IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-47155-1.html
   My bibliography  Save this article

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

Author

Listed:
  • Ernestina Hauptfeld

    (Utrecht University)

  • Nikolaos Pappas

    (Utrecht University)

  • Sandra Iwaarden

    (Utrecht University)

  • Basten L. Snoek

    (Utrecht University)

  • Andrea Aldas-Vargas

    (Wageningen University & Research)

  • Bas E. Dutilh

    (Utrecht University
    Friedrich Schiller University)

  • F. A. Bastiaan Meijenfeldt

    (Utrecht University
    NIOZ Royal Netherlands Institute for Sea Research)

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.

Suggested Citation

  • Ernestina Hauptfeld & Nikolaos Pappas & Sandra Iwaarden & Basten L. Snoek & Andrea Aldas-Vargas & Bas E. Dutilh & F. A. Bastiaan Meijenfeldt, 2024. "Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47155-1
    DOI: 10.1038/s41467-024-47155-1
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-47155-1
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-47155-1?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Junjie Qin & Ruiqiang Li & Jeroen Raes & Manimozhiyan Arumugam & Kristoffer Solvsten Burgdorf & Chaysavanh Manichanh & Trine Nielsen & Nicolas Pons & Florence Levenez & Takuji Yamada & Daniel R. Mende, 2010. "A human gut microbial gene catalogue established by metagenomic sequencing," Nature, Nature, vol. 464(7285), pages 59-65, March.
    2. Howard Ochman & Jeffrey G. Lawrence & Eduardo A. Groisman, 2000. "Lateral gene transfer and the nature of bacterial innovation," Nature, Nature, vol. 405(6784), pages 299-304, May.
    3. Peter Menzel & Kim Lee Ng & Anders Krogh, 2016. "Fast and sensitive taxonomic classification for metagenomics with Kaiju," Nature Communications, Nature, vol. 7(1), pages 1-9, September.
    4. Wickham, Hadley, 2007. "Reshaping Data with the reshape Package," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 21(i12).
    5. Alessio Milanese & Daniel R Mende & Lucas Paoli & Guillem Salazar & Hans-Joachim Ruscheweyh & Miguelangel Cuenca & Pascal Hingamp & Renato Alves & Paul I Costea & Luis Pedro Coelho & Thomas S. B. Schm, 2019. "Microbial abundance, activity and population genomic profiling with mOTUs2," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    6. Karthik Anantharaman & Christopher T. Brown & Laura A. Hug & Itai Sharon & Cindy J. Castelle & Alexander J. Probst & Brian C. Thomas & Andrea Singh & Michael J. Wilkins & Ulas Karaoz & Eoin L. Brodie , 2016. "Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system," Nature Communications, Nature, vol. 7(1), pages 1-11, December.
    7. Mohammad Bahram & Falk Hildebrand & Sofia K. Forslund & Jennifer L. Anderson & Nadejda A. Soudzilovskaia & Peter M. Bodegom & Johan Bengtsson-Palme & Sten Anslan & Luis Pedro Coelho & Helery Harend & , 2018. "Structure and function of the global topsoil microbiome," Nature, Nature, vol. 560(7717), pages 233-237, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Lharbi Dridi & Fernando Altamura & Emmanuel Gonzalez & Olivia Lui & Ryszard Kubinski & Reilly Pidgeon & Adrian Montagut & Jasmine Chong & Jianguo Xia & Corinne F. Maurice & Bastien Castagner, 2023. "Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Fiona B. Tamburini & Dylan Maghini & Ovokeraye H. Oduaran & Ryan Brewster & Michaella R. Hulley & Venesa Sahibdeen & Shane A. Norris & Stephen Tollman & Kathleen Kahn & Ryan G. Wagner & Alisha N. Wade, 2022. "Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    3. Cong Wang & Qing-Yi Yu & Niu-Niu Ji & Yong Zheng & John W. Taylor & Liang-Dong Guo & Cheng Gao, 2023. "Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    4. Augustinus, Benno A. & Blum, Moshe & Citterio, Sandra & Gentili, Rodolfo & Helman, David & Nestel, David & Schaffner, Urs & Müller-Schärer, Heinz & Lensky, Itamar M., 2022. "Ground-truthing predictions of a demographic model driven by land surface temperatures with a weed biocontrol cage experiment," Ecological Modelling, Elsevier, vol. 466(C).
    5. Qianqian Su & Jie Li & Jingui Wang & Gang Li & Yang Sun & Xiaoqin Liu & Lan Luo & Xinrui Wang & Guilong Zhang, 2025. "Available Nitrogen as the Determinant of Variability in Soil Microbial Communities Throughout Lycium chinense Growth Zones in the Qaidam Basin, Qinghai, China," Agriculture, MDPI, vol. 15(5), pages 1-22, February.
    6. Hu Liao & Hu Li & Chen-Song Duan & Xin-Yuan Zhou & Qiu-Ping Luo & Xin-Li An & Yong-Guan Zhu & Jian-Qiang Su, 2022. "Response of soil viral communities to land use changes," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Aletheia Atzinger & Jeffrey G Lawrence, 2020. "Selection for ancient periodic motifs that do not impart DNA bending," PLOS Genetics, Public Library of Science, vol. 16(10), pages 1-25, October.
    8. Miller, Christine M.F. & Waterhouse, Hannah & Harter, Thomas & Fadel, James G. & Meyer, Deanne, 2020. "Quantifying the uncertainty in nitrogen application and groundwater nitrate leaching in manure based cropping systems," Agricultural Systems, Elsevier, vol. 184(C).
    9. Wen Zhao & Yali Yin & Shixiong Li & Jingjing Liu & Yiling Dong & Shifeng Su, 2022. "Soil Microbial Community Varied with Vegetation Types on a Small Regional Scale of the Qilian Mountains," Sustainability, MDPI, vol. 14(13), pages 1-15, June.
    10. Kelly J. Whaley-Martin & Lin-Xing Chen & Tara Colenbrander Nelson & Jennifer Gordon & Rose Kantor & Lauren E. Twible & Stephanie Marshall & Sam McGarry & Laura Rossi & Benoit Bessette & Christian Baro, 2023. "O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    11. Ashwag Shami & Rewaa S. Jalal & Ruba A. Ashy & Haneen W. Abuauf & Lina Baz & Mohammed Y. Refai & Aminah A. Barqawi & Hanadi M. Baeissa & Manal A. Tashkandi & Sahar Alshareef & Aala A. Abulfaraj, 2022. "Use of Metagenomic Whole Genome Shotgun Sequencing Data in Taxonomic Assignment of Dipterygium glaucum Rhizosphere and Surrounding Bulk Soil Microbiomes, and Their Response to Watering," Sustainability, MDPI, vol. 14(14), pages 1-21, July.
    12. Sean McKenzie & Hilary Parkinson & Jane Mangold & Mary Burrows & Selena Ahmed & Fabian Menalled, 2018. "Perceptions, Experiences, and Priorities Supporting Agroecosystem Management Decisions Differ among Agricultural Producers, Consultants, and Researchers," Sustainability, MDPI, vol. 10(11), pages 1-19, November.
    13. Ernest D. Osburn & Steven G. McBride & Mohammad Bahram & Michael S. Strickland, 2024. "Global patterns in the growth potential of soil bacterial communities," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    14. Amanda Sörensen Ristinmaa & Albert Tafur Rangel & Alexander Idström & Sebastian Valenzuela & Eduard J. Kerkhoven & Phillip B. Pope & Merima Hasani & Johan Larsbrink, 2023. "Resin acids play key roles in shaping microbial communities during degradation of spruce bark," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    15. Simon A. Schroeter & Alice May Orme & Katharina Lehmann & Robert Lehmann & Narendrakumar M. Chaudhari & Kirsten Küsel & He Wang & Anke Hildebrandt & Kai Uwe Totsche & Susan Trumbore & Gerd Gleixner, 2025. "Hydroclimatic extremes threaten groundwater quality and stability," Nature Communications, Nature, vol. 16(1), pages 1-9, December.
    16. Dong Zhao & Huping Hou & Haiya Liu & Chen Wang & Zhongyi Ding & Jinting Xiong, 2023. "Microbial Community Structure and Predictive Functional Analysis in Reclaimed Soil with Different Vegetation Types: The Example of the Xiaoyi Mine Waste Dump in Shanxi," Land, MDPI, vol. 12(2), pages 1-14, February.
    17. C. J. Torrecilla-Salinas & O. Troyer & M. J. Escalona & M. Mejías, 2019. "A Delphi-based expert judgment method applied to the validation of a mature Agile framework for Web development projects," Information Technology and Management, Springer, vol. 20(1), pages 9-40, March.
    18. Priyanga Dilini Talagala & Rob J Hyndman & Kate Smith-Miles & Sevvandi Kandanaarachchi & Mario A Munoz, 2018. "Anomaly detection in streaming nonstationary temporal data," Monash Econometrics and Business Statistics Working Papers 4/18, Monash University, Department of Econometrics and Business Statistics.
    19. Thelma Dede Baddoo & Zhijia Li & Yiqing Guan & Kenneth Rodolphe Chabi Boni & Isaac Kwesi Nooni, 2020. "Data-Driven Modeling and the Influence of Objective Function Selection on Model Performance in Limited Data Regions," IJERPH, MDPI, vol. 17(11), pages 1-26, June.
    20. S. Emil Ruff & Pauline Humez & Isabella Hrabe Angelis & Muhe Diao & Michael Nightingale & Sara Cho & Liam Connors & Olukayode O. Kuloyo & Alan Seltzer & Samuel Bowman & Scott D. Wankel & Cynthia N. Mc, 2023. "Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems," Nature Communications, Nature, vol. 14(1), pages 1-17, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47155-1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.