MAINT Citation update, closes #2

motu-tool · Dec 19, 2022 · 8c78d95 · 8c78d95
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diff --git a/CITATION.cff b/CITATION.cff
@@ -1,76 +1,47 @@
 cff-version: 1.2.0
 message: If you use this software, please cite it as below.
-title: 'Microbial abundance, activity and population genomic profiling with mOTUs2'
-doi: 10.1038/s41467-019-08844-4
+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: Daniel R.
-    family-names: Mende
-    affiliation: Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawaii at Mānoa, Honolulu, United States
-    orcid: https://orcid.org/0000-0001-6831-4557
   - given-names: Lucas
     family-names: Paoli
     affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
-      & Department of Biology, École normale supérieure, Paris, France
     orcid: https://orcid.org/0000-0003-0771-8309
-  - given-names: Guillem
-    family-names: Salazar
-    affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
-    orcid: https://orcid.org/0000-0002-9786-1493
-  - given-names: Miguelangel
-    family-names: Cuenca
+  - 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/0000-0003-3435-9102
-  - given-names: Pascal 
-    family-names: Hingamp
-    affiliation: Aix Marseille Univ, Université de Toulon, Marseille, France
-  - given-names: Renato
-    family-names: Alves
-    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
-    orcid: https://orcid.org/0000-0002-7212-0234
-  - given-names: Paul I.
-    family-names: Costea
-    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
-    orcid: https://orcid.org/0000-0003-1645-3947
-  - given-names: Luis Pedro
-    family-names: Coelho
-    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
-    orcid: https://orcid.org/0000-0002-9280-7885
-  - given-names: Thomas S. B.
-    family-names: Schmidt 
-    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
-    orcid: https://orcid.org/0000-0001-8587-4177
-  - given-names: Alexandre 
-    family-names: Almeida 
-    affiliation: European Molecular Biology Laboratory, 
-      European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK 
-      & Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
-    orcid: https://orcid.org/0000-0001-8803-0893
-  - given-names: Alex L 
-    family-names: Mitchell
-    affiliation: European Molecular Biology Laboratory, 
-      European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
-  - given-names: Robert D.
-    family-names: Finn
-    affiliation: European Molecular Biology Laboratory, 
-      European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
-    orcid: https://orcid.org/0000-0001-8626-2148
-  - given-names: Jaime 
-    family-names: Huerta-Cepas
-    affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
-      & Centro de Biotecnología y Genómica de Plantas, 
-      Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
-    orcid: https://orcid.org/0000-0003-4195-5025
+    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
@@ -91,74 +62,45 @@ keywords:
 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: Daniel R.
-      family-names: Mende
-      affiliation: Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawaii at Mānoa, Honolulu, United States
-      orcid: https://orcid.org/0000-0001-6831-4557
     - given-names: Lucas
       family-names: Paoli
       affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
-        & Department of Biology, École normale supérieure, Paris, France
       orcid: https://orcid.org/0000-0003-0771-8309
-    - given-names: Guillem
-      family-names: Salazar
+    - 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/0000-0002-9786-1493
-    - given-names: Miguelangel
-      family-names: Cuenca
-      affiliation: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
-      orcid: https://orcid.org/0000-0003-3435-9102
-    - given-names: Pascal 
-      family-names: Hingamp
-      affiliation: Aix Marseille Univ, Université de Toulon, Marseille, France
-    - given-names: Renato
-      family-names: Alves
-      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
-      orcid: https://orcid.org/0000-0002-7212-0234
-    - given-names: Paul I.
-      family-names: Costea
-      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
-      orcid: https://orcid.org/0000-0003-1645-3947
-    - given-names: Luis Pedro
-      family-names: Coelho
-      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
-      orcid: https://orcid.org/0000-0002-9280-7885
-    - given-names: Thomas S. B.
-      family-names: Schmidt 
-      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
-      orcid: https://orcid.org/0000-0001-8587-4177
-    - given-names: Alexandre 
-      family-names: Almeida 
-      affiliation: European Molecular Biology Laboratory, 
-        European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK 
-        & Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
-      orcid: https://orcid.org/0000-0001-8803-0893
-    - given-names: Alex L 
-      family-names: Mitchell
-      affiliation: European Molecular Biology Laboratory, 
-        European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
-    - given-names: Robert D.
-      family-names: Finn
-      affiliation: European Molecular Biology Laboratory, 
-        European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
-      orcid: https://orcid.org/0000-0001-8626-2148
-    - given-names: Jaime 
-      family-names: Huerta-Cepas
-      affiliation: European Molecular Biology Laboratory, Heidelberg, Germany
-        & Centro de Biotecnología y Genómica de Plantas, 
-        Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
-      orcid: https://orcid.org/0000-0003-4195-5025
+      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
@@ -167,20 +109,37 @@ preferred-citation:
       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: "10.1038/s41467-019-08844-4"
-  journal: "Nature Communications"
-  month: 3
-  year: 2019
+  doi: "10.1186/s40168-022-01410-z"
+  journal: "Microbiome"
+  month: 12
+  year: 2022
   title: "Microbial abundance, activity and population genomic profiling with mOTUs2"
-  abstract: 'Metagenomic sequencing has greatly improved our ability to profile the composition 
-  of environmental and host-associated microbial communities. However, the dependency of most methods 
-  on reference genomes, which are currently unavailable for a substantial fraction of microbial species, 
-  introduces estimation biases. We present an updated and functionally extended tool 
-  based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based 
-  operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. 
-  As more than 30% of them could not previously be quantified at this taxonomic resolution, 
-  relative abundance estimates based on mOTUs are more accurate compared to other methods. 
-  As a new feature, we show that mOTUs, which are based on essential housekeeping genes, 
-  are demonstrably well-suited for quantification of basal transcriptional activity of community members. 
-  Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, 
-  which allows for comparing microbial strain populations (e.g., across different human body sites).'
+  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.'
diff --git a/README.md b/README.md
@@ -83,21 +83,20 @@ Or analyze the samples using `Metadata` you have on hand!
 # Citation
 If you use this tool, please cite the following paper:
 ```
-@article{Milanese2019-gw,
-  title     = {Microbial abundance, activity and population genomic profiling
-               with mOTUs2},
-  author    = {Milanese, Alessio and Mende, Daniel R and Paoli, Lucas and
-               Salazar, Guillem and Ruscheweyh, Hans-Joachim and Cuenca,
-               Miguelangel and Hingamp, Pascal and Alves, Renato and Costea,
-               Paul I and Coelho, Luis Pedro and Schmidt, Thomas S B and
-               Almeida, Alexandre and Mitchell, Alex L and Finn, Robert D and
-               Huerta-Cepas, Jaime and Bork, Peer and Zeller, Georg and
-               Sunagawa, Shinichi},
-  journal   = {Nat. Commun.},
-  publisher = {Springer Science and Business Media LLC},
-  volume    = {10},
-  number    = {1},
-  pages     = {1014},
-  month     = {mar},
-  year      = {2019},
+@article{Ruscheweyh2022,
+  doi = {10.1186/s40168-022-01410-z},
+  url = {https://doi.org/10.1186/s40168-022-01410-z},
+  year = {2022},
+  month = dec,
+  publisher = {Springer Science and Business Media {LLC}},
+  volume = {10},
+  number = {1},
+  author = {Hans-Joachim Ruscheweyh and Alessio Milanese and Lucas Paoli and 
+            Nicolai Karcher and Quentin Clayssen and Marisa Isabell Keller and 
+            Jakob Wirbel and Peer Bork and Daniel R. Mende and Georg Zeller and 
+            Shinichi Sunagawa},
+  title = {Cultivation-independent genomes greatly expand taxonomic-profiling 
+           capabilities of {mOTUs} across various environments},
+  journal = {Microbiome}
 }
+```
diff --git a/q2_motus/citations.bib b/q2_motus/citations.bib
@@ -1,38 +1,12 @@
-@ARTICLE{Milanese2019-gw,
-  title     = {Microbial abundance, activity and population genomic profiling
-               with mOTUs2},
-  author    = {Milanese, Alessio and Mende, Daniel R and Paoli, Lucas and
-               Salazar, Guillem and Ruscheweyh, Hans-Joachim and Cuenca,
-               Miguelangel and Hingamp, Pascal and Alves, Renato and Costea,
-               Paul I and Coelho, Luis Pedro and Schmidt, Thomas S B and
-               Almeida, Alexandre and Mitchell, Alex L and Finn, Robert D and
-               Huerta-Cepas, Jaime and Bork, Peer and Zeller, Georg and
-               Sunagawa, Shinichi},
-  abstract  = {Metagenomic sequencing has greatly improved our ability to
-               profile the composition of environmental and host-associated
-               microbial communities. However, the dependency of most methods
-               on reference genomes, which are currently unavailable for a
-               substantial fraction of microbial species, introduces estimation
-               biases. We present an updated and functionally extended tool
-               based on universal (i.e., reference-independent), phylogenetic
-               marker gene (MG)-based operational taxonomic units (mOTUs)
-               enabling the profiling of >7700 microbial species. As more than
-               30\% of them could not previously be quantified at this
-               taxonomic resolution, relative abundance estimates based on
-               mOTUs are more accurate compared to other methods. As a new
-               feature, we show that mOTUs, which are based on essential
-               housekeeping genes, are demonstrably well-suited for
-               quantification of basal transcriptional activity of community
-               members. Furthermore, single nucleotide variation profiles
-               estimated using mOTUs reflect those from whole genomes, which
-               allows for comparing microbial strain populations (e.g., across
-               different human body sites).},
-  journal   = {Nat. Commun.},
-  publisher = {Springer Science and Business Media LLC},
-  volume    = {10},
-  number    = {1},
-  pages     = {1014},
-  month     = {mar},
-  year      = {2019},
-  language  = {en}
-}
+@article{Ruscheweyh2022,
+  doi = {10.1186/s40168-022-01410-z},
+  url = {https://doi.org/10.1186/s40168-022-01410-z},
+  year = {2022},
+  month = dec,
+  publisher = {Springer Science and Business Media {LLC}},
+  volume = {10},
+  number = {1},
+  author = {Hans-Joachim Ruscheweyh and Alessio Milanese and Lucas Paoli and Nicolai Karcher and Quentin Clayssen and Marisa Isabell Keller and Jakob Wirbel and Peer Bork and Daniel R. Mende and Georg Zeller and Shinichi Sunagawa},
+  title = {Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of {mOTUs} across various environments},
+  journal = {Microbiome}
+}