IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-31654-0.html
   My bibliography  Save this article

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination

Author

Listed:
  • Omary Mzava

    (Cornell University)

  • Alexandre Pellan Cheng

    (Cornell University)

  • Adrienne Chang

    (Cornell University)

  • Sami Smalling

    (Cornell University)

  • Liz-Audrey Kounatse Djomnang

    (Cornell University)

  • Joan Sesing Lenz

    (Cornell University)

  • Randy Longman

    (Weill Cornell Medicine, Jill Roberts Center for IBD)

  • Amy Steadman

    (Global Health Labs)

  • Luis G. Gómez-Escobar

    (Weill Cornell Medicine)

  • Edward J. Schenck

    (Weill Cornell Medicine)

  • Mirella Salvatore

    (Weill Cornell Medicine)

  • Michael J. Satlin

    (Weill Cornell Medicine)

  • Manikkam Suthanthiran

    (Weill Cornell Medicine
    New York Presbyterian Hospital–Weill Cornell Medical Center)

  • John R. Lee

    (Weill Cornell Medicine)

  • Christopher E. Mason

    (Weill Cornell Medical College
    WorldQuant Initiative for Quantitative Prediction)

  • Darshana Dadhania

    (Weill Cornell Medicine
    New York Presbyterian Hospital–Weill Cornell Medical Center)

  • Iwijn De Vlaminck

    (Cornell University)

Abstract

Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we present Sample-Intrinsic microbial DNA Found by Tagging and sequencing (SIFT-seq) a metagenomic sequencing assay that is robust against environmental DNA contamination introduced during sample preparation. The core idea of SIFT-seq is to tag the DNA in the sample prior to DNA isolation and library preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. We applied SIFT-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial DNA signatures of sepsis and inflammatory bowel disease in blood.

Suggested Citation

  • Omary Mzava & Alexandre Pellan Cheng & Adrienne Chang & Sami Smalling & Liz-Audrey Kounatse Djomnang & Joan Sesing Lenz & Randy Longman & Amy Steadman & Luis G. Gómez-Escobar & Edward J. Schenck & Mir, 2022. "A metagenomic DNA sequencing assay that is robust against environmental DNA contamination," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31654-0
    DOI: 10.1038/s41467-022-31654-0
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-31654-0
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-31654-0?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. Philip Burnham & Darshana Dadhania & Michael Heyang & Fanny Chen & Lars F. Westblade & Manikkam Suthanthiran & John Richard Lee & Iwijn De Vlaminck, 2018. "Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    2. 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.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Xian Sun & Dongshuo Yin & Fei Qin & Hongfeng Yu & Wanxuan Lu & Fanglong Yao & Qibin He & Xingliang Huang & Zhiyuan Yan & Peijin Wang & Chubo Deng & Nayu Liu & Yiran Yang & Wei Liang & Ruiping Wang & C, 2023. "Revealing influencing factors on global waste distribution via deep-learning based dumpsite detection from satellite imagery," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

    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. 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.
    2. Peng Liu & Jessica Ewald & Zhiqiang Pang & Elena Legrand & Yeon Seon Jeon & Jonathan Sangiovanni & Orcun Hacariz & Guangyan Zhou & Jessica A. Head & Niladri Basu & Jianguo Xia, 2023. "ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    3. Wei Ding & Shougang Wang & Peng Qin & Shen Fan & Xiaoyan Su & Peiyan Cai & Jie Lu & Han Cui & Meng Wang & Yi Shu & Yongming Wang & Hui-Hui Fu & Yu-Zhong Zhang & Yong-Xin Li & Weipeng Zhang, 2023. "Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Daniela S. Aliaga Goltsman & Lisa M. Alexander & Jyun-Liang Lin & Rodrigo Fregoso Ocampo & Benjamin Freeman & Rebecca C. Lamothe & Andres Perez Rivas & Morayma M. Temoche-Diaz & Shailaja Chadha & Nata, 2022. "Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. 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.
    6. J. L. Rolando & M. Kolton & T. Song & Y. Liu & P. Pinamang & R. Conrad & J. T. Morris & K. T. Konstantinidis & J. E. Kostka, 2024. "Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    7. Nailil Husna & Tatsuya Aiba & Shin-Ichiro Fujita & Yoshika Saito & Dai Shiba & Takashi Kudo & Satoru Takahashi & Satoshi Furukawa & Masafumi Muratani, 2024. "Release of CD36-associated cell-free mitochondrial DNA and RNA as a hallmark of space environment response," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    8. 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.
    9. Alexa M. Nicolas & Ella T. Sieradzki & Jennifer Pett-Ridge & Jillian F. Banfield & Michiko E. Taga & Mary K. Firestone & Steven J. Blazewicz, 2023. "A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    10. Márk Szuhaj & Roland Wirth & Zoltán Bagi & Gergely Maróti & Gábor Rákhely & Kornél L. Kovács, 2021. "Development of Stable Mixed Microbiota for High Yield Power to Methane Conversion," Energies, MDPI, vol. 14(21), pages 1-17, November.
    11. Louise B. Sennett & Constance A. Roco & Natalie Y. N. Lim & Joseph B. Yavitt & Peter Dörsch & Lars R. Bakken & James P. Shapleigh & Åsa Frostegård, 2024. "Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N2O emissions," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    12. Manoshi S. Datta & Idan Yelin & Ori Hochwald & Imad Kassis & Liron Borenstein-Levin & Amir Kugelman & Roy Kishony, 2021. "Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    13. Nancy O. Nou & Jonathan K. Covington & Dengxun Lai & Xavier Mayali & Cale O. Seymour & Juliet Johnston & Jian-Yu Jiao & Steffen Buessecker & Damon Mosier & Alise R. Muok & Nicole Torosian & Allison M., 2024. "Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    14. Heleen T. Ouboter & Rob Mesman & Tom Sleutels & Jelle Postma & Martijn Wissink & Mike S. M. Jetten & Annemiek Ter Heijne & Tom Berben & Cornelia U. Welte, 2024. "Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    15. Mason. R. Stothart & Philip. D. McLoughlin & Sarah. A. Medill & Ruth. J. Greuel & Alastair. J. Wilson & Jocelyn. Poissant, 2024. "Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    16. Zheng Sun & Jiang Liu & Meng Zhang & Tong Wang & Shi Huang & Scott T. Weiss & Yang-Yu Liu, 2023. "Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    17. Kaiyuan Zhu & Alejandro A. Schäffer & Welles Robinson & Junyan Xu & Eytan Ruppin & A. Funda Ergun & Yuzhen Ye & S. Cenk Sahinalp, 2022. "Strain level microbial detection and quantification with applications to single cell metagenomics," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    18. Marc Schoeler & Sandrine Ellero-Simatos & Till Birkner & Jordi Mayneris-Perxachs & Lisa Olsson & Harald Brolin & Ulrike Loeber & Jamie D. Kraft & Arnaud Polizzi & Marian Martí-Navas & Josep Puig & Ant, 2023. "The interplay between dietary fatty acids and gut microbiota influences host metabolism and hepatic steatosis," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    19. Harold P. Hodgins & Pengsheng Chen & Briallen Lobb & Xin Wei & Benjamin J. M. Tremblay & Michael J. Mansfield & Victoria C. Y. Lee & Pyung-Gang Lee & Jeffrey Coffin & Ana T. Duggan & Alexis E. Dolphin, 2023. "Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    20. 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.

    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:13:y:2022:i:1:d:10.1038_s41467-022-31654-0. 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.