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

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

Nature Biotechnology

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

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

Nature Communications

Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer

Lisa Derosa, Bertrand Routy, Andrew Maltez Thomas, +40

Nature Medicine

Pd-1 BlockadeMedicineImmunologyColorectal CancerPathology +7

The person-to-person transmission landscape of the gut and oral microbiomes

Mireia Valles‐Colomer, Aitor Blanco‐Míguez, Paolo Manghi, +40

Nature

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

David Wylensek, Thomas C. A. Hitch, Thomas Riedel, +43

Nature Communications

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

Nicolai Karcher, Eleonora Nigro, Michal Punčochář, +14

Genome biology

Population-level impacts of antibiotic usage on the human gut microbiome

Kihyun Lee, Sébastien Raguideau, Kimmo Sirén, +6

Nature Communications

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

Serena Manara, Francesco Asnicar, Francesco Beghini, +9

Genome biology

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

Aitor Blanco‐Míguez, Francesco Beghini, Fabio Cumbo, +22

DysbiosisComparative GenomicsTaxonomyHuman Microbial FloraGenomics +33

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Björn Grüning, Ryan Dale, Andreas Sjödin, +154

Software MaintenanceEngineeringSynthetic EcologyScience GatewayBioinformatics Database +21