Microbiota are communities of microorganisms such as bacteria, archaea, unicellular eukaryotes and viruses. There is a need to better understand these taxa and communities in distinct research fields. For instance, given climate change, microbial species must be studied to better grasp our ecosystems and to properly act against anthropogenic impacts. On another note, the rise of antibiotic resistance is, according to the World Health Organization, one of the major threats to global health security. Furthermore, countless, not yet cultured microbial species are potential sources of medically and biotechnologically relevant compounds.

Challenges in the understanding of microbiota lie in the complexity of the interactions microorganisms have with their biotic and abiotic environments. From a technical point of view, collecting sufficient data for the analysis of microbiomes and their interactomes is a challenging task: multi-omics data have to be stored, processed and integrated to decipher how individual species and microbiomes work, how they interact at a molecular level, and how they benefit humans and the environment. Often researchers do not have the capabilities to process such data as they are overwhelmed with their size and complexity. Until now, there is no unified service managing from data production to the integration of diverse data sets, or exploring functional interactions between microbiota. To address these needs shared by a community, common standards and a consistent research infrastructure to store and translate the data into insights are required.

In this context, NFDI4Microbiota’s mission is to make analysis of multi-omics data related to microbiota consistent, reproducible and accessible to all fields of the life science community.

Main tasks of NFDI4Microbiota

  • Assist researchers with distinct scientific challenges to understand microbial communities and their interspecific interactions.
  • Provide the computational infrastructure, analytical tools and training for the community to compile, analyse and store various data type.
  • Collaborate with data generators to provide seamless data workflows.
  • Promote a direct deposition of measured data and related metadata into the computational infrastructure provided by the consortium.
  • Enable efficient and reproducible processing of data generated via high-throughput sequencing (including single cell sequencing).
  • Enrich data by metadata from databases and by knowledge automatically extracted from the literature, and make the data interoperable.
  • Contribute to the discussion regarding common metadata standards of high-throughput sequencing data and for sampling in the medical and environmental fields.

Integration into NFDI and NFDI4Life Umbrella

NFDI4Microbiota is in exchange with several consortia to work on common standards, interfaces and training. This includes but is not limited to the following consortia:

NFDI4Life Umbrella: collaboration on several cross-disciplinary issues of the life science community.


  • Exploring the possibilities of standardisation and cross-sectional mapping for standardisation of chemical components (e.g., medication), dietary factor or metabolome data.
  • Exchanging about the inclusion of microbiome related data in epidemiological and clinical studies.

NFDI4Biodiversity: collaboration on common metadata standards for sampling.

NFDI4Agri: collaboration on common metadata standards for sampling.

GHGA: collaboration on human microbiome data.

DataPlant: collaboration on metadata for omics data and training.

NFDI4RSE: collaboration on standards and recommendations regarding analysis workflows and training.

Recommended reading

  • Letter of Intent
  • Extended Abstract
  • Poster