Loretta Daddiego, Elio Fantini, Loredana Lopez, Bruna Piccione, Linda Bianco, Fiammetta Alagna, Giovanna Cangiulli, Carlo Fasano, Roberta Latini, Francesco Panara, Paolo Ciucci, Paolo Facella

The gut microbiome is recognized as a key component of wildlife health and resilience, with direct implications for conservation and understanding drivers of human–wildlife coexistence in shared landscapes. The Apennine brown bear (Ursus arctos marsicanus) is a geographically isolated, critically endangered endemic population restricted to the Central Apennines, Italy, estimated at about 60 individuals. This extremely small size makes any non-invasive tool for enhancing health surveillance and risk detection valuable for conservation planning and management. Here we present a gut microbiome survey on free-ranging Apennine brown bears, to establish a robust baseline enhancing the conservation toolkit for this population. Based on 51 fresh (≤ 24 hrs) fecal samples collected in the Abruzzo Lazio and Molise National Park from 08/2024 to10/2025, we performed a metabarcoding analysis targeting the full-length 16S rRNA bacterial gene, by Oxford Nanopore Technologies’ sequencing. By processing each fecal sample 3 times, we produced more than 28 billion bases. These data enable high-resolution taxonomic profiling and support comparative analyses across individuals and sampling contexts. Overall, population taxonomic profiles indicate a gut community frequently dominated by Enterobacteriaceae-associated taxa, with comparatively fewer samples showing a more “eubiotic” configuration with typical commensal anaerobes. We observe substantial between-sample variability, consistent with marked individual and/or ecological (e.g., diet and seasonality) effects. Building on this dataset, we are conducting two expansions: fungal ITS sequencing across all samples to profile the gut mycobiome and long-read shotgun metagenomics on selected samples for functional and strain-level insights. Integrating bacterial and fungal data with conservation efforts will support non-invasive health monitoring and dysbiosis risk detection to enhance the conservation status of Europe's rarest bear lineage.