Microbiome stability in wild and rehabilitated insectivorous bats revealed by shotgun metagenomics

Abstract Background Wildlife rehabilitation can influence host-associated microbiota, yet little is known about how the gut microbiome of insectivorous bats responds to rehabilitation during temporary managed care. This study applied shotgun metagenomics to evaluate the impact of temporary managed care on the gut microbiome of wild and rehabilitated bats in Yorkshire, UK. Results We analysed 25 faecal metagenomes from Myotis daubentonii, Pipistrellus pipistrellus, Nyctalus noctula and N. leisleri , including wild baseline bats and bats sampled during temporary managed care (1-49 days in rehabilitation). Microbial communities clustered strongly by host species and roost location, but not by rehabilitation status. Bacterial alpha diversity did not differ between wild bats, and bats in care (H = 2.30, p = 0.32). Archaeal communities were highly uniform across samples, showing far lower interindividual variation than bacterial communities (12.2% vs. 41.8% coefficient of variation). Rehabilitated bats showed increased relative abundance of Yersiniaceae and Lactobacillaceae , while environmental families such as Pseudomonadaceae and Erwiniaceae decreased, indicating modest but non-disruptive changes consistent with a controlled diet and reduced environmental exposure. Conclusions Across temporary managed care, the core gut microbiome of insectivorous bats remained stable, demonstrating notable microbial resilience. These findings provide an important baseline for monitoring microbiome health in wildlife rehabilitation and supporting post-release conservation programmes in the UK and beyond.