Who is eating what: diet assessment using next generation sequencing

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan

(2012) WASIM SHEHZAD et al.   MOLECULAR ECOLOGY

Making Contact with Sequencing's Fourth Generation

(2011) Jeffrey Perkel   BIOTECHNIQUES

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Generalist predators disrupt parasitoid aphid control by direct and coincidental intraguild predation

(2011) M. Traugott et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

Feeding diets of the Korean water deer (Hydropotes inermis argyropus) based on a 202 bp rbcL sequence analysis

(2011) Baek Jun Kim et al.   CONSERVATION GENETICS

Influence of management practices on large herbivore diet—Case of European bison in Białowieża Primeval Forest (Poland)

(2011) Rafał Kowalczyk et al.   FOREST ECOLOGY AND MANAGEMENT

Which prey sustains cold-adapted invertebrate generalist predators in arable land? Examining prey choices by molecular gut-content analysis

(2011) Bernhard Eitzinger et al.   JOURNAL OF APPLIED ECOLOGY

Eating local: influences of habitat on the diet of little brown bats (Myotis lucifugus)

(2011) E. L. CLARE et al.   MOLECULAR ECOLOGY

Pyrosequencing of prey DNA in reptile faeces: analysis of earthworm consumption by slow worms

(2011) DAVID S. BROWN et al.   Molecular Ecology Resources

Proportion of prey consumed can be determined from faecal DNA using real-time PCR

(2011) ELLA BOWLES et al.   Molecular Ecology Resources

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

(2011) Tiayyba Riaz et al.   NUCLEIC ACIDS RESEARCH

Intrapopulation Variability Shaping Isotope Discrimination and Turnover: Experimental Evidence in Arctic Foxes

(2011) Nicolas Lecomte et al.   PLoS One

jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units

(2011) Martin Jones et al.   PLoS One

Molecular Diet Analysis of Two African Free-Tailed Bats (Molossidae) Using High Throughput Sequencing

(2011) Kristine Bohmann et al.   PLoS One

DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches

(2011) Dáithí C. Murray et al.   PLoS One

Trophic Downgrading of Planet Earth

(2011) James A. Estes et al.   SCIENCE

Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing

(2010) J. K. Harris et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Lycosid spiders and alternative food: Feeding behavior and implications for biological control

(2010) Anna-Karin Kuusk et al.   BIOLOGICAL CONTROL

Qualitative assessment of the diet of European eel larvae in the Sargasso Sea resolved by DNA barcoding

(2010) L. Riemann et al.   Biology Letters

An In silico approach for the evaluation of DNA barcodes

(2010) Gentile Ficetola et al.   BMC GENOMICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?

(2010) Bruce E. Deagle et al.   CONSERVATION GENETICS

New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: chamois diet in autumn as a case study

(2010) Gilles Rayé et al.   ECOLOGICAL RESEARCH

Investigation on Natural Diets of Larval Marine Animals Using Peptide Nucleic Acid-Directed Polymerase Chain Reaction Clamping

(2010) Seinen Chow et al.   MARINE BIOTECHNOLOGY

Prey choice by carabid beetles feeding on an earthworm community analysed using species- and lineage-specific PCR primers

(2010) R. ANDREW KING et al.   MOLECULAR ECOLOGY

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

Maximizing collection and minimizing risk: does vacuum suction sampling increase the likelihood for misinterpretation of food web connections?

(2010) ERIC G. CHAPMAN et al.   Molecular Ecology Resources

Bryophyte DNA sequences from faeces of an arctic herbivore, barnacle goose (Branta leucopsis)

(2010) M. STECH et al.   Molecular Ecology Resources

Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces

(2010) MATT R. K. ZEALE et al.   Molecular Ecology Resources

Detecting ingested plant DNA in soil-living insect larvae

(2010) Karin Staudacher et al.   SOIL BIOLOGY & BIOCHEMISTRY

Development and application of DNA techniques for validating and improving pinniped diet estimates

(2009) Dominic J. Tollit et al.   ECOLOGICAL APPLICATIONS

Analysis of the predator community of a subterranean herbivorous insect based on polymerase chain reaction

(2009) Jonathan G. Lundgren et al.   ECOLOGICAL APPLICATIONS

Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

(2009) Eeva M Soininen et al.   Frontiers in Zoology

Rapid Assessment of the Nutritional Value of Foods Eaten by Mountain Gorillas: Applying Near-Infrared Reflectance Spectroscopy to Primatology

(2009) Jessica M. Rothman et al.   INTERNATIONAL JOURNAL OF PRIMATOLOGY

Universal DNA-Based Methods for Assessing the Diet of Grazing Livestock and Wildlife from Feces

(2009) Anthony Pegard et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Detection of Predation Using qPCR: Effect of Prey Quantity, Elapsed Time, Chaser Diet, and Sample Preservation on Detectable Quantity of Prey DNA

(2009) Donald C. Weber et al.   JOURNAL OF INSECT SCIENCE

DNA evidence of whale sharks (Rhincodon typus) feeding on red crab (Gecarcoidea natalis) larvae at Christmas Island, Australia

(2009) M. G. Meekan et al.   MARINE AND FRESHWATER RESEARCH

Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

(2009) BRUCE E. DEAGLE et al.   MOLECULAR ECOLOGY

Species on the menu of a generalist predator, the eastern red bat (Lasiurus borealis): using a molecular approach to detect arthropod prey

(2009) ELIZABETH L. CLARE et al.   MOLECULAR ECOLOGY

Carbon source accounting for fish using combined DNA and stable isotope analyses in a regulated lowland river weir pool

(2009) CHRISTOPHER M. HARDY et al.   MOLECULAR ECOLOGY

Development of primers for the mitochondrial cytochromecoxidase I gene in digenetic trematodes (Platyhelminthes) illustrates the challenge of barcoding parasitic helminths

(2009) ANNA MOSZCZYNSKA et al.   Molecular Ecology Resources

Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: thetrnL approach

(2009) ALICE VALENTINI et al.   Molecular Ecology Resources

A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces

(2009) EMMANUEL CORSE et al.   Molecular Ecology Resources

DNA-Based Diet Analysis for Any Predator

(2009) Glenn Dunshea   PLoS One

Identification of Amazonian Trees with DNA Barcodes

(2009) Mailyn Adriana Gonzalez et al.   PLoS One

Identification of trophic interactions between Macrolophus caliginosus (Heteroptera: Miridae) and Myzus persicae (Homoptera: Aphididae) using real time PCR

(2008) Jörg E. U. Schmidt et al.   BIOCONTROL

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS

Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system

(2008) G. Dunshea et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

Incorporating uncertainty and prior information into stable isotope mixing models

(2008) Jonathan W. Moore et al.   ECOLOGY LETTERS

Ecosystem Linkages Between Lakes and the Surrounding Terrestrial Landscape in Northeast Iceland

(2008) Claudio Gratton et al.   ECOSYSTEMS

Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs

(2008) Hege Vestheim et al.   Frontiers in Zoology

An aid to the identification of arthropod fragments in the faeces of gamebird chicks (Galliformes)

(2008) S. J. MOREBY   IBIS

Using quantitative real-time PCR to detect salmonid prey in scats of greyHalichoerus grypusand harbourPhoca vitulinaseals in Scotland - an experimental and field study

(2008) I. Matejusová et al.   JOURNAL OF APPLIED ECOLOGY

Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR)

(2008) Christofer Troedsson et al.   MARINE BIOLOGY

Opening a can of worms: unprecedented sympatric cryptic diversity within British lumbricid earthworms

(2008) R. ANDREW KING et al.   MOLECULAR ECOLOGY

INVITED REVIEW: Molecular analysis of predation: a review of best practice for DNA-based approaches

(2008) R. A. KING et al.   MOLECULAR ECOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

DNA barcoding for ecologists

(2008) Alice Valentini et al.   TRENDS IN ECOLOGY & EVOLUTION

Group-specific primers for DNA-based detection of springtails (Hexapoda: Collembola) within predator gut contents

(2007) A. K. KUUSK et al.   Molecular Ecology Resources

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources