehog diet in rural landscapes by DNA sequencing of faeces.

*R&D