WasteFams: a database of protein families from global wastewater microbiomes
8 affiliations
- 1Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming” , Vari 16672 ,
- 2Department of Informatics and Telecommunications, National and Kapodistrian University of Athens , Athens 16122 ,
- 3Division of Basic Sciences, University of Crete Medical School , Heraklion 71110 ,
- 4Medical School of Athens, National and Kapodistrian University of Athens , Goudi 11527 ,
- 5Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute , 1400 Barbara Jordan Blvd., Austin, TX 78723 ,
- 6European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridge CB10 1SD ,
- 7DOE Joint Genome Institute, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, CA 94720 ,
- 8Division of Biological and Life Sciences, Mohamed bin Zayed University of Artificial Intelligence (MBZUAI) , Building 1B, Masdar City, Abu Dhabi SE45 05 ,
Abstract
Wastewater surveillance has emerged as a critical tool for global epidemiology, yet the functional diversity of wastewater microbiomes remains poorly characterized at the protein level. Here, we present WasteFams, the first comprehensive database dedicated to the systematic exploration of protein families in wastewater metagenomic and metatranscriptomic studies worldwide. Integrating data from 580 metagenomes, 132 metatranscriptomes, and 1709 reference genomes (504 metagenomes, 129 metatranscriptomes, and 1151 reference genomes after filtering), WasteFams catalogs 3887 non-redundant protein families (containing ⪰100 members) derived from over 105 million predicted proteins. Each protein family is enriched with multi-layered annotations, including AlphaFold3 structural predictions, taxonomic classifications, and biome-specific metadata. To further expand their functional annotation, we integrated deep genomic context analysis to link protein families to mobile genetic elements, biosynthetic gene clusters, antibiotic resistance genes, and CRISPR elements. Accessible through the EnvoFams portal, WasteFams provides a user-friendly interface featuring advanced search capabilities, sequence and structural similarity tools, and interactive visualization modules. As global initiatives increasingly leverage wastewater for public health and environmental insights, WasteFams can serve as a critical resource for discovering novel microbial functions, monitoring resistance mechanisms, and exploring the biotechnological potential of secondary metabolites within wastewater-engineered ecosystems.
Related
- An advanced LLM-powered article extraction pipeline delivers a database of buffers for protein studies and protein expression conditions.
- SNOOPPI: a sequence-normalized database of on- and off-target protein-protein interactions.
- RNAffinityDB: a curated database of experimental RNA–protein binding affinities
- CEM 2.0: Co-evolution-guided mining of superior extremophilic proteins via a curated proteome database and protein language model.
- ProPepBA: a binding affinity database for canonical and chemically modified protein–peptide interactions
BibTeX
@article{galaras2026wastefams,
title = {{WasteFams: a database of protein families from global wastewater microbiomes}},
author = {Alexandros Galaras and Iro N Chasapi and Eleni Aplakidou and Maria N Chasapi and Efthimia Lamari and Sophia Diplari and Ilias Georgakopoulos-Soares and Evangelos Karatzas and Fotis A Baltoumas and Nikos C Kyrpides and Georgios A Pavlopoulos},
journal = {NAR Genomics and Bioinformatics},
year = {2026},
month = oct,
doi = {10.1093/nargab/lqag127},
url = {https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag127/8971825},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - WasteFams: a database of protein families from global wastewater microbiomes
AU - Alexandros Galaras
AU - Iro N Chasapi
AU - Eleni Aplakidou
AU - Maria N Chasapi
AU - Efthimia Lamari
AU - Sophia Diplari
AU - Ilias Georgakopoulos-Soares
AU - Evangelos Karatzas
AU - Fotis A Baltoumas
AU - Nikos C Kyrpides
AU - Georgios A Pavlopoulos
PY - 2026
DA - 2026/10/22
JO - NAR Genomics and Bioinformatics
DO - 10.1093/nargab/lqag127
UR - https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag127/8971825
AB - Wastewater surveillance has emerged as a critical tool for global epidemiology, yet the functional diversity of wastewater microbiomes remains poorly characterized at the protein level. Here, we present WasteFams, the first comprehensive database dedicated to the systematic exploration of protein families in wastewater metagenomic and metatranscriptomic studies worldwide. Integrating data from 580 metagenomes, 132 metatranscriptomes, and 1709 reference genomes (504 metagenomes, 129 metatranscriptomes, and 1151 reference genomes after filtering), WasteFams catalogs 3887 non-redundant protein families (containing ⪰100 members) derived from over 105 million predicted proteins. Each protein family is enriched with multi-layered annotations, including AlphaFold3 structural predictions, taxonomic classifications, and biome-specific metadata. To further expand their functional annotation, we integrated deep genomic context analysis to link protein families to mobile genetic elements, biosynthetic gene clusters, antibiotic resistance genes, and CRISPR elements. Accessible through the EnvoFams portal, WasteFams provides a user-friendly interface featuring advanced search capabilities, sequence and structural similarity tools, and interactive visualization modules. As global initiatives increasingly leverage wastewater for public health and environmental insights, WasteFams can serve as a critical resource for discovering novel microbial functions, monitoring resistance mechanisms, and exploring the biotechnological potential of secondary metabolites within wastewater-engineered ecosystems.
SN - 2631-9268
ER -