GloMiNe "Preservation of microbial diversity” by Microbiota Vault and MVIF
Microbial ecosystems underpin life on Earth, yet they are increasingly imperiled by human activities, including unsustainable agricultural practices and overuse of antibiotics. These disturbances disrupt microbial networks essential for environmental stability, biodiversity, and animal and human health, contributing to the global rise of chronic diseases and ecosystem degradation. Equitable approaches for the preservation of microbial diversity are urgently needed.
This 5th Global Microbiome Network symposium (GloMiNe 2025) focuses on the challenges and ways ahead. In partnership with the Microbiome Virtual International Forum (MVIF), the Microbiota Vault initiative assembles a community of experts from all over the world to discuss and promote the importance of conservation efforts on microbial biodiversity.
The Topic of this year’s event is "Preservation of microbial diversity”,
The Glomine event held both at the Atlantic and Pacific session with different speakers. Details can be found below.
Atlantic Event
1. The Microbiota Vault
By Prof. Maria Gloria Dominguez Bello, Rutgers, The State University of New Jersey
Industrialization and urbanization are eroding human-associated microbial diversity, contributing to rising immune and metabolic disorders. The Microbiota Vault initiative, modeled after the Seed Vault, offers an equitable global framework to preserve this biodiversity by enabling local capacity, standardized protocols, and secure backup storage. Through the Global Microbiota Network (GloMiNe), pilot repositories, and international outreach, the project connects biodiversity-rich but resource-limited regions with global efforts. These activities lay the foundation for a distributed infrastructure to safeguard microbial heritage for science, health, and future generations.
2. Presentation Launch Phase
By Mr. Youzheng Teo (University of Lausanne) & Dr. Anton Lavrinienko (ETH Zurich)
The Microbiota Vault Initiative (MVI) is a non-profit organization dedicated to safeguarding naturally evolved microbial diversity for future research and potential restoration of microbial diversity. During its two-year launch phase, MVI partnered with Local Working Collections (LWCs) in Benin, Brazil, Ethiopia, Ghana, Laos, Thailand, and Switzerland, depositing more than 1,171 human fecal specimens and 190 fermented-food samples, which are securely stored at −80 °C in a biobank in Zurich. The launch established standardized standard operating procedures (SOPs) for sample collection, transport, and metadata for human stool and fermented foods, and evaluated preservation methods for long-term storage for maintaining microbial viability. The MVI aims to expand microbial research to underrepresented communities to support inclusivity and globally representation.
3. The Role of Philanthropic Foundations and Donors in the Preservation of Invisible Biodiversity
By Dr. Manuel Fankhauser, Seerave Foundation
4. Biobanking of microorganisms from permafrost and glaciers of the Swiss Alps
By Dr. Beat Frey, Swiss Federal Institute for Forest, Snow and Landscape Research
The cold habitats of the Swiss Alps and the Arctic are undergoing change and are at risk of disappearing partially or completely with increasing global temperatures. Along with them, a poorly known diversity of microorganisms that have adapted to life in these supposedly hostile places. Therefore it is important to preserve this unknown microbial diversity. By cryopreserving approx. 1'500 microbial strains from these habitats, some of today's biodiversity can be preserved in biobanks. Here, we focus on the bioprospecting of Alpine and Polar microorganisms stored at long-term in the biobank to discover natural products that could be useful to us. This is especially relevant now, as these environments are among the most rapidly changing due to climate change. Over the past 20 years, we have collected soil, plastic and ice samples from a variety of Alpine and Polar environments. To bioprospect these ecosystems, we have followed two main approaches. The first involves searching our strains in the biobank for biosynthetic gene clusters, responsible for the production of secondary metabolites and genes related to plastic biodegradation by using tools that were developed for mining genomes for these gene clusters. The second approach involves a proof of concept to test of the selected strains in laboratory experiments for the abilities to produce antibiotic compounds and enzymes involved in plastic biodegradation. In both cases, our goal is to identify genes that may encode bioactive compounds or enzymes of interest—such as those with antimicrobial properties that could help us fight microbial infections and polymer degrading enzymes that might sustain a circular economy for plastic waste.
5. Filling the Gaps in Global Microbiome Knowledge from Latin America
By Alejandro Reyes, Universidad de Los Andes
The human gut microbiome is central to health, yet global knowledge remains biased toward high-income countries. Latin America and the Caribbean (LAC), with its exceptional cultural and dietary diversity, rapid urbanization, and dual burden of infectious and chronic diseases, is still underrepresented in public datasets. This gap limits our ability to define context-specific microbial baselines and risks the irreversible loss of unique microbial lineages shaped by traditional lifestyles.
The Latinbiota Consortium was created to address this imbalance through collaborative, regionally led research. To date, more than 600 fecal samples from ten LAC countries have been sequenced, revealing both the extraordinary diversity of ancestral microbiomes and the rapid homogenization of urban communities. These findings echo global concerns about the erosion of VANISH taxa and the restructuring of microbial networks under modernization.
Associated studies have extended this dataset across gradients of rurality and health, including individuals at risk of obesity who maintain primarily rural lifestyles. These efforts emphasize the importance of equity and capacity building, promoting data sovereignty and the active participation of local scientists and communities. By integrating regional leadership with global collaboration, this initiative aims to improve representation in microbiome research and preserve microbial diversity before it is lost.
6. Live Gut Microbiome: Cryopreservation and Assays
By Prof. Daniel Figeys, Quadram Institute
The gut microbiome plays a central role in host responses to dietary, pharmaceutical, and environmental exposures, yet capturing its functional activity ex vivo remains a major challenge. We developed RapidAIM, a high-throughput assay that maintains live human gut microbiomes in 96-well format, enabling systematic screening of the effects of xenobiotics, prebiotics, and nutritional compounds. RapidAIM preserves taxonomic diversity and functional activity, providing reproducible insights into compound–microbiome interactions and has been shown to reproduce effects observed in vivo. To support longitudinal and large-scale applications, we have established protocols for cryopreservation of live gut microbiomes, which maintain the composition, function, and metabolic output of the microbiome after storage. Together, these innovations provide a robust platform for precision microbiome research, enabling reproducible, scalable investigations of how interventions shape microbial ecology and function.
7. From Deserts to Coral Reefs: Preserving Microbial Diversity for One Health in the Arabian Peninsula
By Prof. Alexandre Rosado, King Abdullah University of Science and Technology
Saudi Arabia is at a crossroads, facing mounting pressures from climate change, rapid development, population growth, and global travel. As outlined in Vision 2030, these challenges intensify strain on ecosystem processes and threaten microbiomes, wider ecosystems, and public health. This presentation examines how preserving microbial diversity in deserts, volcanic fields, coral reefs, and mangroves can address environmental and health challenges by supporting the breakdown of pollution, enhancing food security, preventing disease, and promoting ecosystem restoration. Robust microbiomes underpin the One Health and Planetary Health frameworks, which link environmental resilience to the health of humans, animals, and ecosystems. The newly established Microbial Vault at King Abdullah University of Science and Technology (KAUST) consolidates thousands of microbial isolates from extreme and marine environments, creating a biobank that advances biotechnological innovation, the development of new medicines, and health research. Through the protection and application of this microbial diversity, Saudi Arabia has the potential to become a leading example in One Health, sustainability, and pandemic preparedness.
8. Coral probiotics: From the Laboratory to the Real World
By Prof. Raquel Peixoto, King Abdullah University of Science and Technology
Coral reefs face intensifying heatwaves and disease, motivating nature-based interventions that strengthen holobiont resilience. I will present how we developed a practical framework for discovering, formulating, and deploying Beneficial Microorganisms for Corals (BMCs)—“coral probiotics”—from lab to reef. The pipeline integrates (i) strain sourcing with a preference for native, host-associated taxa; (ii) function-anchored screening (e.g., pathogen antagonism, antioxidant capacity, nitrogen/sulfur cycling, stress-response modulation); (iii) consortium design and delivery optimization (solution, microencapsulation); and (iv) staged validation (controlled assays from mesocosms to pilot field trials). I will share results showing reduced bleaching severity, improved survival, and beneficial microbiome restructuring across multiple coral species. A risk-assessment effort addressing non-target effects, ecological fit, supporting transparent go/no-go decisions will also be presented. Finally, I will discuss lessons from real-world applications, and outline how this stewardship approach can scale responsibly to protect and restore reefs under a warming ocean.
9. A genomic catalogue of cultivated gut bacteria from children in non-industrialised populations
By Mr. Bonface Gichuki, University of Cambridge
10. Viral diversity in the human microbiome
By Prof. Curtis Huttenhower, Harvard University
The number of viral particles on Earth outnumber other microbes by an order of magnitude, and the same holds true in the human microbiome. The human-associated virome is typically dominated by phage, which have historically been difficult to identify via either culture or metagenomics. With the launch of the Human Virome Program, a range of new computational and experimental methods are being developed and applied to large populations to establish an improved baseline for virome diversity. I will discuss the HVP as a program, as well as an early look at improved methods for viral profiling from metagenomes and metatranscriptomes, along with their application to identify ecological and individual viral associations with conditions including the inflammatory bowel diseases and colorectal cancer.
11. Cataloging the global microbiome. Very big data for very small things
By Luis Pedro Coelho, Queensland University of Technology
The global microbiome is the collection of all microbes living on planet Earth. To study this system, we have developed approaches and methods to catalog this habitat, resulting in the Global Microbial Gene Catalog, version 1 (GMGCv1) and SPIRE, a collection of metagenome-assembled genomes (MAGs). Recently, we have expanded this work to also include small open reading frames (we currently consider all open reading frames ≥10 amino acids). We first built a catalogue of smorfs, which contains almost 1 billion sequences.
Pacific Event
1. The Microbiota Vault
By Prof. Maria Gloria Dominguez Bello, Rutgers, The State University of New Jersey
Industrialization and urbanization are eroding human-associated microbial diversity, contributing to rising immune and metabolic disorders. The Microbiota Vault initiative, modeled after the Seed Vault, offers an equitable global framework to preserve this biodiversity by enabling local capacity, standardized protocols, and secure backup storage. Through the Global Microbiota Network (GloMiNe), pilot repositories, and international outreach, the project connects biodiversity-rich but resource-limited regions with global efforts. These activities lay the foundation for a distributed infrastructure to safeguard microbial heritage for science, health, and future generations.
2. Experiences from the Microbiota Vault Pilot Project
By Prof. Adrian Egli, University of Zurich
Built on the “Collect-Preserve-Enable” concept, the 2022-24 Microbiota Vault pilot proved that a global back-up for human microbiome diversity is technically and legally feasible. A –80 °C/N₂ biobank in Zurich, now receives material from eight partner collections (five human gut, three fermented-food) and secured ~2 000 specimens spanning five continents. Sixteen harmonised cryo- and lyophilisation SOPs, validated on infant-to-adult faecal samples over one year, ensure consistent preservation quality. Minimal metadata and a cloud 16S-V4 analysis pipeline deliver immediate research utility, while standard MTAs and a consortium agreement provide equitable governance. With launch-phase milestones met, the project is ready to scale (2025-27) and aims now to further expand with higher geographic coverage.
3. Social Microbiome Gradient Across the Rural-to-Urban Transition in Indonesia.
By Dr. Safarina Malik, Mochtar Riady Institute for Nanotechnology
Indonesia, a densely populated and culturally diverse country, is undergoing rapid transition from traditional to urban lifestyles, a change that may disrupt established host-microbe relationships and influence disease risk. In this study, we analysed metagenomic data from 116 individuals representing a gradient of lifestyles, including transitional hunter-gatherers, rural agriculturalists, and urban dwellers.
Our analysis revealed extensive taxonomic novelty among village-specific, non-spore-forming microbes, suggesting geography-dependent transmission. We also observed a clear rural-to-urban gradient in microbiome composition, with diversity declining alongside urbanisation and complex genus-level taxonomic shifts. Notably, population of origin had a stronger association with microbiome composition than dietary patterns, highlighting the importance of non-dietary factors in shaping gut microbial communities.
By including underrepresented Southeast Asian populations, this study contributes to a more globally inclusive understanding of the human gut microbiome and helps address longstanding biases toward Western urban cohorts.
4. Global perspectives on human milk and infant microbiomes
By Dr. Meghan Azad, University of Manitoba
Breastfeeding is a key driver of infant microbiome development. Human milk composition, including its microbiome, varies across cultures and geographies according to local environments and lifestyle practices. These variations in human milk are fundamental to shaping and understanding variations in infant microbiome development and associated health outcomes globally.
5. Disentangling the exposome’s impact on the gut microbiome and health
By Thomas Sharpton, Oregon state university
Extensive evidence demonstrates that gut microbes can mediate how exposure to environmental agents, including nutrients, pollutants, and parasites, impacts health. Consequently, the effort to manage vertebrate health benefits from defining how different environmental agents interact with the microbiome to drive physiology. This effort, however, remains bottlenecked by the extensive scope and variation of exposure. The zebrafish model system offers an opportunity to alleviate this bottleneck and study these interactions at scale, as it affords access to large sample sizes, automated exposure and phenotyping platforms, and short generation times. In this presentation, I summarize the utility and potential for the zebrafish model system to accelerate our understanding of how the exposome and microbiome interact to impact health. I also introduce key zebrafish research analytical and experimental tools that we and others innovated to this end, including longitudinal sampling designs, high-throughput germ-free fish assays, and strategies for multi-omic data integration. Finally, I will discuss recent research we have conducted that exemplifies the utility and impact of this model system for microbiome research. This discussion will include our recent characterization of how exposure to pollutants affects zebrafish gut microbiome assembly to impact larval fish behavior, and underscores the importance of defining the environmental determinants of dysbiosis in the effort to resolve and preserve health-promoting gut microbiota.
6. Precision Microbiome Health Care
By Dr. Jack GIlbert, University of California, San Diego
The human microbiome is a high dimensional and dynamic part of our physiology that plays a key role in managing health and individualized responses to diet and medicine. The immune system controls our interaction with the microbial world, and the microbial communities in our bodies are central to modulating the immune response. Changes in the human microbiome and their metabolism have substantial influence on atopy, neurological disorders, metabolic disorders, and a range of complex conditions and disease states. Diet is incredibly important in shaping human health and the microbiome, altering both composition and metabolic activity, resulting in changes in immune, endocrine, and neurological systems. Measuring diet through surveys, apps, or photographs has become indispensable to our efforts to associate microbiome composition with physiological response to specific dietary components. Microbiome-Wide Association Studies (MWAS) combined with novel quantitative multi-omic approaches and automated at-home sampling devices are enabling us to use AI techniques to determine personalized responses to nutrition that drive diseases states and treatment efficacy. Through these innovations we are finally realizing the paradigm of precision medicine for facilitating patient care.
7. Preservation of the global early life microbiota: Can a synergism with human milk reveal beneficial strains?
By Prof. David Mills, University of California, Davis
It is well established that the developing infant gut microbiota influences numerous aspects of later health. During breastfeeding, early-life bifidobacterial populations that grow on milk glycans are associated with improved immune function, reduced gut inflammation, and lower pathogen levels. With weaning, the gut microbiome shifts in composition, driven largely by the introduction of solid foods and the expansion of new microbial groups and functions. Industrialization has been linked to a global decline in early-life bifidobacteria, highlighting the need to understand and preserve the bacterial strains and functions that co-evolved to metabolize milk glycans in the infant gut. In addition to protecting the infant during breastfeeding, introducing keystone bifidobacterial populations into infants who lack them may also help support optimal development during the transition to weaning**.**
8. Surveying the faecal microbiomes of Australian marsupials
By Dr. Kate Bowerman, The University of Queensland
Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where despite their iconic status, direct sequencing-based analyses remain limited. Here we present a metagenomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80%) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalyptus folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages were observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.
9. Microbiome spectra and prevalent colibactin-associated mutational process in Japanese colorectal cancer
By Dr. Takuji Yamada, Institute of Science Tokyo
The rising incidence of colorectal cancer (CRC), particularly among younger patients, has become a major public health concern in Japan and worldwide. While the association between the gut microbiota and CRC is well recognized, its molecular basis remains unclear. We aimed to clarify this relationship by integrating whole-genome sequencing (WGS) and transcriptome data from CRC tissues with whole-genome metagenomic sequencing (WGMS) of fecal samples.
We applied explainable artificial intelligence (AI) analysis to classify CRC into four microbiome-based subtypes and examined their clinical and molecular characteristics. Colibactin-associated mutational signatures (SBS88 and ID18) were analyzed as potential early clonal events.
One subtype was enriched in younger patients and associated with poor prognosis. WGS revealed colibactin-associated mutational signatures in 97 of 138 patients (70.3%), with a higher prevalence in the younger subtype. APC hotspot mutations and frameshift deletions matching the colibactin-specific motif were observed in 12 patients (8.7%). CRCs with colibactin signatures were characterized by an immunosuppressive tumor microenvironment.
Colibactin exposure is a common yet potentially modifiable risk factor for CRC in the Japanese population. Our findings highlight the potential of microbiome-based subclassification to provide clinical and biological insights into CRC, particularly in younger patients.
10. Preserving microbial diversity: An Australian perspective
By Prof. Francine Marques, Victorian Heart Institute
Preserving human microbiome diversity can be approached from different angles: 1) preserving microbial species, 2) preserving information (i.e., the metagenomes and metadata associated with it), and 3) helping future generations maintain a healthy, diverse microbiome. In this presentation, we will discuss some of the key elements and challenges of each.
11. Rational Engineering of Live Bacterial Therapeutics from a Human Microbiome Biobank
By Dr. Calum Walsh, The University of Melbourne
Multidrug-resistant organisms (MDROs) frequently colonise the gut, limiting treatment options. Here, we present the Centre for Pathogen Genomics Microbiome Culture Collection (CMC), a >2,000-isolate, genomically characterised biobank of human gut commensals supporting the rational design of live bacterial therapeutics (LBTs). Leveraging genome-level resolution to assess safety and functional potential, we assemble small, complementary consortia intended to restore colonisation resistance and disrupt MDRO niches, with carbapenem-resistant Klebsiella pneumoniae (CRE-Kp) as a priority target. Using in vitro and in vivo assays, we show that rationally designed consortia reproducibly suppress CRE-Kp growth, with several combinations driving rapid decline of pathogen abundance and preventing rebound. These findings illustrate how genomically-resolved culture resources can be translated into mechanism-informed, precision LBT candidatesm with the CMC serving as a valuable resource for accelerating MDRO decolonisation strategies by linking isolate-level genomics with consortium design and functional testing against high-priority threats.