Cited by 2,202Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyEnvironmental DNA in Biodiversity Studies

Shotgun metagenomics, from sampling to analysis

Open access
Quince, Christopher, Walker, Alan W, Simpson, Jared T, Loman, Nicholas J, Segata, Nicola·2017·Nature Biotechnology

Abstract

Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples or environments containing organisms with limited similarity to sequenced genomes, are needed. Understanding the functions and characterizing specific strains of these communities offers biotechnological promise in therapeutic discovery and innovative ways to synthesize products using microbial factories and can pinpoint the contributions of microorganisms to planetary, animal and human health.

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  • Sequence-based methods are not perfect; biases can be introduced at every step of sequence-based studies, from sample collection and storage, through laboratory-based steps such as DNA extraction, to choice of bioinformatic pipelines and reference databases.

    “While sequence-based methods have been transformative for microbiome research, they are not perfect. Biases can be introduced at every step of sequence-based studies, from sample collection and storage, through laboratory-based steps such as DNA extraction, to choice of bioinformatic pipelines and reference databases used to analyse the data 33 .”

    From Human microbiome myths and misconceptions (2023) · cites this paper as [33]

  • Sequencing depth is essential for deciphering microbial composition of a sample, but deeper sequencing comes with higher costs and analytical complexity.

    “Specifically, the depth of sequencing is essential for deciphering the microbial composition of a sample, but deeper sequencing comes with higher costs and analytical complexity. 132”
  • Shotgun metagenomics has not experienced widespread use because of limitations including issues related to sequencing depth and partial incompleteness of available reference databases.

    “Despite its use for more than 15 years, shotgun metagenomics has still not experienced widespread use because of some limitations, including issues related to sequencing depth and partial incompleteness of available reference databases.”
  • Shotgun metagenomics is replacing 16S rRNA gene sequencing and provides higher taxonomic resolution and insight into functions encoded by the microbial community.

    “Although earlier studies were mostly based on 16S rRNA gene sequencing, the technique is being replaced by shotgun metagenomics, which bypasses amplification steps and provides higher taxonomic resolution and insight into the functions encoded by the microbial community. 132”
  • The visibility of species with particularly high genetic diversity within individual communities remains limited; in most cases, only the most dominant strain of each taxon per community is currently analyzable.

    “The visibility of species with particularly high genetic diversity within individual communities also remains limited; in most cases, only the most dominant strain of each taxon per community is currently analyzable, again for both experimental (e.g. sequencing depth) and analytical reasons (Quince et al., 2017).”

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Research works printed but not linked: 1

  1. [53]53. Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19, 455-477 (2012).

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Authors
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N.
Affiliations
  • University of Warwick (GB)
  • University of Aberdeen (GB)
  • Ontario Institute for Cancer Research (CA)
  • University of Birmingham (GB)
  • University of Trento (IT)
Corresponding author
Segata, Nicola
Venue
Nature Biotechnology
Published
2017-09
Volume
35
Issue
9
Pages
833-844
ISSN
  • 0733-222X (ISSN-L)
  • 1087-0156
  • 1546-1696
OpenAlex
W2754579667
Cited by
2,202
References
135
Citations by year
2026: 414 · 2025: 319 · 2024: 292 · 2023: 240 · 2022: 265 · 2021: 231 · 2020: 215 · 2019: 141 · 2018: 72 · 2017: 8 · 2015: 2
FWCI
11.17
Type
journal article
Language
en
Update notices
erratum (2017-12-01)
Open access
Locations
  • Nature Biotechnology (publishedVersion)
  • PubMed (publishedVersion)
  • Aberdeen University Research Archive (Aberdeen University) (submittedVersion)
  • University of Birmingham Research Portal (University of Birmingham) (submittedVersion, other-oa)
  • Iris (University of Trento) (submittedVersion, other-oa)
  • UEA Digital Repository (University of East Anglia) (submittedVersion)
  • Warwick Research Archive Portal (University of Warwick) (submittedVersion)
Funders
  • Rural and Environment Science and Analytical Services Division
  • Government of Ontario
  • European Commission (618833)
  • University of Aberdeen
  • Ministero dell’Istruzione, dell’Università e della Ricerca (FIR RBFR13EWWI, RBFR13EWWI)
  • Fondazione Cassa Di Risparmio Di Trento E Rovereto (2013.0239, Rif.Int.2013.0239)
  • Medical Research Council (MR/M501621/1, MR/L015080/1, L015080, MR/M50161X/1)
  • Biotechnology and Biological Sciences Research Council (BB/L027801/1)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Keywords
shotgun metagenomics, microbial communities, metagenome assembly, unculturable microorganisms, strain characterization, microbial function, therapeutic discovery, microbial biotechnology, environmental microbiology
MeSH terms
Animals, Humans, Biomedical Research, Metagenomics, High-Throughput Nucleotide Sequencing, Microbiota

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