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

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 do...

Full description

Saved in:
Bibliographic Details
Published in:Molecular ecology resources 2023-01, Vol.23 (1), p.222-232
Main Authors: Biderre‐Petit, Corinne, Charvy, Jean‐Christophe, Bronner, Gisèle, Chauvet, Marina, Debroas, Didier, Gardon, Hélène, Hennequin, Claire, Jouan‐Dufournel, Isabelle, Moné, Anne, Monjot, Arthur, Ravet, Viviane, Vellet, Agnès, Lepère, Cécile
Format: Article
Language:English
Subjects:
Anthropogenic factors
Aquatic ecosystems
Archaea
Biodiversity and Ecology
Biological properties
Biological samples
Climate change
Ecological function
Ecology, environment
Environmental Sciences
Eukaryotes
Fresh water
freshwater
Freshwater ecosystems
Geographical locations
Human influences
Life Sciences
Microbial activity
Microbiomes
Microorganisms
omics data
Spatial distribution
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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 resilience, especially through meta‐analysis studies. This collection also highlights different sort of errors in published works (e.g., wrong coordinates, sample type, material, spelling).
ISSN:1755-098X
1755-0998
DOI:10.1111/1755-0998.13692