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MICROWINE - Microbial metagenomics and the modern wine industry

Deliverables

Training event 2

Successful implementation of training event month 12: Communication and Presentation 1 (UW)

PhD theses submission

Ensure all PhD theses submitted.

Publications for each WP (WP3-WP5)

Submission of at least 2 peer review research papers per ESR. Lead partner: WP lead

Training events 3

Successful implementation of training events - month 18: - Abiotic Influences on Viticulture (UCPH) - Grape Harvesting and Biological Monitoring during Fermentation (ChrHa) - Science of Wine and Port Production (AESBUC) - Origins of Viticulture (INRA)

Training events 1

Successful implementation of training events - month 7: - Kickoff conference: 21st Century Challenges to Viticulture (AU). - 21st Century Approaches to Viticiulture and Understanding Wine Quality (ChrHa)

Training events 4

Successful implementation of training events - month 24 - Midterm conference: Meeting Viticulture challenges through Novel Technological Developments (AU) - Communciation and Presentation 2 (UCPH) - Research Management, Career Planning, Grant Writing (UCPH) - Entrepreneurschip (ChrHa) - Genomics - from Microbe to Vine (DTU)

Training event 5

Successful implementation of training event - month 30 - Applied Snesory Analysis (DLR-RLP) - Aroma Analytics (UNIZAR)

Training event 6

Successful implementation of training events - month 36. - Bio-informatics and modelling (VU) - Symbiosis - Biology and Methodology (INRIA)

Training event 7

Successful implementation of training event - month 42: Final Conference MICROWINE 2020 - State of the Art Solutions for Viticulture

Publications

Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

Author(s): Alex Gobbi; Ifigeneia Kyrkou; Elisa Filippi; Lea Ellegaard-Jensen; Lars Hestbjerg Hansen; Lars Hestbjerg Hansen
Published in: Scientific Reports, 10, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-56741-z

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

Author(s): Sarah Siu Tze Mak, Shyam Gopalakrishnan, Christian Carøe, Chunyu Geng, Shanlin Liu, Mikkel-Holger S Sinding, Lukas F K Kuderna, Wenwei Zhang, Shujin Fu, Filipe G Vieira, Mietje Germonpré, Hervé Bocherens, Sergey Fedorov, Bent Petersen, Thomas Sicheritz-Pontén, Tomas Marques-Bonet, Guojie Zhang, Hui Jiang, M Thomas P Gilbert
Published in: GigaScience, 6/8, 2017, Page(s) 1-13, ISSN 2047-217X
Publisher: Oxford Academic
DOI: 10.1093/gigascience/gix049

Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model

Author(s): Ifigeneia Kyrkou, Taneli Pusa, Lea Ellegaard-Jensen, Marie-France Sagot, Lars Hestbjerg Hansen
Published in: Frontiers in Microbiology, 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.02141

Multi-omics and potential applications in wine production

Author(s): Kimmo Sirén, Sarah Siu Tze Mak, Ulrich Fischer, Lars Hestbjerg Hansen, M Thomas P Gilbert
Published in: Current Opinion in Biotechnology, 56, 2019, Page(s) 172-178, ISSN 0958-1669
Publisher: Elsevier BV
DOI: 10.1016/j.copbio.2018.11.014

Assessing the impact of plant genetic diversity in shaping the microbial community structure of Vitis vinifera phyllosphere in the Mediterranean

Author(s): Prashant Singh, Alex Gobbi, Sylvain Santoni, Lars H Hansen, Patrice This, Jean-Pierre Péros
Published in: Frontiers in Life Science, 11/1, 2018, Page(s) 35-46, ISSN 2155-3769
Publisher: Taylor and Francis Inc.
DOI: 10.1080/21553769.2018.1552628

Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach

Author(s): Prashant Singh, Sylvain Santoni, Patrice This, Jean-Pierre Péros
Published in: Microorganisms, 6/4, 2018, Page(s) 96, ISSN 2076-2607
Publisher: mdpi
DOI: 10.3390/microorganisms6040096

Automated supervised learning pipeline for non-targeted GC-MS data analysis

Author(s): Kimmo Sirén, Ulrich Fischer, Jochen Vestner
Published in: Analytica Chimica Acta: X, 1, 2019, Page(s) 100005, ISSN 2590-1346
Publisher: Elsevier B.V.
DOI: 10.1016/j.acax.2019.100005

Distribution of Oenococcus oeni populations in natural habitats

Author(s): Lorentzen, Marc Lucas, Patrick
Published in: Applied Microbiolology and Biotechnology, 103, 2019, Page(s) 0175-7598/2937-2945, ISSN 1432-0614
Publisher: Springer Berlin Heidelberg
DOI: 10.1007/s00253-019-09689-z

Metabolic Games

Author(s): Taneli Pusa, Martin Wannagat, Marie-France Sagot
Published in: Frontiers in Applied Mathematics and Statistics, 5, 2019, ISSN 2297-4687
Publisher: Front. Appl. Math. Stat.
DOI: 10.3389/fams.2019.00018

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must

Author(s): Kimmo Sirén, Sarah Siu Tze Mak, Chrats Melkonian, Christian Carøe, Jan Hendrik Swiegers, Douwe Molenaar, Ulrich Fischer, M. Thomas P. Gilbert
Published in: Frontiers in Microbiology, 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.00697

Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR

Author(s): Alex Gobbi, Rui G. Santini, Elisa Filippi, Lea Ellegaard-Jensen, Carsten S. Jacobsen, Lars H. Hansen
Published in: PLOS ONE, 14/4, 2019, Page(s) e0200979, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0200979

Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Author(s): Marc P. Lorentzen, Hugo Campbell-Sills, Tue S. Jorgensen, Tue K. Nielsen, Monika Coton, Emmanuel Coton, Lars Hansen, Patrick M. Lucas
Published in: BMC Genomics, 20/1, 2019, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-019-5692-3

Changes in the Composition of the Lactic Acid Bacteria Behavior and the Diversity of Oenococcus oeni Isolated from Red Wines Supplemented with Selected Grape Phenolic Compounds

Author(s): Ingrid Collombel, Francisco Campos, Tim Hogg
Published in: Fermentation, 5/1, 2019, Page(s) 1, ISSN 2311-5637
Publisher: MDPI
DOI: 10.3390/fermentation5010001

Modulating Fermentative, Varietal and Aging Aromas of Wine Using non-Saccharomyces Yeasts in a Sequential Inoculation Approach

Author(s): Inès Oliveira; Vicente Ferreira
Published in: Microorganisms, 12 per year, 2019, Page(s) 1-23, ISSN 2076-2607
Publisher: MDPI AG
DOI: 10.3390/microorganisms7060164

Epicoccum layuense a potential biological control agent of esca-associated fungi in grapevine

Author(s): Giovanni Del Frari, Ana Cabral, Teresa Nascimento, Ricardo Boavida Ferreira, Helena Oliveira
Published in: PLOS ONE, 14/3, 2019, Page(s) e0213273, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0213273

Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture

Author(s): Chrats Melkonian, Willi Gottstein, Sonja Blasche, Yongkyu Kim, Martin Abel-Kistrup, Hentie Swiegers, Sofie Saerens, Nathalia Edwards, Kiran R. Patil, Bas Teusink, Douwe Molenaar
Published in: Frontiers in Microbiology, 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.01347

Endotherapy of infected grapevine cuttings for the control of Phaeomoniella chlamydospora and Phaeoacremonium minimum

Author(s): GioVAnni DEL FRARI, João COSTA, HeLenA OLIVEIRA and RiCARdo BOAVIDA FERREIRA
Published in: Phytopathologia Mediterranea, 2018, ISSN 1593-2095
Publisher: Firenze University Press
DOI: 10.14601/phytopathol_mediterr-23515

Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms

Author(s): Giovanni Del Frari, Alex Gobbi, Marie Rønne Aggerbeck, Helena Oliveira, Lars Hestbjerg Hansen, Ricardo Boavida Ferreira
Published in: Frontiers in Plant Science, 10, 2019, ISSN 1664-462X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fpls.2019.00910

Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus plantarum—A Novel Lineage of Lactobacillus Phages Comprising Five New Members

Author(s): Ifigeneia Kyrkou, Alexander Byth Carstens, Lea Ellegaard-Jensen, Witold Kot, Athanasios Zervas, Amaru Miranda Djurhuus, Horst Neve, Martin Hansen, Lars Hestbjerg Hansen
Published in: Viruses, 11/7, 2019, Page(s) 611, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v11070611

MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network

Author(s): Pusa, Taneli; Ferrarini, Mariana Galvao; Andrade, Ricardo; Mary, Arnaud; Marchetti-Spaccamela, Alberto; Stougie, Leen; Sagot, Marie-France
Published in: Bioinformatics, 2019, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz584

New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni.

Author(s): Ingrid Collombel; Chrats Melkonian; Douwe Molenaar; Francisco M. Campos; Tim Hogg; Tim Hogg
Published in: Frontiers in Microbiology, 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.02597

"Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, \""Silenusvirus\""."

Author(s): Ifigeneia Kyrkou; Alexander Byth Carstens; Alexander Byth Carstens; Lea Ellegaard-Jensen; Witold Kot; Witold Kot; Athanasios Zervas; Amaru Miranda Djurhuus; Amaru Miranda Djurhuus; Horst Neve; Charles M. A. P. Franz; Martin Hansen; Lars Hestbjerg Hansen; Lars Hestbjerg Hansen
Published in: Scientific Reports, 10, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1101/728261

Understanding the phyllosphere microbiome assemblage in grape species (<em>Vitaceae</em>) with amplicon sequence data structures

Author(s): Singh, Prashant; Santoni, Sylvain; Weber, Audrey; This, Patrice; Peros, Jean-Pierre
Published in: Scientific Reports, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-50839-0

Control of Bacteria for Sustainable Viticulture and Vinification Practices

Author(s): Ifigeneia Kyrkou
Published in: PhD thesis, 2018
Publisher: Aarhus University

Microbial Assemblage in Grapevine's Phyllosphere: Who is the driver ?

Author(s): Prashant Singh
Published in: 2018
Publisher: Montpellier Supagro

Vineyard soils evaluation. Combining elemental analysis via X-ray fluorescence core scanner and microbial DNA sequencing to assess soil vertical stratification

Author(s): Rui Santini
Published in: PhD Thesis, 2018
Publisher: University of Copenhagen

Riesling, ferments, microbes −The development and application of NGS tools in the context of winemaking

Author(s): Sarah ST Mak
Published in: PhD Thesis, 2018
Publisher: University of Copenhagen

Multi-omics Methods to unravel Microbial Diversity in Fermentation of Riesling Wines

Author(s): Kimmo Sirén
Published in: PhD Thesis, 2019
Publisher: Technical University of Kaiserlautern

Mathematical modelling of the impacts of environment using metabolic networks and game theory

Author(s): Henri Taneli Pusa
Published in: PhD Thesis, 2019
Publisher: University of Lyon 1, France, and Sapienza University of Rome, Italy

Diversité et caractéristiques génomiques d'Oenococcus oeni

Author(s): Marc Lorentzen
Published in: PhD Thesis, 2019
Publisher: University of Bordeaux

Contribution of wine microorganisms to the aroma composition of wine and its sensory impact

Author(s): Ines Pereira Biscaia de Oliveira
Published in: PhD Thesis, 2019
Publisher: Universidad de Zaragoza

Grape Evolution in the Human Environment

Author(s): Hsiao-Lei Liu
Published in: PhD Thesis, 2019
Publisher: University of Warwick

Analysis of grape wine microbiota from different wine producing regions and thier plant growth promoting properties

Author(s): Mónica Oyuela Aguilar
Published in: PhD Thesis, 2019
Publisher: UNLP

Metagenomics in wine fermentation

Author(s): Franziska Klinke
Published in: PhD Thesis, 2019
Publisher: Technical University of Denmark (DTU)

Exploring the molecular basis of microbial wine-terroir

Author(s): Alex Gobbi
Published in: PhD thesis, 2019
Publisher: Aarhus University

Frontiers in the control of pathogenic fungi associated with the esca disease complex

Author(s): Giovanni Del Frari
Published in: 2019
Publisher: University of Lisbon

Post-alcoholic fermentation micro-ecology of wines: the role of phenolic composition and the effects on quality

Author(s): Ingrid Collombel
Published in: 2018
Publisher: University of Porto

Seasonal microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

Author(s): Gobbi Alex, Kyrkou Ifigeneia, Filippi Elisa, Ellegaard-Jensen Lea, Hansen Lars Hestbjerg
Published in: Bioxriv, 2018
Publisher: Bioxriv
DOI: 10.1101/523977

Analysing complex metagenomic data with MicroWineBar

Author(s): Franziska Klincke, Martin Abel-Kistrup, Sofie Maria Gilberte Saerens, Simon Rasmussen
Published in: Biorxiv, 2019
Publisher: Biorxiv
DOI: 10.1101/742684

Datasets

Additional file 8: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Author(s): Lorentzen, Marc; Campbell-Sills, Hugo; Jorgensen, Tue; Nielsen, Tue; Coton, Monika; Coton, Emmanuel; Hansen, Lars; Lucas, Patrick
Published in: figshare

Additional file 9: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Author(s): Lorentzen, Marc; Campbell-Sills, Hugo; Jorgensen, Tue; Nielsen, Tue; Coton, Monika; Coton, Emmanuel; Hansen, Lars; Lucas, Patrick
Published in: figshare

Additional file 11: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Author(s): Lorentzen, Marc; Campbell-Sills, Hugo; Jorgensen, Tue; Nielsen, Tue; Coton, Monika; Coton, Emmanuel; Hansen, Lars; Lucas, Patrick
Published in: figshare

Additional file 12: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Author(s): Lorentzen, Marc; Campbell-Sills, Hugo; Jorgensen, Tue; Nielsen, Tue; Coton, Monika; Coton, Emmanuel; Hansen, Lars; Lucas, Patrick
Published in: figshare

Additional file 10: of Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

Author(s): Lorentzen, Marc; Campbell-Sills, Hugo; Jorgensen, Tue; Nielsen, Tue; Coton, Monika; Coton, Emmanuel; Hansen, Lars; Lucas, Patrick
Published in: figshare

Oenococcus oeni genome assembly - wine CiEs

Author(s): Ahmad A. Zeidan; Ingrid Collombel; Chrats Melkonian
Published in: Zenodo