Data_Sheet_1_Dynamics of Gut Microbiota Diversity During the Early Development of an Avian Host: Evidence From a Cross-Foster Experiment.docx

Despite the increasing knowledge on the processes involved in the acquisition and development of the gut microbiota in model organisms, the factors influencing early microbiota successions in natural populations remain poorly understood. In particular, little is known on the role of the rearing environment in the establishment of the gut microbiota in wild birds. Here, we examined the influence of the nesting environment on the gut microbiota of Great tits (Parus major) by performing a partial cross-fostering experiment during the intermediate stage of nestling development. We found that the cloacal microbiota of great tit nestlings underwent substantial changes between 8 and 15 days of age, with a strong decrease in diversity, an increase in the relative abundance of Firmicutes and a shift in the functional features of the community. Second, the nesting environment significantly influenced community composition, with a divergence among separated true siblings and a convergence among foster siblings. Third, larger shifts in both microbiota diversity and composition correlated with lower nestling body condition. Our results shed new light on the dynamics of microbial diversity during the ontogeny of avian hosts, indicating that the nest environment continues to shape the gut microbiota during the later stages of nestling development and that the increase in gut diversity between hatching and adulthood may not be as linear as previously suspected. Lastly, the microbiota changes incurred during this period may have implications for nestling body condition which can lead to long-term consequences for host fitness.</p

Data_Sheet_2_Dynamics of Gut Microbiota Diversity During the Early Development of an Avian Host: Evidence From a Cross-Foster Experiment.XLSX

<p>Despite the increasing knowledge on the processes involved in the acquisition and development of the gut microbiota in model organisms, the factors influencing early microbiota successions in natural populations remain poorly understood. In particular, little is known on the role of the rearing environment in the establishment of the gut microbiota in wild birds. Here, we examined the influence of the nesting environment on the gut microbiota of Great tits (Parus major) by performing a partial cross-fostering experiment during the intermediate stage of nestling development. We found that the cloacal microbiota of great tit nestlings underwent substantial changes between 8 and 15 days of age, with a strong decrease in diversity, an increase in the relative abundance of Firmicutes and a shift in the functional features of the community. Second, the nesting environment significantly influenced community composition, with a divergence among separated true siblings and a convergence among foster siblings. Third, larger shifts in both microbiota diversity and composition correlated with lower nestling body condition. Our results shed new light on the dynamics of microbial diversity during the ontogeny of avian hosts, indicating that the nest environment continues to shape the gut microbiota during the later stages of nestling development and that the increase in gut diversity between hatching and adulthood may not be as linear as previously suspected. Lastly, the microbiota changes incurred during this period may have implications for nestling body condition which can lead to long-term consequences for host fitness.</p

Data_Sheet_3_Dynamics of Gut Microbiota Diversity During the Early Development of an Avian Host: Evidence From a Cross-Foster Experiment.XLSX

<p>Despite the increasing knowledge on the processes involved in the acquisition and development of the gut microbiota in model organisms, the factors influencing early microbiota successions in natural populations remain poorly understood. In particular, little is known on the role of the rearing environment in the establishment of the gut microbiota in wild birds. Here, we examined the influence of the nesting environment on the gut microbiota of Great tits (Parus major) by performing a partial cross-fostering experiment during the intermediate stage of nestling development. We found that the cloacal microbiota of great tit nestlings underwent substantial changes between 8 and 15 days of age, with a strong decrease in diversity, an increase in the relative abundance of Firmicutes and a shift in the functional features of the community. Second, the nesting environment significantly influenced community composition, with a divergence among separated true siblings and a convergence among foster siblings. Third, larger shifts in both microbiota diversity and composition correlated with lower nestling body condition. Our results shed new light on the dynamics of microbial diversity during the ontogeny of avian hosts, indicating that the nest environment continues to shape the gut microbiota during the later stages of nestling development and that the increase in gut diversity between hatching and adulthood may not be as linear as previously suspected. Lastly, the microbiota changes incurred during this period may have implications for nestling body condition which can lead to long-term consequences for host fitness.</p

donnees_Dryad

donnees_Drya

Effect of temperature treatment on survival, body growth, body condition, and female reproduction the following year in yearling and adults.

<p>NOTE: Statistics of Likelihood Ratio test compare two models, one with temperature treatment and one simpler model without temperature treatment. Generalized linear mixed models with logit links are used for binomial factors such as survival and gravidity, other variables are modeled with linear mixed models except for clutch size, which is modeled with a Poisson distribution. We provide estimate and standard error of the fixed effects included in the model (temperature treatment, age, and sex). Following Nakagawa and Schielzeth (2013), we also provide marginal (R²m, effect of the fixed effects) and conditional (R²c, effect of the fixed and random effects) R² for our best models, as well as the proportion change in variance (PCV) for the random effects.</p><p>Effect of temperature treatment on survival, body growth, body condition, and female reproduction the following year in yearling and adults.</p

Maternal exposure to predators

Maternal exposure to predator

Potential risk from climate change for common lizard populations across Europe inferred from current maximum temperatures experienced by these populations.

<p>Colors represent “risk profiles” of the populations, from A: imminent risk (purple) to F: low risk (green), see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002281#pbio.1002281.s016" target="_blank">S4 Text</a>, <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002281#pbio.1002281.s011" target="_blank">S6 Table</a>. Populations in risk levels from A to C (purple, red and dark orange) will be threatened by a 2°C increase in temperatures. Populations in risk level D (light orange) will be threatened by a 3°C temperature increase, and risk level E (yellow) will be threatened by a 4°C temperature increase.</p

The Metatron.

<p><b>A</b>: Aerial view of the structure. On the right, top shutters are closed on 17 enclosures. Credits: Quentin Bénard. <b>B</b>: Close view of the structure. On the bottom left, an enclosure with open shutters. On the top right, an enclosure with closed shutters. <b>C</b>: Inside view of one enclosure. <b>D</b>: Entrance of the two half-corridors of one enclosure. <b>E</b>: Pole containing the sensors recording temperature, humidity, and illuminance inside of the enclosure as well as the sprinkler system, protected with plastic and labeled with the patch identification number. <b>F</b>: Pitfall trap at the end of one corridor. <b>G</b>: One of the two ponds set in each enclosure. <b>H</b> and <b>I</b>: Rock and logs allowing for lizard thermoregulation, set in each corner of the enclosures.</p

Effect of temperature treatment on survival, body growth, body condition, and female reproduction the following year in juveniles.

<p>NOTE: Statistics of Likelihood Ratio test compare two models, one with temperature treatment and one simpler model without temperature treatment. Generalized linear mixed models with logit links are used for binomial factors such as survival and gravidity, other variables are modeled with linear mixed models except for clutch size, which is modeled with a Poisson distribution. We provide estimate and standard error of the fixed effects included in the model (temperature treatment and date of birth). Following Nakagawa and Schielzeth (2013), we also provide marginal (R²m, effect of the fixed effects) and conditional (R²c, effect of the fixed and random effects) R² for our best models, as well as the proportion change in variance (PCV) for the random effects.</p><p>Effect of temperature treatment on survival, body growth, body condition, and female reproduction the following year in juveniles.</p

supplementary methods, results and figures supporting the diet experiment from Diet contributes to urban-induced alterations in gut microbiota: experimental evidence from a wild passerine

Urban sprawl increasingly affects the ecology of natural populations, including host–microbiota interactions, with observed differences in the gut microbiota between urban and rural hosts. While different mechanisms could explain this pattern, dietary uptake constitutes a likely candidate. To assess the contribution of diet in explaining urban–rural variation in gut microbiota, we performed an aviary experiment in which urban and rural house sparrows where fed with mimics of urban or rural diets. Before the experiment, rural sparrows hosted more diverse gut communities, with a higher relative abundance of Enterococaceae and Staphylococcaceae and lower abundance of genes involved in xenobiotic degradation and lipid metabolism than their urban counterparts. The experimental diets significantly altered gut microbiota α- and β-diversity and taxonomic composition, with the strongest shifts occurring in individuals exposed to contrasting diets. Overall, diet-induced shifts resembled initial differences between free-ranging urban and rural hosts. Furthermore, rural diet had a positive impact on urban host body mass but only in hosts with the highest initial gut diversity. Overall, our results indicate that diet constitutes an important factor contributing to differences in gut microbiota along the urbanization gradient and provide new insights on possible fitness consequences of a reduced gut diversity in urban settings