Gut microbiome variation and pathogen-associated signatures in a Critically Endangered lemur

Background Anthropogenic environmental change can alter wildlife-associated microbial communities and pathogen dynamics, but whether these effects are consistent across disturbance types remains poorly understood. We investigated gut bacterial and viral community variation, pathogen-associated signatures, microbial functional potential, and blood-associated microbial lineages in the Critically Endangered diademed sifaka ( Propithecus diadema ) across Malagasy landscapes affected by slash-and-burn agriculture and nickel-cobalt mining. Results We sampled 51 diademed sifakas from paired disturbed and relatively undisturbed forests in two Malagasy landscapes: Andasibe, including a site adjacent to a nickel–cobalt mine, and Tsinjoarivo, where forest disturbance is associated with slash-and-burn agriculture. Analyses included faecal 16S rRNA gene amplicon sequencing (n = 36), faecal shotgun metagenomics (n = 39; 366 quality-filtered metagenome-assembled genomes), faecal viromics (n = 14) and blood microbial screening (n = 38). In Andasibe, mine-adjacent sifakas exhibited lower gut bacterial alpha diversity and a different community composition compared with the undisturbed forest, whereas no difference in among-host dispersion was detected. In Tsinjoarivo, bacterial alpha diversity and community composition were similar between disturbed and undisturbed forests, but among-host community dispersion was 21.7% lower in the disturbed population. MAG-based community profiles showed broadly similar patterns, including reduced dispersion in the disturbed Tsinjoarivo population. An Escherichia coli genome carrying virulence-associated genes was recovered from four Andasibe individuals, including three from the mine-adjacent population, although its occurrence was not significantly associated with disturbance. Antimicrobial resistance- and metal-associated gene annotations were concentrated in mine-adjacent individuals, but no individual resistance-associated gene remained significantly enriched after multiple-testing correction. Faecal viromes were dominated by bacteriophage-associated sequences, while blood screening detected divergent piroplasmid and Neoehrlichia lineages in Andasibe, related to microbial groups that include recognised pathogens. Conclusions Gut microbiome responses differed between the two landscape contrasts, with reduced within-host bacterial diversity associated with mine-adjacent habitats in Andasibe and lower among-host community variability in disturbed forests in Tsinjoarivo. These findings suggest that distinct anthropogenic disturbances may drive different patterns of microbiome restructuring rather than a uniform response. The detection of virulence- and resistance-associated genomic features and blood-associated lineages related to recognised pathogen groups highlights the value of integrated microbial surveillance for wildlife conservation and One Health monitoring.