FreshOmics : A manually curated and standardized –omics database for investigating freshwater microbiomes

作者：Corinne Biderre‐Petit, Jean‐Christophe Charvy, Gisèle Bronner, Marina Chauvet, Didier Debroas, Hélène Gardon, Claire Hennequin, Isabelle Jouan‐Dufournel, Anne Moné, Arthur Monjot, Viviane Ravet, Agnès Vellet, Cécile Lepère · 发表于：Molecular Ecology Resources · 年份：2022 · DOI：10.1111/1755-0998.13692 · 被引用次数：3 · 研究领域：Microbial Community Ecology and Physiology、Environmental DNA in Biodiversity Studies、Genomics and Phylogenetic Studies

Freshwater is a critical resource for human survival but severely threatened by anthropogenic activities and climate change. These changes strongly impact the abundance and diversity of the microbial communities which are key players in the functioning of these aquatic ecosystems. Although widely documented since the emergence of high-throughput sequencing approaches, the information on these natural microbial communities is scattered among thousands of publications and it is therefore difficult to investigate the temporal dynamics and the spatial distribution of microbial taxa within or across ecosystems. To fill this gap and in the FAIR principles context we built a manually curated and standardized microbial freshwater -omics database (FreshOmics). Based on recognized ontologies (ENVO, MIMICS, GO, ISO), FreshOmics describes 29 different types of freshwater ecosystems and uses standardized attributes to depict biological samples, sequencing protocols and article attributes for more than 2487 geographical locations across 71 countries around the world. The database contains 24,808 sequence identifiers (i.e., Run_Id / Exp_ID, mainly from SRA/DDBJ SRA/ENA, GSA and MG-RAST repositories) covering all sequence-based -omics approaches used to investigate bacteria, archaea, microbial eukaryotes, and viruses. Therefore, FreshOmics allows accurate and comprehensive analyses of microbial communities to answer questions related to their roles in freshwater ecosystems functioning and re...