Biology subjects

Rebolleda-Gomez, M.

Publications and source records attributed to Rebolleda-Gomez, M..

10 recordsLinked to original sources

bioRxiv2026

Gut microbiome connectivity drives mass host colonization and buffers against antibiotic-induced collapse

Microbial dispersal continually shapes gut microbiomes, seeding communities during assembly and replenishing them after perturbation. Dispersals effect depends on its strength: low dispersal introduces stochasticity and drives divergence, whereas high dispersal increases mixing and promotes convergence. Although this pattern manifests across host-microbe systems, the mechanism by which dispersal alters colonization dynamics to generate such contrasting outcomes remains unclear. Identifying factors that toggle these dualistic effects is essential for predicting and controlling gut microbiome assembly and stability. We addressed this problem in gnotobiotic larval zebrafish, which is a tractable vertebrate model that enables experimental control and quantification of gut bacterial dispersal. To dissect the roles of dispersal, we defined the relationship between inoculation dose and colonization frequency for a model Vibrio cholerae isolate under different dispersal regimes. Strikingly, a dose yielding only 50% colonization in isolated hosts--the CD50--produced nearly universal colonization during co-housing, despite identical host and bacterial densities. Measurements of intestinal growth, carrying capacity, shedding, and environmental persistence were used to construct a quantitative colonization-dispersal model that explained the basis for this shift in colonization outcomes. At the CD50, colonization is inherently probabilistic, but once the first hosts become colonized, they reseed the environment and amplify secondary exposures, creating a feedback loop that rapidly transforms individual-level stochasticity into widespread colonization. We further show that this feedback operates in complex microbiomes, where larger host groups--with more opportunities for recolonization--buffer communities against antibiotic-induced collapse. Together, our findings demonstrate that dispersal regimes are not fixed but dynamically shift as hosts become increasingly connected. By revealing how dispersal and interhost transmission drive mass colonization and stabilize gut communities, our work identifies microbiome connectivity as a central mechanism governing gut microbial assembly and resilience.

microbiology↗

bioRxiv2026

Conserved upper thermal limits and small safety margins in soil copiotrophic bacteria.

One of the key uncertainties in climate change models is how microbes will adapt to rising temperatures. Large-scale comparisons of bacterial thermal performances show a clear boundary between mesophiles and thermophiles. Here, we investigated whether phylogenetic constraints limit the adaptive potential of bacteria to warming soils. Focusing on copiotrophs within Gammaproteobacteria, we found that both thermal optima and upper thermal limits are constrained; variation in these traits decreases above 42{degrees}C across the phylogeny, with minimal influence of present-day bioclimatic variables. This, along with the reduced thermal safety margins found in fluctuating hot climates, suggests that many isolates may already be maladapted to local temperature variability. Our findings indicate that these constraints interact with the geometry of thermal performance curves, imposing a trade-off between high-temperature performance and the risk of substantial fitness losses above Topt. Overall, this work underscores potential limits to thermal adaptation and their implications for bacterial fitness.

evolutionary biology↗

bioRxiv2026

Stress-Induced Cooperation Promotes Tolerance in Resource-Limited Auxotrophic Microbial Consortia

Microbial communities often rely on metabolic cooperation, especially under nutrient limitation, but how antibiotics influence these interactions remains unclear. Here, we show that exposure to chloramphenicol, a ribosome-targeting bacteriostatic antibiotic, promotes cooperation in auxotrophic Escherichia coli consortia. Using a proteome-partition model, we find that chloramphenicol-induced growth inhibition elevates levels of the alarmone ppGpp, shifting proteome allocation toward amino acid biosynthesis and export. This regulatory response enhances cross-feeding and supports cooperative growth, even under antibiotic stress. Laboratory experiments confirm that, under low amino acid availability, co-cultures of leucine and phenylalanine auxotrophs display greater tolerance to chloramphenicol than monocultures. Both our theoretical and experimental results reveal a feedback loop in which antibiotic stress strengthens metabolic interdependence, buffering growth inhibition and enhancing community-level tolerance.

microbiology↗

bioRxiv2025

Plant domestication does not reduce diversity in root microbiomes

O_LIDomestication has profoundly shaped the genetic makeup of numerous plant and animal species. While the effects of plant domestication at the genetic and phenotypic levels are well-documented, its impact on plant microbiome remains less understood. C_LIO_LITwo primary hypotheses have been proposed: 1) the reduction in microbial diversity resulting from the domestication process, and 2) the diminished ability of host plants to control their microbiomes. C_LIO_LIWe conducted a meta-analysis of multiple crops, comparing the root microbiomes of domesticated plants and their wild relatives. Our results indicate that the effects of domestication are species-specific and context-dependent, with most domesticated plants exhibiting increased microbial diversity and more structured communities. C_LIO_LIOverall, this study provides evidence that plant domestication does not lead to a uniform reduction in microbial diversity or a consistently diminished ability of plants to influence their microbiomes. C_LIO_LIBased on these findings, we discuss new perspectives and the need for future studies incorporating native soils and host genetic variation in such experiments, analyzing diversity and microbiome function, and considering how root morphology might affect microbiome recruitment. C_LI

ecology↗

bioRxiv2023

Metabolic similarity and the predictability of microbial community assembly

AbstractWhen 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 similarities in metabolic traits across metabolically similar environments lead to predictable similarities in community composition. To that end, we measured the growth rate and by-product profile of a library of proteobacterial strains in a large number of single nutrient environments. We found that growth rates and secretion profiles were positively correlated across environments when the supplied substrate was metabolically similar. By analyzing hundreds of in-vitro communities experimentally assembled in an array of different synthetic environments, we then show that metabolically similar substrates select for taxonomically similar communities. These findings lead us to propose and then validate a comparative approach for quantitatively predicting the effects of novel substrates on the composition of complex microbial consortia.

ecology↗

bioRxiv2023

Predictive microbial community changes across a temperature gradient

A central challenge in community ecology is predicting the effects of abiotic factors on community assembly. In particular, microbial communities play a central role in the ecosystem, but we do not understand how changing factors like temperature are going to affect community composition or function. One of the challenges is that we do not understand the mechanistic impacts of temperature on different metabolic strategies, nor how this metabolic plasticity could impact microbial interactions. Dissecting the contribution of environmental factors on microbial interactions in natural ecosystems is hindered by our understanding of microbial physiology and our ability to disentangle interactions from sequencing data. Studying the self-assembly of multiple communities in synthetic environments, here we are able to predict changes in microbial community composition based on metabolic responses of each functional group along a temperature gradient. This research highlights the importance of metabolic plasticity and metabolic trade-offs in predicting species interactions and community dynamics across abiotic gradients.

ecology↗

bioRxiv2020

Top-down engineering of complex communities by directed evolution

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 variants of higher function. Above the organismal level, a small number of studies have attempted to artificially select microbial communities and ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is still limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. To address this issue, we have developed a flexible modeling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions, in a wide range of ecological conditions. By artificially selecting hundreds of in-silico microbial metacommunities under identical conditions, we examine the fundamental limits of the two main breeding methods used so far, and prescribe modifications that significantly increase their power. We identify a range of directed evolution strategies that, particularly when applied in combination, are better suited for the top-down engineering of large, diverse, and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search for dynamically stable and ecologically and functionally resilient high-functioning communities.

evolutionary biology↗

bioRxiv2020

Metabolic rules of microbial community assembly

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 unpredictable, and why. The emergent metagenomic structure of communities is often quantitatively convergent in similar habitats, with highly similar fractions of the metagenome being devoted to the same metabolic pathways. By contrast, the species-level taxonomic composition is often highly variable even in replicate environments. The mechanisms behind these patterns are not yet understood. By studying the self-assembly of hundreds of communities in replicate, synthetic habitats, we show that the reproducibility of microbial community assembly reflects an emergent metabolic structure, which is quantitatively predictable from first-principles, genome-scale metabolic models. Taxonomic variability within functional groups arises through multistability in population dynamics, and the species-level community composition is predictably governed by the mutual competitive exclusion of two sub-dominant strains. Our findings provide a mechanistic bridge between microbial community structure at different levels of organization, and show that the evolutionary conservation of metabolic traits, both in terms of growth responses and niches constructed, can be leveraged to quantitatively predict the taxonomic and metabolic structure of microbial communities.

ecology↗

bioRxiv2019

Floral organs act as environmental filters and interact with pollinators to structure the yellow monkeyflower (Mimulus guttatus) floral microbiome.

Assembly of microbial communities is the result of neutral and selective processes. However, the relative importance of these processes is still debated. Microbial communities of flowers, in particular, have gained recent attention because of their potential impact to plant fitness and plant-pollinator interactions. However, the role of selection and dispersal in the assembly of these communities remains poorly understood. We evaluated the role of pollinator-mediated dispersal on the contribution of neutral and selective processes in the assembly of floral microbiomes of the yellow monkeyflower (Mimulus guttatus). We sampled floral organs from flowers in the presence and absence of pollinators within five different serpentine seeps in CA and obtained 16S amplicon data on the epiphytic bacterial communities. Consistent with strong micro-environment selection within flowers we observed significant differences in community composition across floral organs and only a small effect of geographic distance. Pollinator exposure affected the contribution of environmental selection and depended on the rate and \"intimacy\" of interactions with flower visitors. This study provides evidence of the importance of dispersal and within-flower heterogeneity in shaping epiphytic bacterial communities of flowers, and highlights the complex interplay between pollinator behavior, environmental selection and additional abiotic factors in shaping the epiphytic bacterial communities of flowers.

ecology↗

bioRxiv2019

Why evolve reliance on the microbiome for timing of ontogeny?

The timing of life history events has important fitness consequences. Since the 1950s, researchers have combined first principles and data to predict the optimal timing of life history transitions. Recently, a striking mystery has emerged. Such transitions can be shaped by a completely different branch of the tree of life: bacterial species in the microbiome. Probing these interactions using testable predictions from evolutionary theory could illuminate whether and how host-microbiome integrated life histories can evolve and be maintained. Beyond advancing fundamental science, this research program could yield important applications. In an age of microbiome engineering, understanding the contexts that lead to microbiota signaling shaping ontogeny could offer novel mechanisms for manipulations to increase yield in agriculture, or reduce pathogen transmission by affecting vector efficiency. We combine theory and evidence to illuminate the essential questions underlying the existence of Microbiome Dependent Ontogenetic Timing (MiDOT) to fuel research on this emerging topic.

evolutionary biology↗