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CITATION.cff
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cff-version: 1.2.0
message: If you use this software, please cite it as below.
title: 'Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments'
doi: 10.1186/s40168-022-01410-z
authors:
- given-names: Hans-Joachim
family-names: Ruscheweyh
affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
orcid: https://orcid.org/0000-0001-7473-6086
- given-names: Alessio
family-names: Milanese
affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
orcid: https://orcid.org/0000-0002-7050-2239
- given-names: Lucas
family-names: Paoli
affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
orcid: https://orcid.org/0000-0003-0771-8309
- given-names: Nicolai
family-names: Karcher
affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
orcid: https://orcid.org/0000-0001-7894-8182
- given-names: Quentin
family-names: Clayssen
affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
orcid: https://orcid.org/0000-0002-2574-073X
- given-names: Marisa Isabell
family-names: Keller
affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
orcid: https://orcid.org/0000-0001-6831-4557
- given-names: Jakob
family-names: Wirbel
affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
orcid: https://orcid.org/0000-0002-4073-3562
- given-names: Peer
family-names: Bork
affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
& Max Delbrück Centre for Molecular Medicine, Berlin, Germany
& Molecular Medicine Partnership Unit, Heidelberg, Germany
& Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
orcid: https://orcid.org/0000-0002-2627-833X
- given-names: Daniel R.
family-names: Mende
affiliation: Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
orcid: https://orcid.org/0000-0001-6831-4557
- given-names: Georg
family-names: Zeller
affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
orcid: https://orcid.org/0000-0003-1429-7485
- given-names: Sunagawa
family-names: Shinichi
affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
orcid: https://orcid.org/0000-0003-3065-0314
version: 3.0.3
date-released: 2022-07-13
repository-code: https://github.com/motu-tool/mOTUs
license: GNU General Public License v3.0
keywords:
- "Metagenomics"
- "Microbiome"
- "Software"
preferred-citation:
type: article
authors:
- given-names: Hans-Joachim
family-names: Ruscheweyh
affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
orcid: https://orcid.org/0000-0001-7473-6086
- given-names: Alessio
family-names: Milanese
affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
orcid: https://orcid.org/0000-0002-7050-2239
- given-names: Lucas
family-names: Paoli
affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
orcid: https://orcid.org/0000-0003-0771-8309
- given-names: Nicolai
family-names: Karcher
affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
orcid: https://orcid.org/0000-0001-7894-8182
- given-names: Quentin
family-names: Clayssen
affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
orcid: https://orcid.org/0000-0002-2574-073X
- given-names: Marisa Isabell
family-names: Keller
affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
orcid: https://orcid.org/0000-0001-6831-4557
- given-names: Jakob
family-names: Wirbel
affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
orcid: https://orcid.org/0000-0002-4073-3562
- given-names: Peer
family-names: Bork
affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
& Max Delbrück Centre for Molecular Medicine, Berlin, Germany
& Molecular Medicine Partnership Unit, Heidelberg, Germany
& Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
orcid: https://orcid.org/0000-0002-2627-833X
- given-names: Daniel R.
family-names: Mende
affiliation: Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
orcid: https://orcid.org/0000-0001-6831-4557
- given-names: Georg
family-names: Zeller
affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
orcid: https://orcid.org/0000-0003-1429-7485
- given-names: Sunagawa
family-names: Shinichi
affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
orcid: https://orcid.org/0000-0003-3065-0314
doi: "10.1186/s40168-022-01410-z"
journal: "Microbiome"
month: 12
year: 2022
title: "Microbial abundance, activity and population genomic profiling with mOTUs2"
abstract: 'Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify
the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data
generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of
isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not
been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during
taxonomic profiling, particularly in samples from underexplored environments. To address this issue,
we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling
of metagenomes. As such, it supports the identification and quantification of both “known” and “unknown”
species based on a set of select marker genes.
We present mOTUs3, a command line tool that enables the profiling of metagenomes for >33,000 species-level
operational taxonomic units. To achieve this, we leveraged the reconstruction of >600,000 draft genomes,
most of which are metagenome-assembled genomes (MAGs), from diverse microbiomes, including soil,
freshwater systems, and the gastrointestinal tract of ruminants and other animals,
which we found to be underrepresented by reference genomes. Overall, two thirds of all species-level taxa
\lacked a reference genome. The cumulative relative abundance of these newly included taxa was low in
well-studied microbiomes, such as the human body sites (6–11%). By contrast, they accounted for
substantial proportions (ocean, freshwater, soil: 43–63%) or even the majority (pig, fish, cattle: 60–80%)
of the relative abundance across diverse non-human-associated microbiomes.
Using community-developed benchmarks and datasets, we found mOTUs3 to be more accurate than other
methods and to be more congruent with 16S rRNA gene-based methods for taxonomic profiling.
Furthermore, we demonstrate that mOTUs3 increases the resolution of well-known microbial groups
into species-level taxa and helps identify new differentially abundant taxa in comparative metagenomic studies.
We developed mOTUs3 to enable accurate species-level profiling of metagenomes. Compared to other methods,
it provides a more comprehensive view of prokaryotic community diversity, in particular for currently
underexplored microbiomes. To facilitate comparative analyses by the research community, it is released
with >11,000 precomputed profiles for publicly available metagenomes and is
freely available at: https://github.com/motu-tool/mOTUs.'