Exploring Bird Gut Microbiota Through Opportunistic Fecal Sampling: Ecological and Evolutionary Perspectives
ABSTRACT Wetland ecosystems are facing alarming rates of destruction and degradation, posing significant challenges for avian populations reliant on these habitats. Bird health is closely linked to the composition of their intestinal microbiota, which is primarily influenced by local conditions, pri...
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Wiley
2025-04-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.71291 |
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| author | Laura Fablet Aurélie Bonin Diane Zarzoso‐Lacoste Vincent Dubut Laurence Walch |
| author_facet | Laura Fablet Aurélie Bonin Diane Zarzoso‐Lacoste Vincent Dubut Laurence Walch |
| author_sort | Laura Fablet |
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| description | ABSTRACT Wetland ecosystems are facing alarming rates of destruction and degradation, posing significant challenges for avian populations reliant on these habitats. Bird health is closely linked to the composition of their intestinal microbiota, which is primarily influenced by local conditions, primarily through diet. Building on our previous work identifying dietary variations among bird populations in marshes within a Ramsar site along the Somme and Avre rivers (France), this pilot study aimed to assess the relevance of using fecal samples collected from the ground to characterize avian intestinal microbiota via 16S rRNA metabarcoding. We hypothesized that this noninvasive sampling method would capture how bird traits and environmental factors shape fecal microbiota composition. Sampling was conducted during the breeding season at seven locations (six within the Ramsar site and one on its outskirts) spanning rural or peri‐urban environments. A total of 52 fecal samples from nine bird species or families, predominantly waterbirds, were analyzed for bacterial composition. At the phylum level, Firmicutes and Proteobacteria were predominant, with the relative abundance of genera such as Clostridium, Rothia, Bacillus, Caldilinea and Pseudomonas varying among bird species. The potential enteropathogen Campylobacter was primarily detected in samples from peri‐urban sites. Multivariate analyses revealed significant variations in bacterial composition associated with bird trophic guild, ecology, body length, pond surface and habitat location. Additionally, a weak correlation was observed between host phylogeny and microbiota composition. Although the limited sample size, particularly for some species, constrains the robustness of these findings, the observed trends align with ecological expectations. This study highlights the potential of opportunistically collected fecal samples as a low‐impact tool for exploring the relationship between bird gut microbiota and their habitat. |
| format | Article |
| id | doaj-art-28bd9041edbb4f2bbd1dcf62ebf5cfb2 |
| institution | OA Journals |
| issn | 2045-7758 |
| language | English |
| publishDate | 2025-04-01 |
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| series | Ecology and Evolution |
| spelling | doaj-art-28bd9041edbb4f2bbd1dcf62ebf5cfb22025-08-20T02:35:33ZengWileyEcology and Evolution2045-77582025-04-01154n/an/a10.1002/ece3.71291Exploring Bird Gut Microbiota Through Opportunistic Fecal Sampling: Ecological and Evolutionary PerspectivesLaura Fablet0Aurélie Bonin1Diane Zarzoso‐Lacoste2Vincent Dubut3Laurence Walch4Sorbonne Université, CNRS, IRD, INRAE Université Paris Est Créteil, Université Paris Cité, Institute of Ecology and Environmental Sciences (IEES‐Paris) Paris FranceARGALY Sainte Hélène du Lac FranceUMR CNRS 7058 Ecologie et Dynamique Des Systèmes Anthropisés (EDYSAN) Université de Picardie Jules Verne Amiens FranceAix Marseille Univ Avignon Université, CNRS, IRD, IMBE Marseille FranceSorbonne Université, CNRS, IRD, INRAE Université Paris Est Créteil, Université Paris Cité, Institute of Ecology and Environmental Sciences (IEES‐Paris) Paris FranceABSTRACT Wetland ecosystems are facing alarming rates of destruction and degradation, posing significant challenges for avian populations reliant on these habitats. Bird health is closely linked to the composition of their intestinal microbiota, which is primarily influenced by local conditions, primarily through diet. Building on our previous work identifying dietary variations among bird populations in marshes within a Ramsar site along the Somme and Avre rivers (France), this pilot study aimed to assess the relevance of using fecal samples collected from the ground to characterize avian intestinal microbiota via 16S rRNA metabarcoding. We hypothesized that this noninvasive sampling method would capture how bird traits and environmental factors shape fecal microbiota composition. Sampling was conducted during the breeding season at seven locations (six within the Ramsar site and one on its outskirts) spanning rural or peri‐urban environments. A total of 52 fecal samples from nine bird species or families, predominantly waterbirds, were analyzed for bacterial composition. At the phylum level, Firmicutes and Proteobacteria were predominant, with the relative abundance of genera such as Clostridium, Rothia, Bacillus, Caldilinea and Pseudomonas varying among bird species. The potential enteropathogen Campylobacter was primarily detected in samples from peri‐urban sites. Multivariate analyses revealed significant variations in bacterial composition associated with bird trophic guild, ecology, body length, pond surface and habitat location. Additionally, a weak correlation was observed between host phylogeny and microbiota composition. Although the limited sample size, particularly for some species, constrains the robustness of these findings, the observed trends align with ecological expectations. This study highlights the potential of opportunistically collected fecal samples as a low‐impact tool for exploring the relationship between bird gut microbiota and their habitat.https://doi.org/10.1002/ece3.71291avian healthbacterial compositionbird communitiesfreshwater ecosystemsmolecular ecology |
| spellingShingle | Laura Fablet Aurélie Bonin Diane Zarzoso‐Lacoste Vincent Dubut Laurence Walch Exploring Bird Gut Microbiota Through Opportunistic Fecal Sampling: Ecological and Evolutionary Perspectives Ecology and Evolution avian health bacterial composition bird communities freshwater ecosystems molecular ecology |
| title | Exploring Bird Gut Microbiota Through Opportunistic Fecal Sampling: Ecological and Evolutionary Perspectives |
| title_full | Exploring Bird Gut Microbiota Through Opportunistic Fecal Sampling: Ecological and Evolutionary Perspectives |
| title_fullStr | Exploring Bird Gut Microbiota Through Opportunistic Fecal Sampling: Ecological and Evolutionary Perspectives |
| title_full_unstemmed | Exploring Bird Gut Microbiota Through Opportunistic Fecal Sampling: Ecological and Evolutionary Perspectives |
| title_short | Exploring Bird Gut Microbiota Through Opportunistic Fecal Sampling: Ecological and Evolutionary Perspectives |
| title_sort | exploring bird gut microbiota through opportunistic fecal sampling ecological and evolutionary perspectives |
| topic | avian health bacterial composition bird communities freshwater ecosystems molecular ecology |
| url | https://doi.org/10.1002/ece3.71291 |
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