An atlas of colonization factors in the mouse gut microbiome reveals phylogenetically structured repertoires and infection-stage-associated variation during Toxoplasma gondii infection in mice

ABSTRACT Colonization factors (CFs) comprise CF-associated gene families related to microbial establishment, persistence, host interaction, and gut ecological fitness, but their organization and variation in the mouse gut microbiome remain poorly defined. We integrated the Mouse Gut Genome Catalogue and the Mouse Gut Protein Catalogue, clustered at 90% amino acid identity, to define CF repertoires. A total of 79 conserved CF families, comprising over 2.4 million homologs, were identified across 112,951 genomes from 2,824 microbial species. Species-level CF-associated gene profiles exhibited a clear phylogeny-associated pattern and separated microbial species into two groups with distinct genome-scale functional profiles. Across the cecum and small intestine, CF profiles differed among control, acute, and chronic infection groups in dominant CF abundance, diversity, richness, and overall composition. CF profiles were significantly concordant with taxonomic profiles and associated with microbial community variation. Differential abundance analyses identified tissue- and stage-associated CF features. Exploratory machine-learning analyses showed high classification performance across all feature sets in the cecum, with the genus-level model yielding the highest median performance, whereas species- and genus-level taxonomic profiles provided stronger discrimination than CF profiles in the small intestine. This study provides a reference-based atlas of CF-associated gene repertoires and a CF-centered framework relating these repertoires to microbial phylogeny, genome-scale functional profiles, and infection-stage-associated variation in a murine Toxoplasma gondii infection model. CF-associated gene profiles can complement taxonomic and functional descriptions of the mouse gut microbiome, although the biological roles of individual CF-associated genes require experimental validation. IMPORTANCE Studies of the mouse gut microbiome commonly emphasize taxonomic composition, whereas the ecological traits associated with microbial establishment and persistence in the murine intestine remain less well characterized. By profiling CF-associated gene repertoires across control, acute, and chronic infection groups in mice, we show that infection-stage-associated differences in murine gut microbial community structure are accompanied by differences in colonization- and fitness-associated gene profiles. CF composition was associated with microbial community structure and functional potential, and CF-based features captured intestinal-region- and infection-stage-associated variation within this mouse data set. The principal contribution of this study is a reference-based, CF-centered framework that complements conventional taxonomic and functional profiling in murine infection models and provides a foundation for future mechanistic investigations of microbial colonization.