Biology subjects

Talavera-Marcos, S.

Publications and source records attributed to Talavera-Marcos, S..

3 recordsLinked to original sources

bioRxiv2025

Computational simulation of ecological drift for generating functional minimal microbiomes identifies key experimental and biotic factors influencing success

We describe a top-down engineering approach that leverages ecological drift to generate Minimal Microbiomes; microbial consortia that are relatively simple, cohesive, and functionally complete. This process can be applied to any microbial ecosystem, provided that the target microbiome can be experimentally mimicked. Empirical support for this approach has emerged from multiple independent studies. Here, we use simulations across diverse scenarios, significantly varying niche structures and biotic interactions, to explore the experimental conditions and source microbiome characteristics that favor successful outcomes. Our results indicate that the effectiveness of this approach is constrained by several factors, and that perfect outcomes should not be routinely expected. Nevertheless, despite its drawbacks, this strategy remains a powerful tool for simplifying microbiomes and isolating key co-adapted populations, enabling the construction of low-diversity consortia that retain community function and present ecological cohesion.

microbiology↗

bioRxiv2025

Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex microbiomes

Metagenomic analysis can generate hypotheses about microbiome interactions and function, yet mechanistic understanding is only possible through precise experimentation manipulating its microbiota composition. The high-throughput isolation of microbiome members thus represents a core resource in this field of research. Here, we present and test a culturomics pipeline based on the use of the limiting dilution method with multi-well plates, an optical plate reader, and barcoded sequencing for phylogenetic identification, and offer modularity by proposing different protocols and possibilities along the pipeline. Most importantly, we provide all scripts required for process automation using an affordable pipetting robot, along with associated estimates of financial and labor costs.

microbiology↗

bioRxiv2024

Coupled phylogenetic and functional enrichment in the tomato rhizosphere microbiome

Plant-microbe interactions occur mainly in the rhizosphere, a hot spot of microbial activity and diversity. Given that the outcome of such interactions can significantly impact plant productivity, we require a better understanding of the rhizosphere microbiome if knowledge-based microbiome modification strategies are to be successfully deployed in the future. Here, we aimed to gain a better understanding of the assembly process of the tomato rhizosphere microbiome and its potential composition-function relationships. Among other things, we studied community assembly through the lens of a conceptual framework for the phylogenetically constrained assembly of microbial communities, while assessing community function based on the predicted minimal metagenome of the microbial ecosystem. We observed a systematic enrichment in terms of phylogeny and predicted functional content in the rhizosphere and were able to delimit phylogenetic signal in the ecosystem with 12 functionally coherent phylogenetic groups present in all samples which together accounted for a large fraction of the total community. Our analyses indicated that these groups included a significantly larger content of the ecosystems minimal metagenome than expected by chance. Thus, our study suggests that community assembly followed coupled phylo-functional selection independent of host genetics, and we expect the same phenomenon to occur in other rhizosphere microbiomes. This knowledge provides a thrust in our understanding of how community composition-phylogeny-function relationships drive the assembly process of the rhizosphere microbiome and should help guide the design of synthetic rhizosphere microbiomes for both research and commercial purposes.

microbiology↗