Microbiome and Citizen Science
A special MVIF event, with talks and panel discussion by:
- Dr. Jérôme Waldispühl, McGill University, Canada
- Dr. Daniel McDonald, UCSD, USA
- Dr. Mikayla Borton, Colorado State University, USA
- Dr. Sarah Ahannach, University of Antwerp, Belgium
The discussion session will be chaired by:
- Pacific event: Dr. Jack Gilbert, UC San Diego School of Medicine, USA
- Atlantic event: Dr. Saara Suominen, IOC-UNESCO, The Netherlands
The panel will follow a session of contributed talks. Details about the contributed talks can be found below.
1. Leveling Up Citizen Science for (meta)genomic research
by Dr. Jérôme Waldispühl, McGill University, Canada
Over the past decade, citizen science computer games have become a popular practice for engaging the public in research activities. This methodology had a noticeable impact in molecular and cell biology, where millions of online volunteers contributed to the classification and annotation of scientific data, but also to solve advanced optimization problems requiring human supervision. Yet, despite promising results, the deployment of citizen science initiatives through academic/professional web pages faces serious limitations. Indeed, the volume of human attention needed to process massive data sets and make state-of-the-art scientific contributions rapidly outpaces the participation and availability of online volunteers. To overcome this challenge, citizen science must transcend its “natural habitat” and reach out to the entire gaming communities. To address this challenge, we propose to build partnerships with commercial video game companies that already assembled large communities of gamers. In this talk, we describe how this approach can transform the impact of citizen science in (meta)genomics. We discuss our experience from Phylo, an online puzzle for gene alignment, to Borderlands Science, a massively multiplayer online game for microbiome data analysis. We show how to embeds citizen science tasks into a virtual universe to engage new user bases. These principles have profound implications for future citizen science initiatives seeking to meet the growing demands of biology.
2. Translating the Microbiome through Microsetta
by Dr. Daniel McDonald, UCSD, USA
The Microsetta Initiative is the globally focused microbiome citizen science successor to the American Gut Project. Representing over 30,000 microbiome samples, with comprehensive phenotypic and diet information, Microsetta is an unparalleled open access compendium of microbiome data. Here, I talk about the state of Microsetta, examples of microbiome results across populations, how you can use these data, and where we are going into the future.
3. From Drops to Data: Harnessing Community Science to Decode Aquatic Microbiomes Across the Globe
by Dr. Mikayla Borton, Colorado State University, USA
Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept, we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures, so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.
4. Citizen science as an instrument for women’s health research
by Dr. Sarah Ahannach, University of Antwerp, Belgium
Women’s health research is receiving increasing attention globally, but considerable knowledge gaps remain. Across many fields of research, active involvement of citizens in science has emerged as a promising strategy to help align scientific research with societal needs. Citizen science offers researchers the opportunity for large-scale sampling and data acquisition while engaging the public in a co-creative approach that solicits their input on study aims, research design, data gathering and analysis. Here, we argue that citizen science has the potential to generate new data and insights that advance women’s health. Based on our experience with the international Isala project, which used a citizen-science approach to study the female microbiome and its influence on health, we address key challenges and lessons for generating a holistic, community-centered approach to women’s health research. We advocate for interdisciplinary collaborations to fully leverage citizen science in women’s health toward a more inclusive research landscape that amplifies underrepresented voices, challenges taboos around intimate health topics and prioritizes women’s involvement in shaping health research agendas.
Contributed Talks
1. Le French Gut – le microbiote français: a prospective French citizen science study aiming to analyze 100,000 fecal samples with associated nutritional and clinical data
by Dr. Patrick Veiga and Dr. Mathieu Almeida, Metagenopolis, INRAE, France
Le French Gut – Le microbiote français is a large-scale national study aiming to explore the links between gut microbiota, diet, environmental factors, and health in the French population. The objective is to collect and analyze 100,000 stool samples from adults—and soon from children and teenagers. Participation is entirely home-based, involving self-collected stool samples, online questionnaires, and linkage with the French national health data system. To achieve this large-scale recruitment target, we adapted both pre-analytical and analytical platforms to ensure scalability, robustness, and adherence to high-quality standards. Recruitment strategies and communication channels were also diversified and optimized to effectively engage a broad population. This project will help to : i) advance our understanding of how environmental factors—including diet—shape the gut microbiome, ii) support the development of precision nutrition and personalized medicine strategies, and iii) identify predictive biomarkers of chronic diseases. Launched in 2022, the study has already enrolled over 25,000 participants as of March 2025. In this presentation, we will provide an overview of the project and discuss the scientific, technical, and operational challenges involved in its implementation.
2. ECHO: Bridging Citizen Participation and Scientific Analysis in Soil Health
by Dr. Claudia Cappello, Free University of Bozen-Bolzano, Italy
ECHO is a Research and Innovation Action co-funded by the EU under Horizon Europe and UK Research and Innovation (UKRI). Running from June 2023 to May 2027, ECHO engages European citizens in soil health by raising awareness, generating data, and fostering stewardship. It complements existing soil monitoring efforts while empowering citizens in data collection and decision-making.
Built on three principles—engaging citizens in soil protection, empowering them with knowledge, and enabling their participation in policy—ECHO develops inclusive citizen science initiatives across Europe. The project addresses cultural and language differences, with 28 initiatives assessing 16,500 sites.
A key outcome is ECHOREPO, an open-access data repository benefiting scientists, policymakers, landowners, and the public. ECHO promotes engagement through an interactive platform, an Ambassador network, and the ECHO app. It provides educational materials and creative collaborations to enhance public participation.
ECHO collects data on eight key soil health indicators, including pollutants, soil organic carbon, structure, nutrients, pH, biodiversity, vegetation cover, and landscape heterogeneity. Citizens use the ECHO app to record GPS data, photos, and assess soil health. Two additional samples undergo laboratory analysis for microbial diversity and heavy metal content. The app also supports real-time data recording, geolocation tracking, and interaction between Ambassadors and participants.
By 2027, ECHO will expand to all EU countries, providing low-cost tools and standardized protocols. While simplified methods may introduce variability, comparative assessments will refine data integration. Ultimately, ECHO aims to enhance citizen science credibility in environmental monitoring, supporting informed soil health policies and sustainable land management.