Francesco Beghini

The paper examines how social network cycles influence microbial strain-sharing in Honduran villages, finding that microbial transmission often occurs within clustered groups but not always aligned with social ties.

The paper develops PolyProf, a method to profile polymorphic toxin systems in metagenomes, showing it predicts microbiome development and disease-related dysbiosis.

The paper characterizes gut microbiomes in rural Honduras, identifying novel species and host-microbiome associations through metagenomic sequencing and genomic data integration.

Marker genes for 26,970 species-level genome bins, 4,992 defined only by metagenome-assembled genomes, let MetaPhlAn 4 quantify uncharacterized species and beat MetaPhlAn 3, mOTUs and Bracken on synthetic benchmarks.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

The paper introduces curatedMetagenomicData, a resource providing curated metagenomic profiles for analysis in R with minimal bioinformatic expertise.