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Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis

Author

Listed:
  • Simon A. Hardwick

    (Garvan Institute of Medical Research
    UNSW Sydney)

  • Wendy Y. Chen

    (Garvan Institute of Medical Research
    UNSW Sydney)

  • Ted Wong

    (Garvan Institute of Medical Research)

  • Bindu S. Kanakamedala

    (Garvan Institute of Medical Research)

  • Ira W. Deveson

    (Garvan Institute of Medical Research
    UNSW Sydney)

  • Sarah E. Ongley

    (UNSW Sydney
    The University of Newcastle)

  • Nadia S. Santini

    (Centre for Marine Bioinnovation UNSW Sydney
    Universidad Nacional Autonoma de Mexico)

  • Esteban Marcellin

    (The University of Queensland)

  • Martin A. Smith

    (Garvan Institute of Medical Research
    UNSW Sydney)

  • Lars K. Nielsen

    (The University of Queensland)

  • Catherine E. Lovelock

    (The University of Queensland)

  • Brett A. Neilan

    (UNSW Sydney
    The University of Newcastle)

  • Tim R. Mercer

    (Garvan Institute of Medical Research
    UNSW Sydney
    Altius Institute for Biomedical Sciences)

Abstract

The complexity of microbial communities, combined with technical biases in next-generation sequencing, pose a challenge to metagenomic analysis. Here, we develop a set of internal DNA standards, termed “sequins” (sequencing spike-ins), that together constitute a synthetic community of artificial microbial genomes. Sequins are added to environmental DNA samples prior to library preparation, and undergo concurrent sequencing with the accompanying sample. We validate the performance of sequins by comparison to mock microbial communities, and demonstrate their use in the analysis of real metagenome samples. We show how sequins can be used to measure fold change differences in the size and structure of accompanying microbial communities, and perform quantitative normalization between samples. We further illustrate how sequins can be used to benchmark and optimize new methods, including nanopore long-read sequencing technology. We provide metagenome sequins, along with associated data sets, protocols, and an accompanying software toolkit, as reference standards to aid in metagenomic studies.

Suggested Citation

  • Simon A. Hardwick & Wendy Y. Chen & Ted Wong & Bindu S. Kanakamedala & Ira W. Deveson & Sarah E. Ongley & Nadia S. Santini & Esteban Marcellin & Martin A. Smith & Lars K. Nielsen & Catherine E. Lovelo, 2018. "Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05555-0
    DOI: 10.1038/s41467-018-05555-0
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    Cited by:

    1. Helen M. Gunter & Scott E. Youlten & Andre L. M. Reis & Tim McCubbin & Bindu Swapna Madala & Ted Wong & Igor Stevanovski & Arcadi Cipponi & Ira W. Deveson & Nadia S. Santini & Sarah Kummerfeld & Peter, 2024. "A universal molecular control for DNA, mRNA and protein expression," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Helen M. Gunter & Scott E. Youlten & Bindu Swapna Madala & Andre L. M. Reis & Igor Stevanovski & Ted Wong & Sarah K. Kummerfield & Ira W. Deveson & Nadia S. Santini & Esteban Marcellin & Tim R. Mercer, 2022. "Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing," Nature Communications, Nature, vol. 13(1), pages 1-11, December.

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