Gene catalogue and MAGs from the ALADDIN birth cohort

This repository contains the complete set of metagenome-assembled genomes (MAGs; n = 17,133) and the non-redundant gene catalogue generated from shotgun metagenomic sequencing of 547 faecal samples from 56 children and their mothers. Raw sequencing data are deposited in the SRA under BioProject PRJEB84944. This resource accompanies the manuscript by Myers, P.N. and Dehli, R.K. et al., titled “Early-life colonisation by aromatic lactate-producing bifidobacteria lowers the risk of allergic sensitisation”. MAGs are provided in FASTA format, with one MAG per file, named: <MGS>__<samplename>.fna.gz Genes in the non-redundant gene catalogue follow the naming structure: <samplename>__C<contig_number>_L=<contig-length>_<gene_number_on_contig>_c<gene-cluster-size> Completeness, contamination, and strain heterogeneity estimates generated with CheckM (v1.0.18) are provided in the accompanying file CheckM_results.tsv. Note: MAGs were identified using a non-classical, metagenomic-species-based binning workflow, which is described in detail in the Supplementary Methods of the manuscript. For comparison, MAGs binned using a standard per-sample workflow from the same dataset have also been deposited under BioProject PRJEB84944 and are described in Chatzigiannidou, I. et al. Temporal dynamics and microbial interactions shaping the gut resistome in early infancy. Nat Commun 16, 8139 (2025). https://doi.org/10.1038/s41467-025-63401-6