Healthy Microbiome

The “Healthy Microbiome” demonstrator

icon of the microbiome demonstrator

Advancing diet-microbiome studies

The human microbiome, consisting of trillions of microorganisms residing in our bodies, plays a crucial role in digestion, immune function, and even mental health. By exploring the intricate relationship between our diet and our microbiome, we can learn how what we eat influences our gut microbiome and, in turn, impacts our overall health and well-being, paving the way for advancements in personalised nutrition and healthcare.

In the FNS-Cloud project, we developed a powerful platform to streamline and enhance the analysis of microbiomes in relation to diet. Our goal is to consolidate fragmented FNS-data from various sources into a seamless workflow, ultimately improving our understanding of the interaction between diet and the microbiome.

Our open-source online tools enable researchers to easily find and merge microbiome-related datasets stored in public repositories. With just a few clicks, users can access a wealth of valuable information, empowering them to conduct comprehensive analyses and download relevant data.

Discover the tools below 👇👇👇

A FAIR data management platform

FAIRSPACE is an open-source research data management platform that adheres to the FAIR principles (Findability, Accessibility; Interoperability and Reusability). It was customised to become the FNS-Cloud metadata browser that allows microbiome and food data exploration within public resources. It brings datasets from different repositories together and links them at sample level.

Accessible from the FNS-Cloud Tools Catalogue.

Developed by The Hyve

View FAIRSPACE in Tools Catalogue

Access the FAIRSPACE user guide on myFNScloud

Metadata submission form
A web-based tool to enhance microbiome studies

The form allows data curators to submit additional metadata (intervention, glucose monitoring data, and food or nutrition intake information) for existing public studies stored in the European Nucleotide Archive (ENA).

You can also submit metadata for microbiome studies not uploaded to the ENA database. This type of submission supports Ontology based input for many metadata fields.

Accessible from the FNS-Cloud Tools Catalogue.

Developed by ScaleFocus

View Form in Tools Catalogue

Data analysis scripts
A Notebook for data pre-processing and exploration

A series of scripts were developed to help answer the research questions. They can be used to analyse data and metadata using R, Python or Julia. A JupyterHub environment is integrated within Fairspace to allow users to run some of those predefined scripts for data pre-processing and exploratory analysis.

Accessible from the FAIRSPACE platform.

Developed by Quadram Institute

Target audience

Researchers in nutritional science, and anyone with an interest in diet and gut microbiome.

Use cases

To design the platform and demonstrate its potential use by researchers, the team worked around the three following research questions: 

  1. Does a diet rich in plant bioactives affect our gut microbiome, and how?
    — with the aim
    to demonstrate the user pathway and the handling of emerging metagenomics datasets and bioinformatic analytical pipelines.
  2. Does our baseline gut microbiome define how species composition shifts upon dietary interventions?
    — with the aim to demonstrate how to find, access and merge datasets from different diet & microbiome studies.
  3. Does our gut microbiome contribute to our metabolic response to foods? Can we predict metabolic responses to foods using microbiome data? Is there more to food than nutrients?
    — with the aim to demonstrate how users can access multiple datasets and a machine-learning prediction tool.

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