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Bouilloud M, Galan M, Pradel J, Loiseau A, Ferrero J, Gallet R, Roche B, Charbonnel N. Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota. Anim Microbiome 2024; 6:16. [PMID: 38528597 DOI: 10.1186/s42523-024-00301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.
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Affiliation(s)
- Marie Bouilloud
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France.
- Centre de Biologie pour la Gestion des Populations, 750 Avenue Agropolis, 34988, Montferrier sur Lez, France.
| | - Maxime Galan
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Julien Pradel
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Anne Loiseau
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Julien Ferrero
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Romain Gallet
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Benjamin Roche
- MIVEGEC, IRD, CNRS, Univ Montpellier, Montpellier, France
| | - Nathalie Charbonnel
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
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Ding SS, Fox JL, Gordus A, Joshi A, Liao JC, Scholz M. Fantastic beasts and how to study them: rethinking experimental animal behavior. J Exp Biol 2024; 227:jeb247003. [PMID: 38372042 PMCID: PMC10911175 DOI: 10.1242/jeb.247003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Humans have been trying to understand animal behavior at least since recorded history. Recent rapid development of new technologies has allowed us to make significant progress in understanding the physiological and molecular mechanisms underlying behavior, a key goal of neuroethology. However, there is a tradeoff when studying animal behavior and its underlying biological mechanisms: common behavior protocols in the laboratory are designed to be replicable and controlled, but they often fail to encompass the variability and breadth of natural behavior. This Commentary proposes a framework of 10 key questions that aim to guide researchers in incorporating a rich natural context into their experimental design or in choosing a new animal study system. The 10 questions cover overarching experimental considerations that can provide a template for interspecies comparisons, enable us to develop studies in new model organisms and unlock new experiments in our quest to understand behavior.
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Affiliation(s)
- Siyu Serena Ding
- Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
| | - Jessica L. Fox
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Andrew Gordus
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Abhilasha Joshi
- Departments of Physiology and Psychiatry, University of California, San Francisco, CA 94158, USA
| | - James C. Liao
- Department of Biology, The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Monika Scholz
- Max Planck Research Group Neural Information Flow, Max Planck Institute for Neurobiology of Behavior – caesar, 53175 Bonn, Germany
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Bendová B, Piálek J, Ďureje Ľ, Schmiedová L, Čížková D, Martin JF, Kreisinger J. How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies. BMC Microbiol 2020; 20:194. [PMID: 32631223 PMCID: PMC7336484 DOI: 10.1186/s12866-020-01859-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/16/2020] [Indexed: 02/08/2023] Open
Abstract
Background The vertebrate gastrointestinal tract is colonised by microbiota that have a major effect on the host’s health, physiology and phenotype. Once introduced into captivity, however, the gut microbial composition of free-living individuals can change dramatically. At present, little is known about gut microbial changes associated with adaptation to a synanthropic lifestyle in commensal species, compared with their non-commensal counterparts. Here, we compare the taxonomic composition and diversity of bacterial and fungal communities across three gut sections in synanthropic house mouse (Mus musculus) and a closely related non-synanthropic mound-building mouse (Mus spicilegus). Results Using Illumina sequencing of bacterial 16S rRNA amplicons, we found higher bacterial diversity in M. spicilegus and detected 11 bacterial operational taxonomic units with significantly different proportions. Notably, abundance of Oscillospira, which is typically higher in lean or outdoor pasturing animals, was more abundant in non-commensal M. spicilegus. ITS2-based barcoding revealed low diversity and high uniformity of gut fungi in both species, with the genus Kazachstania clearly dominant. Conclusions Though differences in gut bacteria observed in the two species can be associated with their close association with humans, changes due to a move from commensalism to captivity would appear to have caused larger shifts in microbiota.
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Affiliation(s)
- Barbora Bendová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Dagmar Čížková
- Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jean-Francois Martin
- CBGP, Montpellier SupAgro, INRA, CIRAD, IRD, Univ Montpellier, Montferrier-sur-Lez, France
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
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