StrainPhlAn

Strain-level Metagenomic Profiling

What is StrainPhlAn?

StrainPhlAn is a tool for strain-level profiling and tracking of specific microbial species across metagenomic samples. It reconstructs strain-level sequences directly from shotgun metagenomic data and uses phylogenetic analysis to track strains across individuals, time points, or conditions.

StrainPhlAn answers the question: “Are the same strains present across these samples?”

StrainPhlAn is distributed as part of the MetaPhlAn package.

📄 GitHub
📖 Wiki
🗞️ Paper: Truong et al. 2017, Nature Genetics

When to Use StrainPhlAn

Use StrainPhlAn when you want to:

Track whether the same microbial strain is shared between individuals (e.g., mother-infant transmission)
Monitor strain dynamics over time in longitudinal studies
Investigate within-species genetic variation
Identify the source of a specific strain

Installation

StrainPhlAn is bundled with MetaPhlAn:

conda create -n metaphlan -c biobakery metaphlan
conda activate metaphlan

Workflow

StrainPhlAn runs in two main steps after MetaPhlAn profiling:

Step 1: Sample-to-marker extraction

Extract consensus marker sequences from each sample’s MetaPhlAn alignment:

# Run MetaPhlAn saving the SAM alignment
metaphlan sample.fastq.gz \
  --input_type fastq \
  -s sample.sam.bz2 \
  -o sample_profile.txt \
  --nproc 8

# Extract sample markers
sample2markers.py \
  -i sample.sam.bz2 \
  -r marker_db/ \
  -o sample_markers/ \
  -n 8

Step 2: StrainPhlAn tree construction

# Get species-specific markers
extract_markers.py \
  -c s__Eggerthella_lenta \
  -o marker_dir/

# Build the phylogenetic tree
strainphlan \
  -s sample_markers/*.pkl \
  -m marker_dir/s__Eggerthella_lenta.fna \
  -o strainphlan_output/ \
  -n 8 \
  -c s__Eggerthella_lenta

Output Files

File	Contents
`*.tre`	Phylogenetic tree of strain relationships
`*.aln`	Aligned marker sequences
`*.info`	Run statistics and sample information

Tips & Gotchas

Warning

Minimum coverage — StrainPhlAn requires sufficient coverage of the target species in each sample. Samples with very low abundance of the target species will be excluded. The default minimum coverage is 20%.

Tip

Save SAM files from MetaPhlAn by always using the -s flag. Once deleted, you cannot re-extract strain markers without re-running MetaPhlAn.

Tip

Add reference genomes to the tree using the --references option. This allows you to place metagenomic strains relative to known isolates.

strainphlan \
  -s sample_markers/*.pkl \
  -m marker_dir/s__Lactobacillus_reuteri.fna \
  -r reference_genomes/*.fna \
  -o strainphlan_output/ \
  -c s__Lactobacillus_reuteri

--- title: "StrainPhlAn" subtitle: "Strain-level Metagenomic Profiling" --- ## What is StrainPhlAn? **StrainPhlAn** is a tool for strain-level profiling and tracking of specific microbial species across metagenomic samples. It reconstructs strain-level sequences directly from shotgun metagenomic data and uses phylogenetic analysis to track strains across individuals, time points, or conditions. StrainPhlAn answers the question: **"Are the same strains present across these samples?"** StrainPhlAn is distributed as part of the **MetaPhlAn** package. - 📄 [GitHub](https://github.com/biobakery/MetaPhlAn) - 📖 [Wiki](https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-4) - 🗞️ [Paper: Truong et al. 2017, *Nature Genetics*](https://www.nature.com/articles/ng.3802) --- ## When to Use StrainPhlAn Use StrainPhlAn when you want to: - Track whether the same microbial **strain** is shared between individuals (e.g., mother-infant transmission) - Monitor strain dynamics over time in longitudinal studies - Investigate within-species genetic variation - Identify the source of a specific strain --- ## Installation StrainPhlAn is bundled with MetaPhlAn: ```bash conda create -n metaphlan -c biobakery metaphlan conda activate metaphlan ``` --- ## Workflow StrainPhlAn runs in two main steps after MetaPhlAn profiling: ### Step 1: Sample-to-marker extraction Extract consensus marker sequences from each sample's MetaPhlAn alignment: ```bash # Run MetaPhlAn saving the SAM alignment metaphlan sample.fastq.gz \ --input_type fastq \ -s sample.sam.bz2 \ -o sample_profile.txt \ --nproc 8 # Extract sample markers sample2markers.py \ -i sample.sam.bz2 \ -r marker_db/ \ -o sample_markers/ \ -n 8 ``` ### Step 2: StrainPhlAn tree construction ```bash # Get species-specific markers extract_markers.py \ -c s__Eggerthella_lenta \ -o marker_dir/ # Build the phylogenetic tree strainphlan \ -s sample_markers/*.pkl \ -m marker_dir/s__Eggerthella_lenta.fna \ -o strainphlan_output/ \ -n 8 \ -c s__Eggerthella_lenta ``` --- ## Output Files | File | Contents | |------|----------| | `*.tre` | Phylogenetic tree of strain relationships | | `*.aln` | Aligned marker sequences | | `*.info` | Run statistics and sample information | --- ## Tips & Gotchas ::: {.callout-warning} **Minimum coverage** — StrainPhlAn requires sufficient coverage of the target species in each sample. Samples with very low abundance of the target species will be excluded. The default minimum coverage is 20%. ::: ::: {.callout-tip} **Save SAM files** from MetaPhlAn by always using the `-s` flag. Once deleted, you cannot re-extract strain markers without re-running MetaPhlAn. ::: ::: {.callout-tip} **Add reference genomes** to the tree using the `--references` option. This allows you to place metagenomic strains relative to known isolates. ```bash strainphlan \ -s sample_markers/*.pkl \ -m marker_dir/s__Lactobacillus_reuteri.fna \ -r reference_genomes/*.fna \ -o strainphlan_output/ \ -c s__Lactobacillus_reuteri ``` ::: --- ## Further Reading - [StrainPhlAn4 tutorial](https://github.com/biobakery/biobakery/wiki/strainphlan4) - [Truong et al. 2017, *Nature Genetics*](https://www.nature.com/articles/ng.3802) - [Pasolli et al. 2019, *Cell*](https://www.cell.com/cell/fulltext/S0092-8674(19)30001-7)