This thematic meeting was organised by PORBIOTA/LifeWatch Portugal, DNAqua-Net and EnvMetaGen project at CIBIO-InBIO. LifeWatch ERIC supported the organisation as part of its IJI (Internal Joint Initiative) on NIS (Non-indigenous and Invasive Species). More than 30 participants from nine EU countries (Belgium, Estonia, Germany, Greece, Italy, Norway, Portugal, Slovenia, Spain and Switzerland) with different backgrounds discussed their requirements for a shared metabarcoding database. CIBIO-InBIO (Research Center in Biodiversity and Genetic Resources), is a research centre which focusses on biodiversity and evolutionary biology. The institute has a large ecological, taxonomical and biogeographical knowledge with a focus on Iberian and Mediterranean biological heritage. It also offers advanced training of MSc and PhD level students and short-term training courses.
Day one (26/02/2020) starts with a welcome by Pedro Beja (Vice Scientific Coordinator of INBIO-CIBIO) and an introduction about the CIBIO facilities. This introduction was followed by a presentation of Florian Leese, Chair of DNAqua-Net, who explained how eDNA and metagenomics are used to estimate the quality of different waterbodies. After which Christos Arvanditis, CEO of LifeWatch ERIC, explained how LifeWatch is active in large scale data capture, connecting scientists and involved in citizen science projects/training programs. Juan M. González, CTO of LifeWatch ERIC, gave a short presentation on how bioinformatic platforms could be integrated in the LifeWatch ERIC e-infrastructure. Rafael C. Jiménez, explained how to combine metagenomic data with different scientists into an easy to use online platform and stressed the importance of cooperation between all parties involved. Rocia Bautista Moreno finishes the first day’s lectures with an introduction of SCBI (Technology park in Malaga) and their expert bioinformatic capacities (Picasso super computer, Next seq500, Miseq, Illumina sequencing, Epigenetics …)
The meeting is concluded with a guided tour of the CIBIO facilities.
Day two (27/02/2020) starts with a presentation by Pedro Beja about NGS optimisation and challenges, an in dept introduction about the different projects currently present at the CIBIO institute and the need for a standardized online platform/network were NGS data and pipelines can be shared.
The day proceeds with presentations of the different participants:
- CNR-IBIOM representatives discuss the need for: standardized bioinformatic protocols to mainstream molecular methods, curated species reference databases and a European open science cloud.
- Christina Pavloudi and Haris Zafeiropoulos, of the Hellenic centre for Marine research, give a short introduction about their work on invasive species.
- Alberto Pallavicini, of the Department of Life Sciences (Slovenia), focusses on the problems of misidentified sequences on GenBank (especially for lichens and plants) for automatic protocols.
- Short introduction of BopCo and JEMU projects by Sophie Gombeer and Carl Vangestel
- Nataša Šibanc (Slovenia), explains her work on plant/fungi diversity in changing forests, indicator species, mating behaviour/systems. She stresses the need for a reliable database to compare differences in time.
- Matjaž Gregorič (Slovenia), focusses on rare plants and arachnids, wherein eDNA is extracted for tracking of invasive species and monitoring of pollinators.
- Jennifer Leonard of the Evolutionary genetics group (Seville) explains her research on Iberian wolves and African golden wolves and the tracking of mammals (tree squirrels) in Borneo. Here specific individuals are genotyped using microsatellites.
- Martha Goberna Estelles presents her work on soil microbiota and microbial communities.
- Pascal Hablutzel gives an introduction on how VLIZ monitors aquatic systems.
- Representatives of DNAqua-Net stress once again the need for standardized protocols, for a flexible system able to adapt to new technologies and able to correct/erase errors in sequences.
- Nuno Fonseca, CIBIO-INBIO (Porto), discusses input (flexibility, multiple formats), Metadata (csv files, which primers? Flexible pipelines), Reference databases and output (which format?, interactive figures, downloadable …)
Day three (28/02/2020) What should be the characteristics of online bioinformatic platforms in LifeWatch-ERIC?
Presentations and issues raised on the previous days are now used for a large scale discussion during which all suggestions and comments of present representatives are recorded.
Topics of discussion:
- Metabarcoding analysis pipelines should be standardized
- User friendly web interface!
- Inputs (metadata, sequence data should be complete before uploading …)
- Databases should be strictly checked!
- Outputs: ASV/OUT tables, taxonomy keys, sequences (fasta) …
- Downstream analysis (Data normalization, diversity analyses, taxonomic composition, phylogenetic inference …)
- Mapping (species distributions, biodiversity indices)
- Data sharing (openness, embargo …)
- Web-interfacing and API (like Galaxy, LANIAKEA …)
The suggestions of the participants were recorded and will be included in the next phase of the construction of the bioinformatic platform.