Metabarcoding

   

We support metabarcoding at the Facility, including identification of species in mixed samples, studies of environmental DNA (eDNA), screening for parasites and diet analysis.

     

Examples of the projects we have supported or are currently supporting are listed below.
Publications arising from this work can be found here.

   

Identification of species in mixed samples (eg water, soil, nests, insect drop-traps & faecal samples)

We use an Illumina MiSeq Sequencer for investigations of species diversity in mixed samples such as investigating the bacterial communities found in water pipes or bacteria in bird nests or to identify the species present in communities of insects in drop-traps.

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PI: Penelope Watt, University of Sheffield, Visitor: Joe Llanos
The effects of ley cropping on earthworm diversity and abundance.

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PI: Sophie Reichert, University of Sheffield; Visitors: Diogo Santos, Carly Lynsdale
Identifying MHC variation as an indicator of resistance to specific parasite fauna of Asian elephants (Elephas maximus).

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PI: Julia Day, University College London; Visitor: Chris Doble
Testing eDNA metabarcoding approaches for surveying Lake Tanganyika’s hyper-diverse littoral fish communities.

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PI: Isabel Douterelo Soler, University of Sheffield, Visitors: Isabel Douterelo Soler and Carolina Calero
Impact of climate change on the microbial ecology of drinking water distribution systems.

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PI: Paul Ashton, Edge Hill University, Visitor: Andy Devaynes
Bacterial communities of Blue Tit nest boxes.

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PI: Rob Freckleton, University of Sheffield, Visitor: Rob Goodsell
Investigating the drivers of arthropod diversity in agro-ecosystems using metabarcoding.

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PI: Joby Boxall, University of Sheffield, Visitor: Kat Fish
The impact of disinfection upon biofilm microbial communities within drinking water distribution systems.

  

Environmental DNA (eDNA) detection

We possess a QuantStudio 12K Flex Real-time PCR System (the all-in-one qPCR instrument). This is used for environmental DNA (eDNA) typing, such as screening water samples for the presence of a specific species, eg Great Crested Newt DNA.  

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PI: Jim Groombridge, University of Kent, Visitor: Andy Buxton
Environmental DNA as an assessment tool for population size estimates of the Great Crested Newt (Triturus cristatus).

We use a MiSeq Sequencer for detecting multiple species from environmental samples, such as the detection of fish in lakes from water samples.

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PI: Julia Day, University College London, Visitor: Chris Doble
Testing eDNA metabarcoding approaches for surveying Lake Tanganyika’s hyper-diverse littoral fish communities.

    

Parasite detection

We use a MiSeq Sequencer for detecting multiple parasite species from faecal or environmental samples.

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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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Simon Goodman, University of Leeds, Visitor: Rebecca Thomas
Molecular epidemiology of multi-parasite co-infections in Turtle Doves.

    

Diet Analysis

We use an Illumina MiSeq Sequencer for obtaining sequences from mixed samples where multiple species are present - for example, DNA-based studies of diet from fecal material. We have supported diet studies of a wide range of species including carnivores, omnivores, piscivores and herbivores. These include otter, pika, hedgehog, bats (Bechsteins bat, Natterers bat, pipistrelle), multiple birds (passerines, doves and pigeons, penguin, crane, diver, shearwater), fish and reptiles (tortoise and skink). In 2018 we will support diet studies of the snow leopard and golden wolf in an aim to assist the conservation of these species.

Examples of the many diet studies we have supported and are currently supporting are listed here.