{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T18:10:28Z","timestamp":1789755028993,"version":"4.0.1"},"reference-count":26,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"George and Marie Vergottis Postdoctoral Fellowship"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Lysosomal pathways influence host\u2013microbe interactions, but the microbiome consequences of lysosomal dysfunction remain incompletely defined. LAMP2 is required for autophagosome\u2013lysosome fusion, and pathogenic variants in\n                      <jats:italic>LAMP2<\/jats:italic>\n                      cause Danon disease. Whether\n                      <jats:italic>Lamp2<\/jats:italic>\n                      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.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We performed shotgun metagenomic sequencing on 50 fecal samples from male\n                      <jats:italic>Lamp2<\/jats:italic>\n                      knockout (\n                      <jats:italic>Lamp2<\/jats:italic>\n                      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 (&lt;3\u2009\u00d7\u200910\n                      <jats:sup>5<\/jats:sup>\n                      classified genus-level reads) were excluded from primary inference (primary set: n\u2009=\u200948). 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\u2013Hochberg false discovery rate.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      In the primary set (48 samples from 27 cages),\n                      <jats:italic>Lamp2<\/jats:italic>\n                      KO and WT mice showed similar genus-level alpha diversity and overall community composition (PERMANOVA using Aitchison and Bray\u2013Curtis 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-\u03b2-L-rhamnose biosynthesis) showed an exploratory association (FDR q\u2009&lt;\u20090.10) within the 50 most abundant pathways.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      In this controlled mouse cohort, we did not detect robust, cage-independent shifts in fecal microbiome composition or inferred functional pathway profiles associated with\n                      <jats:italic>Lamp2<\/jats:italic>\n                      deficiency under standard SPF husbandry and chow; given the sample size, smaller or compartment-specific effects cannot be excluded.\n                    <\/jats:p>\n                  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