Microbiome stability in wild and rehabilitated insectivorous bats revealed by shotgun metagenomics
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
Wildlife rehabilitation can alter host-associated microbial communities, yet the effects of temporary managed care on the gut microbiome of insectivorous bats remain poorly understood. We used shotgun metagenomic sequencing to investigate gut microbiome composition in wild and rehabilitated bats from Yorkshire, United Kingdom. A total of 25 faecal metagenomes were analysed from four bat species (Myotis daubentonii, Pipistrellus pipistrellus, Nyctalus noctula, and Nyctalus leisleri), including wild baseline individuals
and bats undergoing temporary managed care for 1-49 days. Microbial community structure clustered primarily according to host species and roost location, with no
significant separation associated with rehabilitation status. Among bats in managed care, bacterial alpha diversity did not differ significantly with time in care (H = 2.30, p = 0.32). Archaeal communities displayed markedly lower interindividual variation than bacterial
communities (coefficient of variation: 12.2% vs. 41.8%), indicating a highly conserved archaeal microbiome across hosts. Rehabilitated bats exhibited modest compositional shifts in bacterial communities, including increased relative abundances of Yersiniaceae and Lactobacillaceae and reduced abundances of environmentally associated taxa such as Pseudomonadaceae and Erwiniaceae. These changes may reflect controlled dietary provision and reduced environmental exposure during care. Overall, no marked rehabilitation- associated differences in gut microbiome diversity or community structure were detected under the current sampling design. These findings are consistent with microbiome stability during temporary managed care, although longitudinal studies are required to confirm microbiome dynamics within individual bats. Nonetheless, this study provides an initial baseline for future microbiome-informed wildlife rehabilitation studies.
and bats undergoing temporary managed care for 1-49 days. Microbial community structure clustered primarily according to host species and roost location, with no
significant separation associated with rehabilitation status. Among bats in managed care, bacterial alpha diversity did not differ significantly with time in care (H = 2.30, p = 0.32). Archaeal communities displayed markedly lower interindividual variation than bacterial
communities (coefficient of variation: 12.2% vs. 41.8%), indicating a highly conserved archaeal microbiome across hosts. Rehabilitated bats exhibited modest compositional shifts in bacterial communities, including increased relative abundances of Yersiniaceae and Lactobacillaceae and reduced abundances of environmentally associated taxa such as Pseudomonadaceae and Erwiniaceae. These changes may reflect controlled dietary provision and reduced environmental exposure during care. Overall, no marked rehabilitation- associated differences in gut microbiome diversity or community structure were detected under the current sampling design. These findings are consistent with microbiome stability during temporary managed care, although longitudinal studies are required to confirm microbiome dynamics within individual bats. Nonetheless, this study provides an initial baseline for future microbiome-informed wildlife rehabilitation studies.
Date Issued
2026-07-01
Date Acceptance
2026-06-23
Citation
Microorganisms, 2026, 14 (7)
ISSN
2076-2607
Publisher
MDPI AG
Journal / Book Title
Microorganisms
Volume
14
Issue
7
Copyright Statement
© 2026 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.
License URL
Identifier
10.3390/microorganisms14071403
Subjects
bat microbiome
metagenomics
microbial ecology
rehabilitation
Myotis daubentonii
Pipistrellus pipistrellus
gut microbiota
Publication Status
Published
Article Number
1403
Date Publish Online
2026-06-25