Miguel D. Fernández-de-Bobadilla

The paper shows microbial community function is predictable due to coordinated interactions across species, not because interactions are simple.

BacTaxID provides a universal framework for bacterial classification using whole-genome k-mer sketches, achieving concordance with species and sub-species systems and capturing strain-level diversity.

This paper shows that higher-order interactions in microbial communities are undetectable due to noise and statistical constraints, not because they are biologically insignificant.

This paper isolates and characterizes viable Bdellovibrio from human fecal samples, revealing genomic conservation and prey specialization in the human gut microbiome.

The study analyzes the gut resistome of the Wayampi, revealing similar antibiotic resistance gene richness to Europeans but higher metal resistance gene diversity, highlighting shared and distinct resistance patterns.

The paper investigates the long-term dynamics of Serratia marcescens complex in hospital sinks, identifying persistent strains linked to outbreaks and revealing new insights into their ecology and resistance gene acquisition.

PATO is a toolkit for pangenome analysis that efficiently handles thousands of genomes, offering fast and accurate methods for core-genome definition, population structure, and gene sharedness networks.