MetaPhlAn

Metagenomic Phylogenetic Analysis

What is MetaPhlAn?

MetaPhlAn (Metagenomic Phylogenetic Analysis) is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It uses a database of clade-specific marker genes to rapidly and accurately determine the taxonomic composition of a metagenome.

MetaPhlAn answers the question: “Who is in this community and at what abundance?”

Current version: MetaPhlAn 4

When to Use MetaPhlAn

Use MetaPhlAn when you have shotgun metagenomic reads and you want to:

  • Determine which species/strains are present
  • Get relative abundance estimates at multiple taxonomic levels
  • Detect novel or uncharacterized species
  • Feed taxonomic profiles downstream into HUMAnN or StrainPhlAn
Note

MetaPhlAn works only with shotgun metagenomics data. For 16S amplicon data, use QIIME2 or DADA2 for taxonomic profiling.

Installation

Via pip

pip install metaphlan

Database

Download the marker gene database:

metaphlan --install --index mpa_vOct22_CHOCOPhlAnSGB_202212

Basic Usage

metaphlan sample.fastq.gz \
  --input_type fastq \
  --nproc 8 \
  -o sample_profile.txt

Paired-end reads

metaphlan sample_R1.fastq.gz,sample_R2.fastq.gz \
  --input_type fastq \
  --nproc 8 \
  -o sample_profile.txt

Key options

Option Description
--input_type Input type: fastq, fasta, bowtie2out, sam
--nproc Number of CPU threads
-o Output profile file
--bowtie2out Save Bowtie2 output for reuse
--tax_lev Taxonomic level to profile (a=all, k=kingdom, p=phylum, …)
--add_viruses Include viral organisms
--unknown_estimation Estimate fraction of unknown organisms

Output Files

The main output is a tab-separated profile file with columns:

Column Description
#clade_name Full taxonomic lineage string
NCBI_tax_id NCBI taxonomy identifier
relative_abundance Relative abundance (0–100%)
additional_species Species grouped under this clade

Merging multiple samples

merge_metaphlan_tables.py \
  sample1_profile.txt \
  sample2_profile.txt \
  sample3_profile.txt \
  -o merged_profiles.txt

Taxonomic Levels

MetaPhlAn profiles at all standard taxonomic levels:

Prefix Level
k__ Kingdom
p__ Phylum
c__ Class
o__ Order
f__ Family
g__ Genus
s__ Species
t__ Strain/SGB

Tips & Gotchas

Tip

Reuse Bowtie2 alignments — Save the --bowtie2out file and reuse it with --input_type bowtie2out if you need to re-profile without re-aligning.

Warning

Human/host reads should be removed before running MetaPhlAn. Use KneadData (also from Biobakery) for host decontamination.

Tip

MetaPhlAn4 introduced SGBs (Species-level Genome Bins), which allows profiling of novel uncharacterized species not in reference databases.

Further Reading