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Host‐Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban–Rural Ecotone

Alessandra Giacomini, Maklarin B. Lakim Orcid Logo, Fred Y. Y. Tuh Orcid Logo, Matthew Hitchings Orcid Logo, Sofia Consuegra del Olmo Orcid Logo, Tamsyn Uren Webster Orcid Logo, Konstans Wells Orcid Logo

Molecular Ecology, Volume: 34, Issue: 11

Swansea University Authors: Alessandra Giacomini, Matthew Hitchings Orcid Logo, Sofia Consuegra del Olmo Orcid Logo, Tamsyn Uren Webster Orcid Logo, Konstans Wells Orcid Logo

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DOI (Published version): 10.1111/mec.17782

Abstract

Global change and urbanisation profoundly alter wildlife habitats, driving native animals into novel habitats while increasing the co-occurrence between native and invasive species. Host-microbiome associations are shaped by host traits and environmental features, but little is known about their pla...

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Published in: Molecular Ecology
ISSN: 0962-1083 1365-294X
Published: Wiley 2025
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URI: https://cronfa.swan.ac.uk/Record/cronfa69337
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spelling 2025-06-02T15:04:45.5584868 v2 69337 2025-04-24 Host‐Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban–Rural Ecotone a9529ee248e80d338ab3e6fedb2197eb Alessandra Giacomini Alessandra Giacomini true false be98847c72c14a731c4a6b7bc02b3bcf 0000-0002-5527-4709 Matthew Hitchings Matthew Hitchings true false 241f2810ab8f56be53ca8af23e384c6e 0000-0003-4403-2509 Sofia Consuegra del Olmo Sofia Consuegra del Olmo true false 3ea91c154926c86f89ea6a761122ecf6 0000-0002-0072-9745 Tamsyn Uren Webster Tamsyn Uren Webster true false d18166c31e89833c55ef0f2cbb551243 0000-0003-0377-2463 Konstans Wells Konstans Wells true false 2025-04-24 MRKT Global change and urbanisation profoundly alter wildlife habitats, driving native animals into novel habitats while increasing the co-occurrence between native and invasive species. Host-microbiome associations are shaped by host traits and environmental features, but little is known about their plasticity in co-occurring native and invasive species across urban–rural gradients. Here, we explored gut microbiomes of four sympatric small mammal species along an urban–rural ecotone in Borneo, one of the planet's oldest rainforest regions experiencing recent urban expansion. Host species identity was the strongest determinant of microbiome composition, while land use and spatial proximity shaped microbiome similarity within and among the three rat species. The urban-dwelling rat Rattus rattus had a microbiome composition more similar to that of the native, urban-adapted rat Sundamys muelleri (R. rattus' strongest environmental niche overlap), than to the closely related urban-dwelling R. norvegicus. The urban-dwelling shrew Suncus murinus presented the most distinct microbiome. The microbiome of R. norvegicus was the most sensitive to land use intensity, exhibiting significant alterations in composition and bacterial abundance across the ecotone. Our findings suggest that environmental niche overlap among native and invasive species promotes similar gut microbiomes. Even for omnivorous urban-dwellers with a worldwide distribution like R. norvegicus, gut microbiomes may change across fine-scale environmental gradients. Future research needs to confirm whether land use intensity can be a strong selective force on mammalian gut microbiomes, influencing the way in which native and invasive species are able to exploit novel environments. Journal Article Molecular Ecology 34 11 Wiley 0962-1083 1365-294X gut microbiota, invasive rats, microbial community ecology, native-invasive species interactions, phylosymbiosis, urban adaptation 1 6 2025 2025-06-01 10.1111/mec.17782 COLLEGE NANME Marketing COLLEGE CODE MRKT Swansea University SU Library paid the OA fee (TA Institutional Deal) Royal Society Industry Fellowship (Grant Number: IF\R1\231030); Swansea University ECR BIOL postgraduate research scholarship 2025-06-02T15:04:45.5584868 2025-04-24T10:31:41.1288853 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Alessandra Giacomini 1 Maklarin B. Lakim 0009-0005-0142-0255 2 Fred Y. Y. Tuh 0000-0001-9558-5782 3 Matthew Hitchings 0000-0002-5527-4709 4 Sofia Consuegra del Olmo 0000-0003-4403-2509 5 Tamsyn Uren Webster 0000-0002-0072-9745 6 Konstans Wells 0000-0003-0377-2463 7 69337__34121__a7893817f6d247d49ef83c12baf396d2.pdf Giacomini_etal_2025_MolEcol.pdf 2025-04-28T10:41:09.7411903 Output 1993952 application/pdf Version of Record true © 2025 The Author(s). This is an open access article under the terms of the Creative Commons Attribution License. true eng http://creativecommons.org/licenses/by/4.0/ 320 Alessandra Giacomini a.giacomini.2156511@swansea.ac.uk true https://doi.org/10.5281/zenodo.15223040 false
title Host‐Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban–Rural Ecotone
spellingShingle Host‐Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban–Rural Ecotone
Alessandra Giacomini
Matthew Hitchings
Sofia Consuegra del Olmo
Tamsyn Uren Webster
Konstans Wells
title_short Host‐Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban–Rural Ecotone
title_full Host‐Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban–Rural Ecotone
title_fullStr Host‐Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban–Rural Ecotone
title_full_unstemmed Host‐Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban–Rural Ecotone
title_sort Host‐Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban–Rural Ecotone
author_id_str_mv a9529ee248e80d338ab3e6fedb2197eb
be98847c72c14a731c4a6b7bc02b3bcf
241f2810ab8f56be53ca8af23e384c6e
3ea91c154926c86f89ea6a761122ecf6
d18166c31e89833c55ef0f2cbb551243
author_id_fullname_str_mv a9529ee248e80d338ab3e6fedb2197eb_***_Alessandra Giacomini
be98847c72c14a731c4a6b7bc02b3bcf_***_Matthew Hitchings
241f2810ab8f56be53ca8af23e384c6e_***_Sofia Consuegra del Olmo
3ea91c154926c86f89ea6a761122ecf6_***_Tamsyn Uren Webster
d18166c31e89833c55ef0f2cbb551243_***_Konstans Wells
author Alessandra Giacomini
Matthew Hitchings
Sofia Consuegra del Olmo
Tamsyn Uren Webster
Konstans Wells
author2 Alessandra Giacomini
Maklarin B. Lakim
Fred Y. Y. Tuh
Matthew Hitchings
Sofia Consuegra del Olmo
Tamsyn Uren Webster
Konstans Wells
format Journal article
container_title Molecular Ecology
container_volume 34
container_issue 11
publishDate 2025
institution Swansea University
issn 0962-1083
1365-294X
doi_str_mv 10.1111/mec.17782
publisher Wiley
college_str Faculty of Science and Engineering
hierarchytype
hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences
document_store_str 1
active_str 0
description Global change and urbanisation profoundly alter wildlife habitats, driving native animals into novel habitats while increasing the co-occurrence between native and invasive species. Host-microbiome associations are shaped by host traits and environmental features, but little is known about their plasticity in co-occurring native and invasive species across urban–rural gradients. Here, we explored gut microbiomes of four sympatric small mammal species along an urban–rural ecotone in Borneo, one of the planet's oldest rainforest regions experiencing recent urban expansion. Host species identity was the strongest determinant of microbiome composition, while land use and spatial proximity shaped microbiome similarity within and among the three rat species. The urban-dwelling rat Rattus rattus had a microbiome composition more similar to that of the native, urban-adapted rat Sundamys muelleri (R. rattus' strongest environmental niche overlap), than to the closely related urban-dwelling R. norvegicus. The urban-dwelling shrew Suncus murinus presented the most distinct microbiome. The microbiome of R. norvegicus was the most sensitive to land use intensity, exhibiting significant alterations in composition and bacterial abundance across the ecotone. Our findings suggest that environmental niche overlap among native and invasive species promotes similar gut microbiomes. Even for omnivorous urban-dwellers with a worldwide distribution like R. norvegicus, gut microbiomes may change across fine-scale environmental gradients. Future research needs to confirm whether land use intensity can be a strong selective force on mammalian gut microbiomes, influencing the way in which native and invasive species are able to exploit novel environments.
published_date 2025-06-01T14:15:33Z
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