The BeeBiome data portal provides easy access to bee microbiome information
Abstract Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition...
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| Language: | English |
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BMC
2025-07-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06229-7 |
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| author | Valentine Rech de Laval Benjamin Dainat Philippe Engel Marc Robinson-Rechavi |
| author_facet | Valentine Rech de Laval Benjamin Dainat Philippe Engel Marc Robinson-Rechavi |
| author_sort | Valentine Rech de Laval |
| collection | DOAJ |
| description | Abstract Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. The challenge of such an approach is that datasets are difficult to find within large generalist repositories and are often not readily accessible, which hinders integrative analyses. Here we present a publicly-available online resource, the BeeBiome data portal ( https://www.beebiome.org ), which provides an overview of and easy access to currently available metagenomic datasets involving bee-associated microbes. Currently the data portal contains 33,678 Sequence Read Archive (SRA) experiments for 278 Apoidea hosts. We present the content and functionalities of this portal. By providing access to all bee microbiomes in a single place, with easy filtering on relevant criteria, BeeBiome will allow faster progress of applied and fundamental research on bee biology and health. It should be a useful tool for researchers, academics, funding agencies, and governments, with beneficial impacts for stakeholders. |
| format | Article |
| id | doaj-art-e4e4347d1a3b48b0b507f31e5d6af622 |
| institution | DOAJ |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-e4e4347d1a3b48b0b507f31e5d6af6222025-08-20T03:06:36ZengBMCBMC Bioinformatics1471-21052025-07-012611810.1186/s12859-025-06229-7The BeeBiome data portal provides easy access to bee microbiome informationValentine Rech de Laval0Benjamin Dainat1Philippe Engel2Marc Robinson-Rechavi3Department of Ecology and Evolution, University of LausanneAgroscope, Swiss Bee Research CentreDepartment of Fundamental Microbiology, University of LausanneDepartment of Ecology and Evolution, University of LausanneAbstract Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. The challenge of such an approach is that datasets are difficult to find within large generalist repositories and are often not readily accessible, which hinders integrative analyses. Here we present a publicly-available online resource, the BeeBiome data portal ( https://www.beebiome.org ), which provides an overview of and easy access to currently available metagenomic datasets involving bee-associated microbes. Currently the data portal contains 33,678 Sequence Read Archive (SRA) experiments for 278 Apoidea hosts. We present the content and functionalities of this portal. By providing access to all bee microbiomes in a single place, with easy filtering on relevant criteria, BeeBiome will allow faster progress of applied and fundamental research on bee biology and health. It should be a useful tool for researchers, academics, funding agencies, and governments, with beneficial impacts for stakeholders.https://doi.org/10.1186/s12859-025-06229-7MicrobiomeBeeDatabaseMetagenomics |
| spellingShingle | Valentine Rech de Laval Benjamin Dainat Philippe Engel Marc Robinson-Rechavi The BeeBiome data portal provides easy access to bee microbiome information BMC Bioinformatics Microbiome Bee Database Metagenomics |
| title | The BeeBiome data portal provides easy access to bee microbiome information |
| title_full | The BeeBiome data portal provides easy access to bee microbiome information |
| title_fullStr | The BeeBiome data portal provides easy access to bee microbiome information |
| title_full_unstemmed | The BeeBiome data portal provides easy access to bee microbiome information |
| title_short | The BeeBiome data portal provides easy access to bee microbiome information |
| title_sort | beebiome data portal provides easy access to bee microbiome information |
| topic | Microbiome Bee Database Metagenomics |
| url | https://doi.org/10.1186/s12859-025-06229-7 |
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