Martin-Bideguren, G. | Search bioRxiv

bioRxiv2025

Beyond the core: endemic microbiota 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 (Calotriton asper) 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 (MAGs), respectively, and examined taxonomic composition, metabolic capacity, and microdiversity across environments. While alpha diversity remained consistent, 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 explained by 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.

microbiology↗

bioRxiv2024

Dietary intervention in captive-bred hares fails to enrich gut microbiomes with wild-like functions

Reintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this possibility, we employed genome-resolved metagenomics to analyse the taxonomic and functional differences in the gut microbiota of wild and captive European hares (Lepus europaeus), as well as to assess the impact of a dietary switch to grass aimed at pre-adapting captive hares to wild conditions. Our analyses recovered 860 metagenome-assembled genomes, with 87% of them representing novel species. We found significant taxonomic and functional differences between the gut microbiota of wild and captive hares, notably the absence of Spirochaetota in captive animals and differences in amino acid and sugar degradation capacities. While the dietary switch to grass induced some minor changes in the gut microbiota, it did not result in a shift towards a more wild-like microbial community. The increased capacity for degrading amino acids and specific sugars observed in wild hares suggest that, instead of bulk grass, dietary interventions tailored to their specific dietary preferences might be necessary for pre-adapting hare gut microbiota to wild conditions. ImportanceThis study sheds light on the critical role of gut microbiota in the success of reintroducing captive-bred animals into the wild. By comparing the gut microbiota of wild and captive European hares, we identified significant taxonomic and functional differences, including the absence of key microbial groups in captive hares. Dietary interventions, such as switching to grass, showed limited success in restoring a wild-like microbiota, highlighting the need for tailored approaches to mimic natural diets. With 87% of recovered microbial genomes representing novel species, this research also enriches our understanding of microbial diversity in wildlife. These findings emphasise that maladapted gut microbiota may hinder the survival and adaptation of reintroduced animals, suggesting that microbiome-targeted strategies could improve conservation efforts and the success of animal rewilding programs.

ecology↗