Freshwater habitats are under increasing pressure from numerous anthropogenic forces, including the introduction of alien species capable of altering ecosystems and threatening native species. Although alien species themself are likely to experience loss of genetic diversity when colonising novel environments, some manage to become invasive, suggesting that other factors might facilitate their adaptive capacity. Using a hologenomic approach, we elucidate population genomic trends, the gut microbiota composition and genome-environment-microbiota interaction in the endemic and endangered Spanish toothcarp (Aphanius iberus) and the highly invasive Eastern mosquitofish (Gambusia holbrooki). We found clear genetic signatures of captive breeding in the populations of A. iberus, while G. holbrooki are characterised by an overall low level of heterozygosity and likely signs of multiple introductions. Gut microbial communities of the two species differed significantly across locations, but no sign of increased microbial plasticity was detected in G. holbrooki. However, we report that the genetic profile of each fish was able to explain a considerable part of the microbiota variation measured across individuals. Using shotgun metagenomics, we observed an overall high functional capacity of the microbiota in both species, but we identified no significant differences in the functional capacity between them. The role of the gut microbiota in invasive species and conservation warrant further research using direct comparisons or controlled mesocosm setups, but based on the results of the current study, the gut microbiota of invasive species

The gut microbiomes that associate with animals can represent labile units of cooperating and competing microbes. This lability, sometimes referred to as metagenomic plasticity, has been posited to have an important role as an additional axis of hosts’ phenotypic plasticity. However, whether and how metagenomic plasticity varies across hosts with different ecological and evolutionary features remains unclear. To address this, we utilised faecal-derived genome-resolved metagenomics and compared how the taxonomic, phylogenetic and functional microbial dynamics varied across a series of disturbances in two mammal species; namely, the insectivorous-specialist, Crocidura russula (N = 29) and the omnivorous-generalist Apodemus sylvaticus (N = 22). Although faecal microbial diversity of both species remained stable, compositional dynamics differed significantly. C. russula exhibited substantially higher variability and directionality of microbial responses, with higher predictability associated with each disturbance, compared to A. sylvaticus. Predictions of functional traits using joint-species distribution modelling supported these observations. C. russula showed strong functional response to perturbations, with marked directional variation of various metabolic functions. In contrast, the significantly higher functional diversity and redundancy of the A. sylvaticus microbiome likely buffered its functional response to perturbations, which remained more constant across time. Our results indicate that the intrinsic properties (e.g., diversity, redundancy) of gut microbiomes associated with animals with different biological attributes shape the taxonomic, phylogenetic, and functional response to environmental stressors. This level of plasticity might affect the capacity of animal hosts to acclimate and adapt to changing environments.