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Food System Microbiomes 2025 International Conference, Nov 25-28, 2025, Wageningen, NL

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SCIENTIFIC PROGRAM

MAIN TOPICS

Interconnectedness of microbiomes across food systems


Microbiomes for global health


Microbiomes for mitigating climate change


Microbiomes for circularity/sustainability

Microbiomes for nutrition and human health


Microbiomes for mitigation of risks in the food system


Novel microbiome concepts, applications and technologies

 

DETAILED PROGRAM

Latest Update: 17.10.2025


Day 1 (Tuesday, November 25th, 2025) 13:00 – 20:00

11:00 - 13:00

Arrival & registration

13:00 - 13:10

Welcome (Angela Sessitsch & Hauke Smidt, MicrobiomeSupport Association)

13:10 - 13:20

Pierre-Mathieu Pelissier (Directorate-General for Research & Innovation, Bioeconomy and Food Systems Unit, EC) - Europe for microbiomes: positioning the EU as a global leader in life sciences by 2030

13:20 - 14:05

Opening lecture: Nicola Segata (University Trento, IT) - Human and food microbiomes within a OneHealth perspective

14:05 - 15:45

Session 1: Interconnectedness of microbiomes across food systems

Chairs: Daniele Daffonchio (University of Turin, IT) and Jan Sikkema (Holomicrobiome Institute, NL)

14:05 - 14:30

Daniele Daffonchio (University of Turin, IT)
The ‘microbial terroir’ promotes fruit quality, plant resilience against stresses and carbon sequestration in fruit tree agroecosystems

14:30 - 14:45

Sijmen Schoustra (Wageningen University & University of Zambia, NL)
Ecological selection shapes microbiomes in traditional fermentation: from ecology inspired experiments to avenues of sustainable development

14:45 – 14:50

Science flash: I Nyoman Sumerta (The University of Melbourne, AU)
Seasonal sap tapping affects microbial community assembly and flavour formation in palm wine fermentation

14:50 – 14:55

Science flash: Chiara Traina (University of Turin, IT)
Interconnections across microbiomes: how do plant holobionts and food fermentations relate? A focus on the taggiasca olive tree ecosystem.

14:55 - 15:20

Jan Sikkema (Holomicrobiome Institute, NL)
The Holomicrobiome Institute: interconnectedness of microbiomes

15:20 - 15:35

Francesca Cristetti (Univeristy of Turin, IT)
Characterization of endophytic and epiphytic microbial communities of Nebbiolo grapes

15:35 – 15:40

Science flash: Despoina Langari (Aristotle University of Thessaloniki, GR)
A multi-omics exploration of microbiome dynamics across fermentation styles of cv. Chalkidiki green olives: revealing microbial interconnectedness in table olive food system

15:40 – 15:45

Science flash: Marco van Es (Bac2nature, NL)
BRIDGING Microbiome Science and Practice: Connecting Soil, Food, and Health Professionals

15:45 - 16:15

Coffee break & Poster Session 1

16:15 - 18:00

Session 2: The many pathways to sustainable food systems powered by microbiomes (ESR session) - Powered by PechaKucha

Chairs: Kevin Jerez-Bogota (Aarhus University, DK) and Ricardo Garavito Duarte (North Carolina State University, USA)
Session sponsor: Applied Microbiology International

16:15 - 16:25

Presentation by session sponsor (TBA)

16:25 - 17:10

PechaKucha Presentations by ESRs

 

Eugenia Dadzie (University of Waterloo, CA)

 

Ricardo Garavito Duarte (North Carolina State University, USA)

 

Shana L. Hepping (Leiden University, NL)

 

Leonardo Menghi (University of Southern Denmark, DK)

 

Ally Miners (University of Waterloo, CA)

 

Sara Pipponzi (AIT Austrian Institute of Technology, AT)

17:10 - 18:00

Moderated discussion

18:00 - 20:00

Welcome reception (included in the registration fee)


Day 2 (Wednesday, November 26th, 2025) 09:00 – 21:00

09:00 - 10:30

Session 3: Microbiomes for global health

Chairs: Gerlinde de Deyn (Wageningen University, NL) and Alexandre Soares Rosado (KAUST, SA)

09:00 - 09:25

Gerlinde De Deyn (Wageningen University, NL)
Soil health, soil microbes and one health

09:25 - 09:40

Jowenna Sim (University of South Australia, AU)
From Soil to Food Chain: Microbial Responses to Triazole Fungicides

09:40 – 09:45

Science flash: Joseph Selvin (Pondicherry University, IN)
Urbanization-Driven Alterations in Sediment Microbial Communities and the Prevalence of Antimicrobial Resistance in Freshwater Ecosystems

09:45 - 10:10

Alexandre S. Rosado (KAUST, SA)
Extreme microbes, the ultimate frontier in environmental restoration and planetary health

10:10 - 10:25

Wisnu Adi Wicaksono (Graz University of Technology, AT)
One Health perspective: Large-scale (meta)genomic analyses elucidate the distribution and horizontal transmission of antimicrobial resistance genes from environmental sources to humans

10:25 – 10:30

Science flash: Elena Crotti (University of Milan, IT)
Uncovering antimicrobial resistance pathways in agri-food ecosystems

10:30 - 11:00

Coffee break & Poster Session 1

11:00 - 12:10

Session 4: Microbiomes for mitigating climate change

Chairs: Eiko Kuramae (Netherlands Institute of Ecology, NL) and Ana Portugal Melo (MIRRI, PT)

11:00 - 11:25

Eiko Kuramae (Netherlands Institute of Ecology (NIOO-KNAW), NL)
Climate costs of domestication: How rice microbiomes shifted from nitrogen fixers to N2O emitters

11:25 - 11:50

Ana Portugal Melo (MIRRI-ERIC, PT)
MIRRI-ERIC and MICROBES-4-CLIMATE: advancing culturomics and synthetic communities for climate action  

11:50 - 12:05

Robin Martens (Wageningen University & Research, NL)
Predicting Microbial Functional Diversity for Decomposition along an Aridity Gradient

12:05 – 12:10

Science flash: Edoardo Zaccaria (Wageningen Livestock Research / Wageningen University, NL)
Microbial seeding as an early-life intervention to reduce methane emissions in dairy cattle

12:10 - 13:00

Session 5: Microbiomes for circularity/sustainability

Chairs: Rosa Doménech (ITENE, ES), Rosa Perez-Gregorio (University of Vigo, ES) and Angela Sessitsch (AIT Austrian Institute of Technology, AT)

12:10 - 12:35

Rosa Doménech (ITENE, ES)
Plant-growth promoting microorganisms to drive wheat microbiome modulation through sustainable practices

12:35 - 12:50

Aranksha Thakor (University of Waterloo, CA)
Engineering Pseudomonas alloputida for Sustainable Bioplastic Production from Dairy Waste

12:50 – 12:55

Science flash: Simone Rampelli (University of Bologna, IT)
From soil to must: Harnessing vineyard microbiomes for circular viticulture and winemaking

12:55 – 13:00

Science flash: Dirkjan Schokker (Wageningen Bioveterinary Research, NL)
Antimicrobial resistance dynamics in black soldier fly larvae valorizing waste streams

13:00 - 14:30

Lunch break & Poster Session 1

14:30 - 16:10

Session 5: Microbiomes for circularity/sustainability

Chairs: Rosa Doménech (ITENE, ES), Rosa Perez-Gregorio (University of Vigo, ES) and Angela Sessitsch (AIT Austrian Institute of Technology, AT)

14:30 - 14:55

Rosa Perez-Gregorio (University of Vigo, ES)
Leveraging bioactive compounds and microbiomes for the development of sustainable, low-immunogenic wheat-based foods

14:55 - 15:10

Elisabetta Chiarini (University of Turin, IT)
Sustainable Kombucha fermentation: Microbial dynamics and chemical profiling from plant-based by-products

15:10 – 15:15

Science flash: Annelein Meisner (Wageningen University & Research, NL)
Steering microbiomes for diseases suppression in soilless cultivations systems via the addition of circular waste streams

15:15 – 15:20

Science flash: Enrique Cubas (ITENE, ES)
Exploiting crop microbiomes as a source of biocontrol and biostimulant microorganisms for sustainable agriculture in the Mediterranean

15:20 - 15:45

Angela Sessitsch (AIT Austrian Institute of Technology, AT)
Microbiome interconnectedness and employing microbiomes for a sustainable and healthy soya-based food system

15:45 - 16:00

Sofia Leonti (Wageningen University and Research, NL)
Facilitators and barriers to farmers’ acceptance of microbiome technology and other similar technologies for sustainable crop production: a review.

16:00 – 16:05

Science flash: Abelardo Margolles (CSIC-IPLA, ES)
Modulation of gut microbiota by oligosaccharide fractions derived from brewer’s spent grain in a dynamic colonic fermentation model

16:05 – 16:10

Science flash: Christian Euler (University of Waterloo, CA)
Synthetic mixotrophic approaches to CO2-free waste upcycling

18:00 -

Conference dinner: De Beekdalhoeve (bus departure from conference venue @16:30)


Day 3 (Thursday, November 27th, 2025) 09:00 – 18:15

09:00 - 10:30

Session 6: Microbiomes for nutrition and human health

Chairs:Stephane Chaillou (INRAE, FR) and Christophe Courtin (KU Leuven, BE)

09:00 - 09:25

Stephane Chaillou (INRAE, FR)
The domino-like heath effect of fermented food-based diet: What strategies for untangling the complexity?

09:25 - 09:40

Maria Batool (University of Reading, GB)
Microbiota changes and growth impacts associated with oral iron supplementation in neonates

09:40 - 09:55

Julien Tap (micalisfme, FR)
Multiscale associations between diet and the gut microbiome in a nationwide French cohort

09:55 - 10:10

Elisa Di Stefano (APC Microbiome Ireland, IE)
Harnessing Bifidobacterium spp. for phytate degradation: activity, regulation, and potential to support early-life nutrition.

10:10 – 10:15

Science flash: Davide Buzzanca (University of Turin, IT)
Development of a plant-based psychobiotic yogurt-like for the gut brain axis

10:15 – 10:20

Science flash: Faezeh Ebrahimi (University of Melbourn, AU)
The bi-directional influence of dietary polyphenol and the regional gastrointestinal microbial population

10:20 – 10:25

Science flash: Ilario Ferrocino (University of Turin, IT)
Effects of probiotic supplementation on symptoms and microbiome characteristics in patients with non-celiac gluten/wheat sensitivity

10:30 - 11:00

Coffee break & Poster Session 2

11:00 - 12:05

Session 6: Microbiomes for nutrition and human health

Chairs:Stephane Chaillou (INRAE, FR) and Christophe Courtin (KU Leuven, BE)

11:00 - 11:25

Christophe Courtin (KU Leuven, BE)
Leveraging food fermentations for health

11:25 - 11:40

Josep Rubert (Wageningen University, NL)
Unveiling microbial lipid signatures: The metabolism of linoleic acid by clostridia and gammaproteobacteria

11:40 - 11:55

Frederick Warren (Quadram Institute, GB)
Spatiotemporal Profiling of the human small intestinal microbiome

11:55 – 12:00

Science flash: Gloria Fackelmann (University of Trento, IT)
Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals

12:00 – 12:05

Science flash: Emma Saltzman (Monash University, AU)
Live bacteria in fresh foods contribute to human gut microbiome diversity

12:15 - 13:30

Regulatory Workshop

Chairs: Yolanda Sanz (CSIC, ES) and Javier Moreno (CSIC, ES)

12:15 - 13:00

Introductory talks

Yolanda Sanz (CSIC, ES)
MicrobiomeSupport Regulatory Task Force introduction

Javier Moreno (CSIC-UAM, ES)
Integrating gut microbiome insights into food safety risk assessments

Rosella Brozzi (EFSA, IT)
Scientific criteria for the characterisation of microorganisms of regulated products in the EU

Sandrine Claus (STARFISH Bioscience, FR)
Developing next-generation biosolutions for agriculture within the EU legislative framework

13:00 - 13:30

Round Table discussion with Rosella Brozzi (EFSA, IT), Sandrine Claus (STARFISH Bioscience, FR), Céline Druart (Pharmabiotic Research Institute, FR), Javier Moreno (CSIC-UAM, ES) and David Yañez (CSIC, ES)

13:00 - 14:30

Lunch break & Poster Session 2

14:30 - 16:00

Project Exhibition & Poster Session 2 (in parallel)

  • Session 1: How food system microbiomes contribute to food transition pathways (Microbiomes4Soy, Tribiome, Wheatbiome)
  • Session 2: How to predict emerging food system risks (HOLiFOOD, FoodSafeR)
  • Session 3: Unlocking microbial potential – accelerating discovery through integrated infrastructure (UNLOCK)
16:30 - 18:10

Session 7: Microbiomes for mitigation of risks in the food system

Chairs: Ine Van der Fels-Klerx (Wageningen Food Safety Research, NL) and Martin Wagner (University of Veterinary Medicine Vienna, AT)

16:30 - 16:55

Ine Van der Fels-Klerx (Wageningen Food Safety Research, NL)
Resilience thinking in management Salmonella spp in the pork supply chain

16:55 - 17:10

Eleftheria Trampari (Quadram Institute Bioscience, GB)
The ecology of persistence: How community complexity and composition shape Salmonella’s survival in the food chain

17:10 – 17:15

Science flash: Mohak Gujare (Wageningen University & Research, NL)
Identifying prognostic microbiome biomarkers to predict post weaning diarrhea (PWD) in piglets and disentangling the effects of confounding factors

17:15 – 17:20

Science flash: Felix Spiegel (FFoQSI GmbH, AT)
Genomic characterization of persistent Listeria monocytogenes in European food processing facilities

17:20 - 17:45

Martin Wagner (Veterinary Medicine, AT)
The microbiome of biofilms in real food systems

17:45 - 18:00

Barbara Drigo (University of South Australia/Adelaide University, AU)
A novel risk assessment framework to address antimicrobial resistance in the Australian and Asia-Pacific vegetable supply chain

18:00 – 18:05

Science flash: Floor van Meer (Wageningen Food Safety Research, NL)
The effect of climate change on food-borne disease outbreaks in the Netherlands

18:05 – 18:10

Science flash: Garance Leroy (IFREMER, FR)
Assessment of a microbiome engineering strategy using Lactic Acid Bacteria as bioprotective cultures to delay the spoilage of Gilthead Seabream (Sparus aurata) fillets


Day 4 (Friday, November 28th, 2025) 09:00 – 13:00

09:00 - 11:10

Session 8: Novel microbiome concepts, applications and technologies

Chairs: Paul Cotter (TEAGASC, IE) and Marnix Medema (Wageningen University, NL)
Session sponsor: Quantum Design Europe

09:00 - 09:10

Presentation by session sponsor (TBA)

09:10 - 09:35

Marnix Medema (Wageningen University, NL)
Deciphering the chemical language of the microbiome using computational omics

09:35 – 09:50

Narciso M. Quijada (Institute of Functional Biology and Genomics (IBFG), ES)
The neglected side of the microbiome: hotspots in food production and the fungal resistome

09:50 – 10:05

Hrituraj Dey (University of Trento, IT)
Extending curatedFoodMetagenomicData(cFMD) for integrated analysis of food microbiomes

10:05 – 10:10

Science flash: Agata Szymanek (Perseus Biomics, BE)
Robust microbiome profiling with strain resolution using optical mapping

10:10 – 10:15

Science flash: Ananya Pawan Gupta (universita di torino, IT)
Phenotypic characterisation using BIOLOG: microbial strains from cocoa and their novel application

10:15 – 10:20

Science flash: Lakhansing A. Pardeshi (Wageningen University & Research, NL)
Conservation, evolution and recombination of tailocins in the genus Pectobacterium; and consequences for species and strain level interactions

10:20 - 10:45

Paul D. Cotter (Teagasc, IE)
New developments in studying food-microbiome-gut interactions

10:45 - 11:00

Bhavya Sree Vadlamudi (Wageningen University and Research, NL)
Evolution on autopilot: Engineering functional stability in synthetic microbial communities

11:00 – 11:05

Science flash: Nehir Kizililsoley (WFSR, NL)
Leveraging advanced AI for enhanced food safety through pathogen analysis

11:05 – 11:10

Science flash: Irene Franciosa (University of Turin, IT)
Optimizing long-term storage and propagation strategies for the preservation and reuse of fermented sausage microbiome

11:15 - 11:45

Coffee break & Poster Session 2

11:45 - 12:30

Closing lecture: Michael Wagner (University of Vienna, AT) - TBA

12:30 - 13:00

Poster awards and closing (Hauke Smidt & Tanja Kostic, MicrobiomeSupport Association)

 

Call for Abstract Submissions:

Please note that only poster abstracts are being accepted at this time, through October 31st. We welcome you to submit your abstract for a poster presentation within any of the outlined sessions. This is a great opportunity to showcase your research, insights, and innovations to a diverse and engaged audience.

Please prepare your submissions in accordance with the guidelines provided. The detailed program, including session schedules and presentation formats, will be made available in September 2025 to help you plan your participation.

We look forward to your valuable contributions and to welcoming you at the event.

Food System Microbiomes: Themed Collection Launch

Applied Microbiology International LogoIn a collaboration with our partner Applied Microbiology International, we are excited to announce the launch of a themed collection in the Sustainable Microbiology Journal inspired by the dynamic sessions and cutting-edge research presented at the 2nd Food System Microbiomes International Conference, held in Wageningen, the Netherlands, from November 25 - 28, 2025.

For more details, visit: Microbiology Calls for Papers | Sustainable Microbiology | Oxford Academic.

Please send us an email to office@foodsystemsmicrobiomes.org if you are interested in contributing to this themed collection, so we can arrange an invitation to submit. Publication fees will be waived for conference participants.



Organizing Institutions

 

Microbiome Support Association Logo
AIT Logo
Wageningen Microbiome Center Logo
OEGMBT Logo

 

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