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Shotgun metagenomics, from sampling to analysis
Open accessAbstract
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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“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]
In the citing paper
“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”
From Key determinants of success in fecal microbiota transplantation: From microbiome to clinic (2023) · cites this paper as [132]
In the citing paper
“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.”
From Key determinants of success in fecal microbiota transplantation: From microbiome to clinic (2023) · cites this paper as [132]
In the citing paper
“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”
From Key determinants of success in fecal microbiota transplantation: From microbiome to clinic (2023) · cites this paper as [132]
In the citing paper
“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).”
From Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2021) · cites this paper as Quince et al., 2017
In the citing paper
“Unlike 16S ribosomal RNA sequencing, shotgun metagenomics sequences permit a parallel assessment of all microbial kingdoms (bacterial, fungal, viral) in a given sample.77, 78”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [78]
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Metadata
- 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
- FWCI
- 11.17
- Type
- journal article
- Language
- en
- Update notices
- erratum (2017-12-01)
- Open access
- green
- hdl.handle.net
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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