Shotgun metagenomic profiling of the fecal microbiome in Lamp2 knockout mice reveals limited genotype-associated differences under standard housing

Background Lysosomal pathways influence host–microbe interactions, but the microbiome consequences of lysosomal dysfunction remain incompletely defined. LAMP2 is required for autophagosome–lysosome fusion, and pathogenic variants in LAMP2 cause Danon disease. Whether Lamp2 loss alters the gut microbiome in vivo has not been systematically evaluated using methods that profile both taxonomic composition and microbial functional potential, such as shotgun metagenomics. Methods We performed shotgun metagenomic sequencing on 50 fecal samples from male Lamp2 knockout ( Lamp2 KO) mice and wild-type (WT) littermates sampled at 3, 6, 9, and 12 months under single-genotype cages or mixed-genotype cohousing. Two low-depth libraries (5 classified genus-level reads) were excluded from primary inference (primary set: n = 48). We analyzed genus-level alpha diversity, beta diversity, and differential abundance using compositional, cage-aware mixed-effects models and cage-blocked permutation testing. We analyzed functional pathway profiles using copies-per-million abundances with centered-log-ratio transformation and mixed-effects modeling. We controlled multiple testing using the Benjamini–Hochberg false discovery rate. Results In the primary set (48 samples from 27 cages), Lamp2 KO and WT mice showed similar genus-level alpha diversity and overall community composition (PERMANOVA using Aitchison and Bray–Curtis distances). Primary mixed-effects models detected no genera with differential abundance after false discovery rate correction. Taxonomic profiles were broadly similar between genotypes and were dominated by Bacteroidota and Bacillota. Exploratory within-cage (paired) analyses identified consistent directional differences in a small set of genera, but these signals were not supported by the primary mixed-effects models. Functional pathway profiles were similar between genotypes; one pathway (dTDP-β-L-rhamnose biosynthesis) showed an exploratory association (FDR q  Conclusions In this controlled mouse cohort, we did not detect robust, cage-independent shifts in fecal microbiome composition or inferred functional pathway profiles associated with Lamp2 deficiency under standard SPF husbandry and chow; given the sample size, smaller or compartment-specific effects cannot be excluded.