Announcing MetaPhlAn 4

MetaPhlAn 4 Release Notes

The new MetaPhlAn 4 integrates information from both metagenome assemblies and microbial isolate genomes for improved and more comprehensive metagenomic taxonomic profiling ( From a curated collection of ~1M prokaryotic reference and metagenome-assembled genomes, we defined unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 integrates the novelty of metagenomic assemblies with the sensitivity and fidelity of reference-based analyses, providing efficient metagenomic profiling of uncharacterized species and enabling deeper and more comprehensive microbiome analyses.

What has changed in MetaPhlAn 4:

  • Adoption of the species-level genome bins system (SGBs, as described and available here) expanded with many additional MAGs and SGBs.

  • ~5M new MetaPhlAn marker genes identified from ~1M microbial genomes (~236,600 references and 771,500 metagenomic assembled genomes).

  • Ability to profile 21,978 known (kSGBs) and 4,992 unknown (uSGBs) microbial species.

  • Better representation of not only the human (gut) microbiome but also many other animal and ecological environments.

What has NOT changed in MetaPhlAn 4:

  • MetaPhlAn 4 remains backward compatible with MetaPhlAn 3 databases using the --mpa3 parameter.

  • Markers are used in the same way and relative abundances are computed in the same way.

How to perform a fresh install of MetaPhlAn 4:

What’s next

  • MetaPhlAn 4.1 is currently under development with the addition of new eukaryotic and viral species.

Hi there - congrats on the new version of metaphlan! Are there also plans to update humann3 or are the metaphlan4 profiles compatible with it? Thanks!

Hi @Pierre_Schneeberger
Yes, HUMAnN 3.5 is now available and compatible with MetaPhlAn 4: Announcing HUMAnN 3.5 - #2

That’s awesome - thanks!

Thanks for the update. Looking forward to the update humann version! Any chance you generated a phylogenetic tree from the reference genomes used in the metaphlan4 database?


He had generated the phylogenetic tree with the representative genome of all the SGB present in the database: MetaPhlAn/mpa_vJan21_CHOCOPhlAnSGB_202103.nwk at master · biobakery/MetaPhlAn · GitHub