SeqHub and Microcosm Foods Partner to Share Fermentation Datasets and Advance Open Science
SeqHub, the scientific platform for sharing and exploring biological sequence data, is partnering with Microcosm Foods, a non-profit research organization currently being incubated at the Astera Institute, which is mapping the connections between fermented foods and health.
Together, they are making microbial fermentation datasets more discoverable to accelerate open science and food innovation.
This partnership combines Microcosm's expertise in food and microbial ecosystems with SeqHub's infrastructure for sequence data annotation, sharing and collaboration.
About Microcosm Foods
Microcosm Foods is focused on uncovering the biological importance of fermented foods to human health, and increasing the impact of that knowledge through open datasets and science communication.
About SeqHub
SeqHub is a platform where researchers can easily explore, annotate, and share biological sequence datasets while also working privately with their own data in secure workspaces. This combination of openness and collaboration makes it a natural home for publishing data that benefits both individual labs and the broader scientific community.
About the Dataset
To put this vision into practice, Microcosm is publishing their first dataset as a collection on SeqHub, featuring:
- 1,235 genomes consisting of 5.6 million protein sequences
- Sourced from over 3,000 public samples of fermented food associated metagenomes and isolate genomes
- Curated metadata on the original fermented food samples
- Functional annotations including peptides for bioactivity predictions
- Taxonomic identifications
The collection includes genomes from existing public datasets with curated metadata, offering researchers a valuable resource to explore, compare, and integrate into their own work.
Commitment to Open Science
"At Microcosm, we believe microbes in fermented foods have numerous health benefits that we are only recently beginning to fully understand. Sharing our data on SeqHub is a way to invite the broader scientific community into that journey, accelerating discovery and expanding what's possible when we work together."
Elizabeth McDaniel
Head of Computational Biology, Microcosm Foods
SeqHub and Microcosm share a commitment to open science—a belief that data should be easier to find, understand, and share so that together, we can push the boundaries of what microbes can teach us.
Whether you're an academic researcher, biotech innovator, or part of a global consortium, your contributions matter. Publishing your data on SeqHub not only makes your work more discoverable, it strengthens the collective knowledge we all depend on.
Join Microcosm in building a more open, connected, and impactful scientific community.
Explore Microcosm's Dataset Collection
Dive into 1,235 genomes from fermented foods and discover the microbial diversity that connects food and health.
Frequently Asked Questions
What is Microcosm Foods?
Microcosm Foods is working to fill in the gaps in our understanding of the connections between fermented foods and human biology, and increase the impact of this knowledge through open science and by stimulating innovation in fermented foods.
What is SeqHub?
SeqHub is a collaborative platform where researchers can explore, annotate, share, and manage biological sequence datasets.
What is the goal of the partnership?
To make microbial fermentation datasets more discoverable and advance open science in food and microbiology.
Ready to share your datasets?
Join Microcosm and a growing community of scientists using SeqHub to make their sequence data more discoverable and impactful.