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)
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.
Miniconda
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-forgeIf 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 mOTUs4After installation, you can test whether the tool was installed correctly by executing:
$ motus --helpNote 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
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.
$ motus profileProgram: 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]
$ motus map_taxProgram: 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)
$ motus calc_mgcProgram: 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 calc_mgc command takes a file storing the alignments of sequencing reads
to the mOTUs marker gene database and calculates marker gene cluster abundances.
Usage:
motus calc_mgc -i FILE -o FILE [options]
Input options:
-i, --input-file FILE
Path to BAM file generated after running the motus map_tax command [required]
Output options:
-o, --output-file FILE
Output file name [required]
Algorithm options:
-l, --alignment-length INT
Minimum length of the alignment (bp) (default: 75)
$ motus calc_motuProgram: 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 calc_motu command takes a file containing marker gene cluster
abundances and generates a taxonomic profile.
Usage:
motus calc_motu -i FILE -o FILE [options]
Input options:
-i, --input-file FILE
MGC abundance table generated by the calc_mgc command [required]
-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)
-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]$ motus mergeProgram: 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 merge command takes multiple profiles produced after running the
profile command and combines them into a single table.
Usage:
motus merge -i FILE [FILE ...] -o FILE
Input options:
-i, --input-files FILE [FILE ...]
A list of mOTUs profile files or a text file containing the list of profile
files to be merged, with one line per file [required]
Output options:
-o, --output-file FILE
Output file name [required]
$ motus downloadMGDBProgram: 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 downloadMGDB command downloads the marker gene reference database used
by the profile and map_tax commands.
Usage:
motus downloadMGDB [options]
Options:
-f, --force
Force download even when database is already present
$ motus classifyProgram: 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 classify command takes a list of genome sequence files as input and
assigns these genomes to existing mOTUs in the database.
Usage:
motus classify -i FILE -o FILE [options]
Input options:
-i, --input-file FILE
Text file listing genome sequence files in fastA(.gz) format to classify.
One line per genome file [required]
Output options:
-o, --output-file FILE
Output file name. Each line contains a genome and its associated mOTU [required]
Algorithm options:
-t, --threads INT
Number of threads (default: 1)
$ motus prep_longProgram: 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 prep_long command takes long-read sequencing data and converts it
into the appropriate input format to be used by the profile and map_tax commands.
Usage:
motus prep_long -i FILE -o FILE [options]
Input options:
-i, --input-file FILE
Long-read sequencing file to convert, can be in fastQ/A(.gz) format [required]
Output options:
-o, --output-file FILE
Output file name. This converted file is ready to be used by motus profile [required]
Algorithm options:
-sl, --splitting-length INT
Target fragment length (in bp) for splitting long reads (default: 300)
-ml, --minimum-length INT
Minimum read length after splitting. Shorter reads are discarded (default: 50)
$ motus downloadProgram: 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 download command downloads listed genome files from mOTUs-db.
Usage:
motus download -i FILE -o PATH [options]
motus download -i STR [STR ...] -o PATH [options]
Input options:
-i, --input-genomes FILE/STR
Can be either a list of genome identifiers separated by spaces or a text file
listing the identifiers of genomes for download. One line per genome. The output of
the motus genomes command can be used as input for this command [required]
Output options:
-o, --output-folder PATH
Path to output folder where the downloaded sequences will be saved [required]
-r, --representatives
Download only sequences from representative genomes.
$ motus genomesProgram: 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 genomes command queries the mOTUs-db based on identifiers, functional,
or taxonomic annotations and returns a list of genomes matching indicated query.
Usage:
motus genomes -i FILE -o FILE [options]
motus genomes -i STR [STR ...] -o FILE [options]
Input options:
-i, --input-queries FILE/STR
Can be either a list of search queries or a text file listing search queries
with one line per query. Queries can be genome or mOTUs identifiers, PFAM, KEGG, EGGNOG,
or GTDB taxonomy names. If the query does not exactly match any database entry,
alternative queries will be suggested [required]
Output options:
-o, --output-file FILE
Output file containing a list of genome identifiers matching search queries and their
annotations as indicated by the -d parameter. This output file can be used as input
for the motus download command [required]
-d, --details STR [STR ...]
List of annotations to report. Choose any combination of [KEGG, PFAM, EGGNOG, TAXONOMY],
for example, -d KEGG PFAM.
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