Announcing MetaPhlAn 4

Microbial community profiling MetaPhlAn
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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 (https://doi.org/10.1101/2022.08.22.504593). 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.
2 Likes
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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!

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

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That’s awesome - thanks!

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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?

Best

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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

1 Like
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Hi @Pierre_Schneeberger , I meet with some problems using metaphlan4: when metaphlan4 finished my jobs, It annotated about 200 species in one sample, and the phylum Proteobacteria account for more than 95% of the total species, which was quiet different with our result got from 16S rRNA sequences. The sample was collected from coastal marine sediment and sequence depth was about 10 Gbp. Thanks for your attention and appreciated for your help.

nohup metaphlan …/…/…/…/05.binning/mud03.2021.01.S.paired.R_1.fastq,…/…/…/…/05.binning/mud03.2021.01.S.paired.R_2.fastq --bowtie2out metagenome_mud03S.bowtie2.bz2
–bowtie2db /home/renyanhu/software/Miniconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases --nproc 64 --input_type fastq -o profiled_metagenome_mud03S.txt &