Alexandre Almeida

This study analyzes gut microbiome and resistome diversity in Indigenous Orang Asli communities in Malaysia, finding that urbanization reduces microbial diversity but increases antibiotic resistance gene diversity.

The paper integrates metagenome-assembled genomes with clinical isolates to identify genomic signatures of K. pneumoniae in carriage and disease, revealing distinct diversity and improved classification using machine learning.

The paper presents a gut microbiome dataset from Indonesia, revealing novel species and subspecies linked to rural-to-urban lifestyle transitions and showing that community-level diet differences drive microbiome divergence.

This study analyzes 11,115 global gut metagenomes to identify uncultured species linked to health and disease, finding CAG-170 as a potential biomarker of health.

This study shows that the human whipworm's host specificity is driven by the host microbiome, using a humanized-microbiota mouse model and metagenomic analysis.

VIRify identifies and classifies viral contigs and prophages from metagenomic data with high accuracy across prokaryotic and eukaryotic viruses.

The paper analyzes 1,167 archaeal genomes from the human gut to reveal novel species, genomic adaptations, and correlations with socio-demographic factors.