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Thursday 17 January 2013

Second Metabarcoding Spring School in Crete (13-17 May 2013)

Eric Coissac, KASAPIDIS Panagiotis

In the context of the European project MARBIGEN, the Institute of Marine Biology, Biotechnology and Aquaculture (former Institute of Marine Biology and Genetics) of the Hellenic Centre for Marine Research, organizes the 2nd DNA Metabarcoding Spring School in Crete, Greece.

The advances in next-generation sequencing (NGS) technologies have revolutionized many fields of the biological sciences, including that of biodiversity studies. Many ecological questions rely on the knowledge of the list of species involved in the studied process. Tackling this demand using standard methods of taxonomical identification, is often a difficult task that relies on highly qualified persons. DNA barcoding has introduced the use of short standardized genomic sequences (barcode) as a character in taxonomical identification. DNA metabarcoding uses the same principle that associates DNA sequences to taxa for estimating biodiversity of an environmental sample. Metabarcoding approaches use total and usually degraded DNA from environmental samples to analyze biotic assemblages and can be potentially carried out for any kind of organisms in an ecosystem. These analyses rely on specific genetic markers, called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. As all living organisms spread cells in their environment, a PCR amplicon obtained with adequate primers from the total DNA extracted from an environmental sample, can be consider as a mirror of the biodiversity present in the environment. The pertinent choice of the primer pair allows to focus on a specific group as, for example, plants. Then the sequencing of a large number of individual DNA molecules of the PCR amplicon using NGS technologies allows establishing a list of taxa present in the sample. Metabarcoding can be applied to many ecological studies such as plant community analysis, plankton and benthic community analysis, past ecosystem reconstruction, or diet assessment.

After the success of the 1st DNA Metabarcoding Spring School in French Alps, we organize the 2nd one in Crete, which includes lectures and bioinformatic practical sessions on metabarcoding. The School is open for 20 participants (post-graduate students or researchers) that will attend both lectures and practicals, and for 30 additional participants that will follow only the lectures.

The focus will be mainly on marine biodiversity, however people from all fields of metabarcoding are encouraged to participate.

Main lecturers

  • Chris Bowler (ENS, France)
  • Antony Chariton (CSIRO, Australia)
  • Eric Coissac (LECA, CNRS, France)
  • François Pompanon (LECA, CNRS, France)
  • Xin Zhou (BGI, China)
  • Lucie Zinger (EDB, CNRS, France)

Final program

Monday 13Tuesday 14 Wednesday 15Thursday 16Friday 17
9h - 10h Registration - Welcome Eric Coissac: In silico selection and design of barcodes for DNA metabarcoding François Pompanon: Diet analysis using NGS Antony Chariton: Can metabaroding be used to routinely monitor and assess estuarine environments? Antony Chariton: Environmental monitoring of marine and estuarine sedimentary environments: wins, losses and considerations.
10h - 11h François Pompanon: Introduction to DNA metabarcoding Xin Zhou: Using standard barcode for DNA metabarcoding Chris Bowler: The Tara Ocean Expedition Lucie Zinger: DNA metabarcoding in community ecology Xin Zhou: A PCR free approach of DNA metabarcoding
11h00 - 11h30 Coffee break Coffee break Coffee break Coffee break Coffee break
11h30 - 11h45 Mieke Jansen
DNA metabarcoding in biodiversity research
James Seymour Haile
What’s In the Mix? Piles of Pills and Bags of Bones
Jon Kristoffersen
Comparison of conventional otolith analysis and DNA metabarcoding approach to assess the diet of the Mediterranean Shag from pellets
Kathleen Stoof-Leichsenring
Obtaining genetic diatom diversity from arctic lake sediments
Jakub Kreisinger
Gastrointestinal microbiota of wild and inbred individuals in two House Mouse subspecies assessed using high throughput parallel pyrosequencing
11h45 - 12h00 Raphael Civade
From sampling methodology to Metabarcoding, a new way to use environmental DNA (eDNA) as a tool for fish biodiversity assessment in stream waters
Rodolphe Rougerie
High throughput species identification of insects as ecological indicators using next generation sequencing
Christelle Tougard
Molecular identification of the diet for the Pomatoschistus gobies from Mediterranean lagoons: towards a better management of the lagoonal ecosystems
María Magdalena Fernández Guardiola
Attempting to characterize marine meiofauna using metabarcoding: what we got and what we wish
Vania Patrone
Assessing the diversity and dynamics of microbial communities within the gut
12h00 - 12h15 Kees van Bochove
Protocol optimization for eDNA metabarcoding of macrofauna indicator species listed in the European Water
Kurt Jordaens
The use of DNA metabarcoding to optimize the natural history collections of two Belgian federal institutes
Anna Papadopoulou
DNA-based biodiversity assessment of beetle assemblages: making the transition towards a metabarcoding approach
Cristina Pavloudi
"Next generation biodiversity”: Combination of molecular and morphological approaches to estimate biodiversity in lagoonal sediments
Heidy Schimann
Host preference of fungal communities in a tropical forest: evidences obtained with 454 pyrosequencing of fungal ITS
12h15 - 12h30 Jos Kielgast
eDNA monitoring of aquatic animals based on water samples
Moneeb A. Qablan
Application of NGS to examine genetic diversity of piroplasmids in their definitive host
Tomasz Suchan
Metabarcoding of plant-pollinator networks
Cuong Q. Tang
The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna
Lucie Miché
Impact of metal and spray pollutions on the biodiversity of Astragalus tragacantha associated root-symbionts
12h30 - 12h45 Alexandros Triantafyllidis
Barcoding and Meta-barcoding Research in the Laboratory of Animal Population Genetics of School of Biology of Aristotle University of Thessaloniki
Jerome Murienne
A metabarcoding approach to evaluate the role of biodiversity in disease transmission risks
Jawad Abdelkrim
My way into NGS: From doing old things to a complete change in approach
12h45 - 14h30 Lunch Lunch Lunch Lunch
14h30 - 17h30 Practical Session: Introduction to LINUX Practical Session: Metabarcoding marker design in silico Practical Session: Metabarcoding data analysis I Practical Session: Metabarcoding data analysis II Excursion to Spinalonga (13:30-21:00)


The number of participants will be limited to 20 that will attend both lectures and practical sessions. Thirty (30) more participants will follow only the lectures. Applications including a short CV and a short motivation letter should be sent to spring2013 at metabarcoding.org, with subject: “MARBIGEN DNA Metabarcoding School 2013” no later than 1 March 2013.

Workshop venue

The workshop will be held in the premises of the Hellenic Centre for Marine Research in Crete, Greece in the main building of Thalassokosmos complex (former US base at Gournes, Heraklion).


Accommodation will be provided in hotels in the area of the workshop venue, in special prices for the participants.

Workshop Costs

There are no registration fees for the workshop. Participants will have to pay for their accommodation, meals and travel expenses. The average cost for accommodation and meals for 6 days is not expected to exceed 350 euros.

Twitter : @Metabarcoding
Editorial board
  • BRANDNER Melissa
    • University of Nordland
    • Bodø (Norway)
  • BROCHMANN Christian
    • National Centre for Biosystematics
    • Oslo (Norway)
  • CHARITON Anthony
    • CSIRO Land and Water
    • Lucas Heights NA (Australia)
  • DEAGLE Bruce
    • University of Victoria
    • Victoria (Canada)
  • Eric Coissac
    • LECA
    • Grenoble (France)
  • KASAPIDIS Panagiotis
    • Hellenic Center for Marine Research
    • Irakleion, Crete (Greece)
    • Université de Genève
    • Genève 4 (Switzerland)
  • TABERLET Pierre
    • LECA,
    • Grenoble (France)
    • Centre for GeoGenetics
    • Copenhagen (Denmark)
  • Vodka, Bison and Metabarcoding

    31 July 2015, by BRANDNER Melissa

    The start of last month saw the occurrence of the Fifth Metabarcoding Spring School held in Białowieża National Park , Poland. A variety of scientists attended from all over the globe to learn, share and inspire with unique stories of metabarcoding.
    The scientists at the Mammal Research Institute PAS in Białowieża National Park hosted this year’s workshop. And our hats go off to them for the organizational skills, warmth and hospitality. During the week, experienced metabarcoders gave lectures on their trials and tribulations in the field of metabarcoding, sparking conversations between the attendees. The end of the first day saw flash talks from all participants of the event, creating an icebreaker and showing the wide variety of applications for metabarcoding, including, dietary studies, environmental health, fundamental ecology and exploration of rare and ancient habitats.
    Pierre Taberlet (who is rumoured to run 8000 PCR a day!) taught technical aspects such as DNA extraction in (...)

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