Toward FAIR Representations of Microbial Interactions

mSystems, vol. 7, pp. e0065922

Abstract

Despite an ever-growing number of data sets that catalog and characterize interactions between microbes in different environments and conditions, many of these data are neither easily accessible nor intercompatible. These limitations present a major challenge to microbiome research by hindering the streamlined drawing of inferences across studies. Here, we propose guiding principles to make microbial interaction data more findable, accessible, interoperable, and reusable (FAIR). We outline specific use cases for interaction data that span the diverse space of microbiome research, and discuss the untapped potential for new insights that can be fulfilled through broader integration of microbial interaction data. These include, among others, the design of intercompatible synthetic communities for environmental, industrial, or medical applications, and the inference of novel interactions from disparate studies. Lastly, we envision potential trajectories for the deployment of FAIR microbial interaction data based on existing resources, reporting standards, and current momentum within the community.

Authors 4

1. Alan R. Pacheco

   ETH Zurich · Institute of Microbiology

   Affiliation as printed

   Institute of Microbiology, ETH Zurich, Zurich, Switzerland

2. Charlie Pauvert Aachen Functional Microbiome Research Group Institute of Medical Microbiology

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany

3. Dileep Kishore

   Boston University

   Affiliation as printed

   Bioinformatics Program and Biological Design Center, Boston University, Boston, Massachusetts, USA

4. Daniel Segrè

   Boston University

   Affiliation as printed

   Bioinformatics Program and Biological Design Center, Boston University, Boston, Massachusetts, USA

   Department of Biology, Department of Biomedical Engineering, Department of Physics, Boston University, Boston Massachusetts, USA