Beyond the core microbiome: endemic bacteria drive functional and microdiversity differences across salamander populations

Population-specific variation in animal microbiomes is well documented, yet the functional consequences and underlying mechanisms remain poorly understood. To address this, we conducted genome-resolved metagenomic analyses on gut and skin microbiomes from four populations of Pyrenean brook salamanders (<i>Calotriton asper</i>) inhabiting two distinct environments: Pyrenean subalpine brooks and Atlantic montane streams. From paired faecal and skin swab samples, we reconstructed 539 and 43 metagenome-assembled genomes, respectively, and examined taxonomic composition, metabolic capacity, and microdiversity across environments. Although alpha diversity remained similar across environments, both gut and skin microbiomes exhibited significant differences in community composition and functional potential between environments. Partitioning the gut microbiome into core, endemic, and marginal fractions revealed a dominant core community-shared across environments and accounting for over 85% of reads-that did not drive functional divergence. Instead, functional differences were primarily shaped by low-abundance, population-specific endemic bacteria. Atlantic salamanders hosted endemic taxa with significantly greater metabolic potential and higher strain-level microdiversity than those at the Pyrenees. These patterns were not associated with broad-scale dietary differences and may reflect environmental influences such as temperature and nutrient availability. Our findings highlight the relevance of rare, endemic bacteria in driving microbiome function and underscore the power of genome-resolved metagenomics to uncover functional and evolutionary dynamics in wild host-microbe systems.