Juan Antonio Ugalde

This paper identifies {Phi}ESI, a prophage in Salmonella Infantis, as a competitive factor that helps the emergent lineage outcompete non-emergent strains by selectively lysing susceptible competitors.

NanoVI provides a Bayesian variational inference pipeline for species-level taxonomic classification of full-length 16S rRNA Nanopore reads, achieving comparable accuracy to Emu with faster execution and fewer false positives.

This study develops two microbiome-based health scores to differentiate healthy from lesioned Atlantic salmon using 16S rRNA sequencing of multiple body sites.

The paper characterizes a multidrug-resistant Salmonella Amager strain carrying a blaCTX-M-65-positive plasmid, highlighting its emergence and potential for human infections.

The paper reports the first high-quality nuclear and complete mitochondrial genome assemblies of a clinical Wickerhamomyces anomalus isolate, revealing genomic rearrangements linked to virulence and adaptation.

This study analyzes the global genomic diversity of Moraxella catarrhalis using whole-genome sequencing to identify phylogenetic lineages, antimicrobial resistance, and virulence factors.

This study profiles vaginal microbial communities in Chilean women using full-length 16S rRNA sequencing and self-sampling, revealing Lactobacillus dominance and CST IV patterns.

The paper identifies a new strain of Aeromonas salmonicida lacking the vapA gene, which correlates with reduced virulence and lower serological response in Chilean salmon farms.

BugBuster provides a modular, reproducible workflow for metagenomic data analysis using Nextflow, supporting read, contig, and MAG-level analysis along with resistome and taxonomic profiling.

This study assesses reproducibility in microbiome analysis by evaluating sampling, storage, and laboratory processing variations, finding that subject identity is the largest determinant of variation.