Toward FAIR Representations of Microbial Interactions
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 hinde...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-10-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.00659-22 |
| _version_ | 1828317934428094464 |
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| author | Alan R. Pacheco Charlie Pauvert Dileep Kishore Daniel Segrè |
| author_facet | Alan R. Pacheco Charlie Pauvert Dileep Kishore Daniel Segrè |
| author_sort | Alan R. Pacheco |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T17:34:55Z |
| format | Article |
| id | doaj.art-3ae57ce9f61444ef8adc53ab04254ba1 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-04-13T17:34:55Z |
| publishDate | 2022-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-3ae57ce9f61444ef8adc53ab04254ba12022-12-22T02:37:24ZengAmerican Society for MicrobiologymSystems2379-50772022-10-017510.1128/msystems.00659-22Toward FAIR Representations of Microbial InteractionsAlan R. Pacheco0Charlie Pauvert1Dileep Kishore2Daniel Segrè3Institute of Microbiology, ETH Zurich, Zurich, SwitzerlandFunctional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH, Aachen, GermanyBioinformatics Program and Biological Design Center, Boston University, Boston, Massachusetts, USABioinformatics Program and Biological Design Center, Boston University, Boston, Massachusetts, USAABSTRACT 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.https://journals.asm.org/doi/10.1128/msystems.00659-22microbiomemicrobial interactionsmicrobial ecologydata sharingaccessibilityreproducibility |
| spellingShingle | Alan R. Pacheco Charlie Pauvert Dileep Kishore Daniel Segrè Toward FAIR Representations of Microbial Interactions mSystems microbiome microbial interactions microbial ecology data sharing accessibility reproducibility |
| title | Toward FAIR Representations of Microbial Interactions |
| title_full | Toward FAIR Representations of Microbial Interactions |
| title_fullStr | Toward FAIR Representations of Microbial Interactions |
| title_full_unstemmed | Toward FAIR Representations of Microbial Interactions |
| title_short | Toward FAIR Representations of Microbial Interactions |
| title_sort | toward fair representations of microbial interactions |
| topic | microbiome microbial interactions microbial ecology data sharing accessibility reproducibility |
| url | https://journals.asm.org/doi/10.1128/msystems.00659-22 |
| work_keys_str_mv | AT alanrpacheco towardfairrepresentationsofmicrobialinteractions AT charliepauvert towardfairrepresentationsofmicrobialinteractions AT dileepkishore towardfairrepresentationsofmicrobialinteractions AT danielsegre towardfairrepresentationsofmicrobialinteractions |