Sylvie Estrela
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View article: Nutrient competition predicts gut microbiome restructuring under drug perturbations
Nutrient competition predicts gut microbiome restructuring under drug perturbations Open
Human gut commensal bacteria are routinely exposed to various stresses, including therapeutic drugs, and collateral effects are difficult to predict. To systematically interrogate community-level effects of drug perturbations, we screened …
View article: Metabolic similarity and the predictability of microbial community assembly
Metabolic similarity and the predictability of microbial community assembly Open
When microbial communities form, their composition is shaped by selective pressures imposed by the environment. Can we predict which communities will assemble under different environmental conditions? Here, we hypothesize that quantitative…
View article: Emergent coexistence in multispecies microbial communities
Emergent coexistence in multispecies microbial communities Open
Understanding the mechanisms that maintain microbial biodiversity is a critical aspiration in ecology. Past work on microbial coexistence has largely focused on species pairs, but it is unclear whether pairwise coexistence in isolation is …
View article: Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamics
Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamics Open
Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, we use thousands of microbial communities cultured in vitro from human…
View article: Emergent coexistence in multispecies microbial communities
Emergent coexistence in multispecies microbial communities Open
Microbial communities are highly diverse, and understanding the factors that promote and modulate this diversity is a major area of research in microbial ecology. Recent work has proposed a reductionist perspective to microbial coexistence…
View article: Diversity begets diversity under microbial niche construction
Diversity begets diversity under microbial niche construction Open
Microbial interactions are expected to modulate microbial diversity, but whether they inhibit or stimulate further diversity in complex microbial communities, and how, remains poorly understood. By assembling microbial communities in multi…
View article: The meta-gut: community coalescence of animal gut and environmental microbiomes
The meta-gut: community coalescence of animal gut and environmental microbiomes Open
All animals carry specialized microbiomes, and their gut microbiota are continuously released into the environment through excretion of waste. Here we propose the meta-gut as a novel conceptual framework that addresses the ability of the g…
View article: Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments
Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments Open
A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, we investigate whether comm…
View article: Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology
Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology Open
Recent advances in robotics and affordable genomic sequencing technologies have made it possible to establish and quantitatively track the assembly of enrichment communities in high-throughput. By conducting community assembly experiments …
View article: The meta-gut: Hippo inputs lead to community coalescence of animal and environmental microbiomes
The meta-gut: Hippo inputs lead to community coalescence of animal and environmental microbiomes Open
All animals carry specialized microbiomes, and their gut microbiotas in particular are continuously released into the environment through excretion of waste. Here we propose the meta-gut as a novel conceptual framework that addresses the a…
View article: Directed Evolution of Microbial Communities
Directed Evolution of Microbial Communities Open
Directed evolution is a form of artificial selection that has been used for decades to find biomolecules and organisms with new or enhanced functional traits. Directed evolution can be conceptualized as a guided exploration of the genotype…
View article: Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments
Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments Open
A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, we investigate whether comm…
View article: Top-down engineering of complex communities by directed evolution
Top-down engineering of complex communities by directed evolution Open
Directed evolution has been used for decades to engineer biological systems from the top-down. Generally, it has been applied at or below the organismal level, by iteratively sampling the mutational landscape in a guided search for genetic…
View article: Metabolic rules of microbial community assembly
Metabolic rules of microbial community assembly Open
To develop a quantitative theory that can predict how microbiomes assemble, and how they respond to perturbations, we must identify which descriptive features of microbial communities are reproducible and predictable, which are unpredictab…
View article: Community lifespan, niche expansion and the evolution of interspecific cooperation
Community lifespan, niche expansion and the evolution of interspecific cooperation Open
Natural selection favours individuals who maximise their own reproductive success and that of their close relatives. From this perspective, cooperation that benefits individuals of a different species represents an evolutionary conundrum. …
View article: Emergent simplicity in microbial community assembly
Emergent simplicity in microbial community assembly Open
Interchanging species of similar function Under natural conditions, bacteria form mixed, interacting communities. Understanding how such communities assemble and stabilize is important in a range of contexts, from biotechnological applicat…
View article: Community interactions and spatial structure shape selection on antibiotic resistant lineages
Community interactions and spatial structure shape selection on antibiotic resistant lineages Open
Polymicrobial interactions play an important role in shaping the outcome of antibiotic treatment, yet how multispecies communities respond to antibiotic assault is still little understood. Here we use an individual-based simulation model o…
View article: Emergent Simplicity in Microbial Community Assembly
Emergent Simplicity in Microbial Community Assembly Open
Microbes assemble into complex, dynamic, and species-rich communities that play critical roles in human health and in the environment. The complexity of natural environments and the large number of niches present in most habitats are often…