MOTUs
motus - a tool for marker gene-based OTU (mOTU) profiling
Install / Use
/learn @motu-tool/MOTUsREADME
mOTUs profiler
The mOTU profiler is a computational tool that estimates taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.
The current version of the mOTUs profiler is built on top of the genomic mOTUs database (motus-db) which is constructed from 919K isolate and single cell-amplified (SAGs) genomes and 2.83M metagenome-assembled genomes (MAGs) generated from over 117K metagenomic samples spanning diverse microbiomes, which include (in addition to the human and ocean microbiome) soil, freshwater and gastrointestinal tract microbiomes of ruminants and other animals, environments we found to be greatly underrepresented by reference genomes.
In the current version, 124,295 species-level taxonomic units (mOTUs) were constructed using sequences of 10 single-copy marker genes recovered from these genomes. 30,256 mOTUs are represented by an isolate genome, whereas 94,039 mOTUs are represented by MAGs only.
If you use the mOTUs profiler, please cite:
Reference genome-independent taxonomic profiling of microbiomes with mOTUs3
Hans-Joachim Ruscheweyh* , Alessio Milanese*, Lucas Paoli, Nicolai Karcher, Quentin Clayssen, Marisa Isabell Metzger, Jakob Wirbel, Peer Bork, Daniel R. Mende, Georg Zeller# & Shinichi Sunagawa#
Microbiome (2022)
If you use the mOTUs database, please cite:
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
Marija Dmitrijeva* , Hans-Joachim Ruscheweyh* , Lilith Feer , Kang Li , Samuel Miravet-Verde , Anna Sintsova , Daniel R Mende , Georg Zeller , Shinichi Sunagawa#
Nucleic Acids Research (2025)
📦 Installation
The mOTUs profiler, written in Python 3 (>=3.12), can be executed on a 64-bit Linux or MacOS system. However, there are external dependencies that need to be pre-installed. These dependencies can be manually installed or, more conveniently, using the conda package manager.
Installation with Conda
<details> <summary>Miniconda</summary>The installation using the conda package manager is generally preferable, as it encapsulates the entire installation process into a single command once conda is installed. Execute the following command to install conda:
$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ sh Miniconda3-latest-Linux-x86_64.sh
$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
If working on a MacOS system, the download link has to be replaced by: https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh.
mOTUs is available as a package in bioconda and can be installed in an isolated environment:
$ conda create -n mOTUs4 motus
$ conda activate mOTUs4
🚀 Usage
After installation, you can test whether the tool was installed correctly by executing:
$ motus --help
Note Currently the command to execute mOTUs is python motus/motus.py which will be replaced with motus once the tool is installed via pip.
Program: motus - a tool for marker gene-based OTU (mOTU) profiling
Version: 4.0.4
References:
Profiler: Ruscheweyh, Milanese et al. Cultivation-independent genomes greatly expand
taxonomic-profiling capabilities of mOTUs across various environments. Microbiome (2022).
doi: https://doi.org/10.1186/s40168-022-01410-z
Database: Dmitrijeva, Ruscheweyh et al. The mOTUs online database provides web-accessible
genomic context to taxonomic profiling of microbial communities. Nucleic Acids Research (2025).
doi: https://doi.org/10.1093/nar/gkae1004
Usage:
motus <command> [options]
Commands:
-- Taxonomic profiling
profile Perform taxonomic profiling (map_tax + calc_mgc + calc_motu) in a single step
map_tax Map reads to the marker gene database
calc_mgc Calculate marker gene cluster (MGC) abundance
calc_motu Summarize MGC abundances into a mOTU profile
-- Tool utilities
downloadMGDB Download the mOTUs marker gene database
merge Merge multiple taxonomic profiling results into one table
classify Classify user genomes into mOTUs
prep_long Prepare long reads to be profiled by mOTUs
-- Genome accession
genomes Search the mOTUs-db by keyword (taxonomic, functional)
download Download sequence files from mOTUs-db
Type motus <command> to print the help menu for a specific command
Commands
The profile function in mOTUs is the main function that executes map_tax, calc_mgc, and calc_motu in sequence. It takes short read metagenomic sequencing data as input and generates a taxonomic profile.
Helper functions include download, which provides users with programmatic access to the ~4 million genomes in the motus-db; downloadMGDB, which downloads the marker gene database of mOTUs; merge, which merges multiple taxonomic profiles; and classify, which assigns user-submitted genomes to existing mOTUs.
Profile
$ motus profile
Program: motus - a tool for marker gene-based OTU (mOTU) profiling
Version: 4.0.4
References:
Profiler: Ruscheweyh, Milanese et al. Cultivation-independent genomes greatly expand
taxonomic-profiling capabilities of mOTUs across various environments. Microbiome (2022).
doi: https://doi.org/10.1186/s40168-022-01410-z
Database: Dmitrijeva, Ruscheweyh et al. The mOTUs online database provides web-accessible
genomic context to taxonomic profiling of microbial communities. Nucleic Acids Research (2025).
doi: https://doi.org/10.1093/nar/gkae1004
Summary:
The profile command in mOTUs is the main function that executes map_tax, calc_mgc,
and calc_motu in sequence. It takes short read metagenomic sequencing data as input
and generates a taxonomic profile.
Usage:
motus profile -f FILE [FILE ...] -r FILE [FILE ...] -s FILE [FILE ...] -o FILE [options]
motus profile -f FILE [FILE ...] -r FILE [FILE ...] -o FILE [options]
motus profile -s FILE [FILE ...] -o FILE [options]
Input options:
-f, --forward FILE [FILE ...]
Input file(s) for reads in forward orientation, fastQ/A(.gz)-formatted
-r, --reverse FILE [FILE ...]
Input file(s) for reads in reverse orientation, fastQ/A(.gz)-formatted
-s, --single FILE [FILE ...]
Input file(s) for unpaired reads, fastQ/A(.gz)-formatted
-n, --sample-name STR
Sample name (default: 'unnamed sample')
Output options:
-o, --output-file FILE
Output file name [required]
Algorithm options:
-g, --marker-genes INT
Required number of marker genes for a mOTU to be called present:
1=higher recall, 6=higher precision, 10=maximum (default: 3)
-l, --alignment-length INT
Minimum length of the alignment (bp) (default: 75)
-t, --threads INT
Number of threads (default: 1)
-y, --counting-mode STR
Which scale the abundances are reported in (default: INSERT_SCALED)
Choices: [INSERT_RAW, INSERT_NORM, INSERT_SCALED, BASE_RAW, BASE_NORM]
Map Tax
$ motus map_tax
Program: motus - a tool for marker gene-based OTU (mOTU) profiling
Version: 4.0.4
References:
Profiler: Ruscheweyh, Milanese et al. Cultivation-independent genomes greatly expand
taxonomic-profiling capabilities of mOTUs across various environments. Microbiome (2022).
doi: https://doi.org/10.1186/s40168-022-01410-z
Database: Dmitrijeva, Ruscheweyh et al. The mOTUs online database provides web-accessible
genomic context to taxonomic profiling of microbial communities. Nucleic Acids Research (2025).
doi: https://doi.org/10.1093/nar/gkae1004
Summary:
The map_tax command takes short read metagenomic sequencing data as input and
maps reads to the mOTUs marker gene database.
Usage:
motus map_tax -f FILE [FILE ...] -r FILE [FILE ...] -s FILE [FILE ...] -o FILE [options]
motus map_tax -f FILE [FILE ...] -r FILE [FILE ...] -o FILE [options]
motus map_tax -s FILE [FILE ...] -o FILE [options]
Input options:
-f, --forward FILE [FILE ...]
Input file(s) for reads in forward orientation, fastQ/A(.gz)-formatted
-r, --reverse FILE [FILE ...]
Input file(s) for reads in reverse orientation, fastQ/A(.gz)-formatted
-s, --single FILE [FILE ...]
Input file(s) for unpaired reads, fastQ/A(.gz)-formatted
Output options:
-o, --output-file FILE
Output file name [required]
Algorithm options:
-l, --alignment-length INT
Minimum length of the alignment (bp) (default: 75)
-t, --threads INT
Number of threads (default: 1)
Calc MGC
$ motus calc_mgc
Program: motus - a tool for marker gene-based OTU (mOTU) profiling
Version: 4.0.4
References:
Prof
