bifidoAnnotator: fine-grained annotation of bifidobacterial glycoside hydrolases for human milk glycan utilization

This repository contains two main datasets used in the development and validation of bifidoAnnotator, a specialized tool for fine-grained annotation of bifidobacterial glycoside hydrolases involved in human milk glycan (HMG) utilization. bifDB reference database: A curated MMseqs2 database comprising 22,699 bifidobacterial protein sequences from 13 glycoside hydrolase families (GH2, GH5_18, GH18, GH20, GH29, GH33, GH38, GH42, GH85, GH95, GH112, GH125, and GH136) organized into 122 functional clusters. Each cluster has been manually curated with experimental validation status (experimentally validated, putative function, or hypothetical) based on literature evidence. The database was constructed from 2,333 bifidobacterial genomes and serves as the reference for bifidoAnnotator's hierarchical annotation workflow. AIMS bifidobacterial proteomes: A collection of 49 bifidobacterial proteomes derived from metagenome-assembled genomes (MAGs) reconstructed from fecal and oral samples collected from mothers (34 weeks gestation) and their infants (1 and 6 months of age) participating in the Amsterdam Infant Microbiome Study (AIMS). These proteomes represent 8 bifidobacterial species and were used to demonstrate bifidoAnnotator's capabilities in revealing strain-level functional variation and species-specific HMG utilization patterns. Both datasets are essential for reproducing the analyses presented in the associated publication and enable researchers to apply bifidoAnnotator for detailed functional profiling of bifidobacterial communities.