Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Ernestina Hauptfeld; Nikolaos Pappas; Sandra van Iwaarden; Basten L. Snoek; Andrea Aldas-Vargas; Bas E. Dutilh; F. A.Bastiaan von Meijenfeldt

doi:10.1038/s41467-024-47155-1

Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Ernestina Hauptfeld
, Nikolaos Pappas
, Sandra van Iwaarden
, Basten L. Snoek
, Andrea Aldas-Vargas
, Bas E. Dutilh^*
, F. A.Bastiaan von Meijenfeldt^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.

Original language	English
Article number	3373
Number of pages	12
Journal	Nature Communications
Volume	15
Issue number	1
DOIs	https://doi.org/10.1038/s41467-024-47155-1
Publication status	Published - 20 Apr 2024

Bibliographical note

Publisher Copyright:
© The Author(s) 2024.

Funding

This work was supported by the European Research Council (Consolidator Grant 865694: DiversiPHI to B.E.D.), the Deutsche Forschungsgemeinschaft under Germany\u2019s Excellence Strategy (EXC 2051; Project-ID 390713860 to B.E.D.) and the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt Professorship founded by the German Federal Ministry of Education and Research (to B.E.D.). We thank Nora B. Sutton and her group for providing us with groundwater metagenomes to use for this manuscript. We thank Jan Kees van Amerongen for critical technical support. We thank the members of TBB at the University of Utrecht for their valuable input on the text.

Funders	Funder number
Bundesministerium für Bildung und Forschung
Universiteit Utrecht
Alexander von Humboldt-Stiftung
European Research Council	865694
Deutsche Forschungsgemeinschaft	390713860

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title = "Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes",

abstract = "Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT\_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.",

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AU - Aldas-Vargas, Andrea

AU - Dutilh, Bas E.

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Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Abstract

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