Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Francesco Beghini, Lauren J. McIver, Aitor Blanco‐Míguez, +14

eLife

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Edoardo Pasolli, Francesco Asnicar, Serena Manara, +15

Cell

DysbiosisGeneticsGenomicsHigh Throughput SequencingMetagenomes Spanning Age +15

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

Pamela Ferretti, Edoardo Pasolli, Adrian Tett, +42

Cell Host & Microbe

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Aitor Blanco‐Míguez, Francesco Beghini, Fabio Cumbo, +23

Nature Biotechnology

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

Andrew Maltez Thomas, Paolo Manghi, Francesco Asnicar, +36

Nature Medicine

Choline DegradationDysbiosisMedicinePathologyColorectal Cancer +8

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

Francesco Asnicar, Sarah Berry, Ana M. Valdes, +36

Nature Medicine

BiologyMicrobiome BiologyDysbiosisHabitual DietHost-microbe Interactions +12

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini, +15

Nature Communications

Critical Assessment of Metagenome Interpretation: the second round of challenges

Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, +100

Nature Methods

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis

Adrian Tett, Edoardo Pasolli, Stefania Farina, +11

npj Biofilms and Microbiomes

Large-scale comparative metagenomics of <i>Blastocystis</i>, a common member of the human gut microbiome

Francesco Beghini, Edoardo Pasolli, Tin Duy Truong, +3

The ISME Journal